https://launchpad.net/ubuntu/+archive/test-rebuild-20201216-hirsute-lto/+build/20599634 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-074 4.15.0-132-generic #136-Ubuntu SMP Tue Jan 12 15:01:53 UTC 2021 aarch64 Buildd toolchain package versions: launchpad-buildd_194~476~ubuntu18.04.1 python3-lpbuildd_194~476~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.7 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 26 Jan 04:31:06 ntpdate[1640]: adjust time server 10.211.37.1 offset 0.000997 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-20599634 --image-type chroot /home/buildd/filecache-default/d1fb963478283f19fe8f83381d93195a7691df38 Creating target for build PACKAGEBUILD-20599634 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-20599634 Starting target for build PACKAGEBUILD-20599634 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-20599634 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu hirsute main' 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu hirsute main' 'deb http://ftpmaster.internal/ubuntu hirsute main universe' Overriding sources.list in build-PACKAGEBUILD-20599634 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-20599634 Adding trusted keys to build-PACKAGEBUILD-20599634 Warning: apt-key is deprecated. Manage keyring files in trusted.gpg.d instead (see apt-key(8)). OK Warning: apt-key is deprecated. Manage keyring files in trusted.gpg.d instead (see apt-key(8)). /etc/apt/trusted.gpg -------------------- pub rsa1024 2009-10-22 [SC] 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid [ unknown] Launchpad Toolchain builds /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-cdimage.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 8439 38DF 228D 22F7 B374 2BC0 D94A A3F0 EFE2 1092 uid [ unknown] Ubuntu CD Image Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2018-archive.gpg ------------------------------------------------------ pub rsa4096 2018-09-17 [SC] F6EC B376 2474 EDA9 D21B 7022 8719 20D1 991B C93C uid [ unknown] Ubuntu Archive Automatic Signing Key (2018) RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-20599634 Updating target for build PACKAGEBUILD-20599634 Get:1 http://ftpmaster.internal/ubuntu hirsute InRelease [269 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu hirsute InRelease [23.8 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu hirsute InRelease [23.8 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute/main arm64 Packages [1360 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main Translation-en [513 kB] Get:6 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu hirsute/main arm64 Packages [19.6 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/universe arm64 Packages [12.7 MB] Get:8 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu hirsute/main Translation-en [10.0 kB] Get:9 http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu hirsute/main arm64 Packages [2092 B] Get:10 http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu hirsute/main Translation-en [2012 B] Get:11 http://ftpmaster.internal/ubuntu hirsute/universe Translation-en [5420 kB] Fetched 20.4 MB in 7s (2899 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libisl22 libperl5.30 perl-modules-5.30 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libisl23 libperl5.32 libxxhash0 perl-modules-5.32 The following packages will be upgraded: adduser apt base-files base-passwd bash binutils binutils-aarch64-linux-gnu binutils-common bsdutils coreutils cpp-10 dash dpkg dpkg-dev fakeroot g++-10 gcc-10 gcc-10-base gpg gpg-agent gpgconf gpgv grep gzip init init-system-helpers libacl1 libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libgcc-10-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgssapi-krb5-2 libidn2-0 libip4tc2 libitm1 libk5crypto3 libkrb5-3 libkrb5support0 liblsan0 liblz4-1 libmount1 libmpc3 libncurses6 libncursesw6 libnpth0 libp11-kit0 libpcre2-8-0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libssl1.1 libstdc++-10-dev libstdc++6 libsystemd0 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login mount ncurses-base ncurses-bin openssl passwd patch perl perl-base readline-common sensible-utils systemd systemd-sysv systemd-timesyncd sysvinit-utils tar tzdata util-linux 114 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 85.2 MB of archives. After this operation, 58.5 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcrypt-dev arm64 1:4.4.17-1ubuntu1 [109 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu hirsute/main arm64 dpkg arm64 1.20.7.1ubuntu11 [2472 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute/main arm64 libc6-dev arm64 2.32-0ubuntu6 [1723 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute/main arm64 libc-dev-bin arm64 2.32-0ubuntu6 [28.7 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcrypt1 arm64 1:4.4.17-1ubuntu1 [80.8 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main arm64 linux-libc-dev arm64 5.8.0-36.40+21.04.1 [1118 kB] Get:7 http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu hirsute/main arm64 dpkg-dev all 1.20.7.1ubuntu11 [2169 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtirpc-common all 1.3.1-1 [7452 B] Get:9 http://ftpmaster.internal/ubuntu hirsute/main arm64 libk5crypto3 arm64 1.17-10ubuntu1 [79.6 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgssapi-krb5-2 arm64 1.17-10ubuntu1 [112 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute/main arm64 libkrb5-3 arm64 1.17-10ubuntu1 [314 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute/main arm64 libkrb5support0 arm64 1.17-10ubuntu1 [30.2 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main arm64 libssl1.1 arm64 1.1.1f-1ubuntu5 [1157 kB] Get:14 http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu hirsute/main arm64 libdpkg-perl all 1.20.7.1ubuntu11 [1557 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtirpc-dev arm64 1.3.1-1 [185 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtirpc3 arm64 1.3.1-1 [73.3 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute/main arm64 libisl23 arm64 0.23-1 [586 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcc1-0 arm64 10.2.1-6ubuntu1 [46.7 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute/main arm64 libctf0 arm64 2.35.50.20210106-1ubuntu2 [89.9 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute/main arm64 libctf-nobfd0 arm64 2.35.50.20210106-1ubuntu2 [92.5 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute/main arm64 binutils-aarch64-linux-gnu arm64 2.35.50.20210106-1ubuntu2 [2514 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute/main arm64 libbinutils arm64 2.35.50.20210106-1ubuntu2 [618 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute/main arm64 binutils-common arm64 2.35.50.20210106-1ubuntu2 [216 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute/main arm64 binutils arm64 2.35.50.20210106-1ubuntu2 [3364 B] Get:25 http://ftpmaster.internal/ubuntu hirsute/main arm64 gcc-10-base arm64 10.2.1-6ubuntu1 [19.7 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgcc-s1 arm64 10.2.1-6ubuntu1 [34.6 kB] Get:27 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgomp1 arm64 10.2.1-6ubuntu1 [93.7 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute/main arm64 libitm1 arm64 10.2.1-6ubuntu1 [24.2 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute/main arm64 libatomic1 arm64 10.2.1-6ubuntu1 [9812 B] Get:30 http://ftpmaster.internal/ubuntu hirsute/main arm64 libasan6 arm64 10.2.1-6ubuntu1 [2026 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute/main arm64 liblsan0 arm64 10.2.1-6ubuntu1 [800 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtsan0 arm64 10.2.1-6ubuntu1 [1970 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute/main arm64 libubsan1 arm64 10.2.1-6ubuntu1 [765 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute/main arm64 g++-10 arm64 10.2.1-6ubuntu1 [8917 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute/main arm64 libstdc++-10-dev arm64 10.2.1-6ubuntu1 [1719 kB] Get:36 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgcc-10-dev arm64 10.2.1-6ubuntu1 [915 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute/main arm64 gcc-10 arm64 10.2.1-6ubuntu1 [15.8 MB] Get:38 http://ftpmaster.internal/ubuntu hirsute/main arm64 cpp-10 arm64 10.2.1-6ubuntu1 [7783 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute/main arm64 libstdc++6 arm64 10.2.1-6ubuntu1 [461 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute/main arm64 libmpc3 arm64 1.2.0-1 [42.3 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main arm64 libzstd1 arm64 1.4.8+dfsg-1 [274 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/main arm64 libc6 arm64 2.32-0ubuntu6 [2246 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/main arm64 base-files arm64 11ubuntu16 [60.4 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute/main arm64 bash arm64 5.1-1ubuntu1 [632 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute/main arm64 bsdutils arm64 1:2.36.1-1ubuntu2 [82.6 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute/main arm64 coreutils arm64 8.32-4ubuntu2 [1258 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main arm64 tar arm64 1.32+dfsg-1 [262 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/main arm64 dash arm64 0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1 [84.1 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main arm64 grep arm64 3.6-1 [147 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main arm64 gzip arm64 1.10-2ubuntu2 [92.6 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main arm64 login arm64 1:4.8.1-1ubuntu8 [217 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main arm64 libncurses6 arm64 6.2+20201114-2 [92.6 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/main arm64 libncursesw6 arm64 6.2+20201114-2 [120 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtinfo6 arm64 6.2+20201114-2 [81.6 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute/main arm64 ncurses-bin arm64 6.2+20201114-2 [168 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute/main arm64 perl-modules-5.32 all 5.32.0-6 [2754 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute/main arm64 libperl5.32 arm64 5.32.0-6 [3875 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/main arm64 perl arm64 5.32.0-6 [225 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute/main arm64 perl-base arm64 5.32.0-6 [1430 kB] Get:60 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgdbm6 arm64 1.19-2 [26.5 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgdbm-compat4 arm64 1.19-2 [6020 B] Get:62 http://ftpmaster.internal/ubuntu hirsute/main arm64 util-linux arm64 2.36.1-1ubuntu2 [1034 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute/main arm64 libdebconfclient0 arm64 0.256ubuntu1 [6148 B] Get:64 http://ftpmaster.internal/ubuntu hirsute/main arm64 base-passwd arm64 3.5.48 [46.6 kB] Get:65 http://ftpmaster.internal/ubuntu hirsute/main arm64 init-system-helpers all 1.59 [38.2 kB] Get:66 http://ftpmaster.internal/ubuntu hirsute/main arm64 libc-bin arm64 2.32-0ubuntu6 [520 kB] Get:67 http://ftpmaster.internal/ubuntu hirsute/main arm64 ncurses-base all 6.2+20201114-2 [18.4 kB] Get:68 http://ftpmaster.internal/ubuntu hirsute/main arm64 sysvinit-utils arm64 2.96-5ubuntu1 [20.4 kB] Get:69 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxxhash0 arm64 0.8.0-2 [16.9 kB] Get:70 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgcrypt20 arm64 1.8.7-2ubuntu1 [354 kB] Get:71 http://ftpmaster.internal/ubuntu hirsute/main arm64 liblz4-1 arm64 1.9.3-0ubuntu1 [52.0 kB] Get:72 http://ftpmaster.internal/ubuntu hirsute/main arm64 systemd-sysv arm64 247.1-4ubuntu1 [10.3 kB] Get:73 http://ftpmaster.internal/ubuntu hirsute/main arm64 libaudit-common all 1:2.8.5-3ubuntu3 [4048 B] Get:74 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcap-ng0 arm64 0.7.9-2.2build1 [10.5 kB] Get:75 http://ftpmaster.internal/ubuntu hirsute/main arm64 libaudit1 arm64 1:2.8.5-3ubuntu3 [38.1 kB] Get:76 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpcre2-8-0 arm64 10.35-2ubuntu1 [172 kB] Get:77 http://ftpmaster.internal/ubuntu hirsute/main arm64 libselinux1 arm64 3.1-2build2 [65.4 kB] Get:78 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsemanage-common all 3.1-1build2 [10.0 kB] Get:79 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsemanage1 arm64 3.1-1build2 [80.6 kB] Get:80 http://ftpmaster.internal/ubuntu hirsute/main arm64 passwd arm64 1:4.8.1-1ubuntu8 [770 kB] Get:81 http://ftpmaster.internal/ubuntu hirsute/main arm64 adduser all 3.118ubuntu5 [156 kB] Get:82 http://ftpmaster.internal/ubuntu hirsute/main arm64 systemd-timesyncd arm64 247.1-4ubuntu1 [26.4 kB] Get:83 http://ftpmaster.internal/ubuntu hirsute/main arm64 libapparmor1 arm64 3.0.0-0ubuntu5 [34.3 kB] Get:84 http://ftpmaster.internal/ubuntu hirsute/main arm64 libblkid1 arm64 2.36.1-1ubuntu2 [124 kB] Get:85 http://ftpmaster.internal/ubuntu hirsute/main arm64 libudev1 arm64 247.1-4ubuntu1 [63.3 kB] Get:86 http://ftpmaster.internal/ubuntu hirsute/main arm64 libdevmapper1.02.1 arm64 2:1.02.167-1ubuntu4 [110 kB] Get:87 http://ftpmaster.internal/ubuntu hirsute/main arm64 libuuid1 arm64 2.36.1-1ubuntu2 [21.0 kB] Get:88 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcryptsetup12 arm64 2:2.3.4-1ubuntu1 [177 kB] Get:89 http://ftpmaster.internal/ubuntu hirsute/main arm64 libidn2-0 arm64 2.3.0-5 [51.3 kB] Get:90 http://ftpmaster.internal/ubuntu hirsute/main arm64 libp11-kit0 arm64 0.23.22-1 [183 kB] Get:91 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgnutls30 arm64 3.7.0-5ubuntu1 [844 kB] Get:92 http://ftpmaster.internal/ubuntu hirsute/main arm64 libip4tc2 arm64 1.8.5-3ubuntu4 [18.2 kB] Get:93 http://ftpmaster.internal/ubuntu hirsute/main arm64 libseccomp2 arm64 2.4.3-1ubuntu6 [42.6 kB] Get:94 http://ftpmaster.internal/ubuntu hirsute/main arm64 mount arm64 2.36.1-1ubuntu2 [117 kB] Get:95 http://ftpmaster.internal/ubuntu hirsute/main arm64 systemd arm64 247.1-4ubuntu1 [3670 kB] Get:96 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsystemd0 arm64 247.1-4ubuntu1 [254 kB] Get:97 http://ftpmaster.internal/ubuntu hirsute/main arm64 libapt-pkg6.0 arm64 2.1.18 [814 kB] Get:98 http://ftpmaster.internal/ubuntu hirsute/main arm64 gpgv arm64 2.2.20-1ubuntu2 [185 kB] Get:99 http://ftpmaster.internal/ubuntu hirsute/main arm64 apt arm64 2.1.18 [1268 kB] Get:100 http://ftpmaster.internal/ubuntu hirsute/main arm64 init arm64 1.59 [6164 B] Get:101 http://ftpmaster.internal/ubuntu hirsute/main arm64 libacl1 arm64 2.2.53-9 [16.7 kB] Get:102 http://ftpmaster.internal/ubuntu hirsute/main arm64 libattr1 arm64 1:2.4.48-6 [12.6 kB] Get:103 http://ftpmaster.internal/ubuntu hirsute/main arm64 libmount1 arm64 2.36.1-1ubuntu2 [137 kB] Get:104 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsmartcols1 arm64 2.36.1-1ubuntu2 [88.6 kB] Get:105 http://ftpmaster.internal/ubuntu hirsute/main arm64 sensible-utils all 0.0.14 [13.5 kB] Get:106 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcap2 arm64 1:2.44-1 [16.7 kB] Get:107 http://ftpmaster.internal/ubuntu hirsute/main arm64 readline-common all 8.1-1 [54.1 kB] Get:108 http://ftpmaster.internal/ubuntu hirsute/main arm64 libreadline8 arm64 8.1-1 [129 kB] Get:109 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsqlite3-0 arm64 3.34.0-1 [542 kB] Get:110 http://ftpmaster.internal/ubuntu hirsute/main arm64 openssl arm64 1.1.1f-1ubuntu5 [600 kB] Get:111 http://ftpmaster.internal/ubuntu hirsute/main arm64 tzdata all 2020f-1ubuntu2 [294 kB] Get:112 http://ftpmaster.internal/ubuntu hirsute/main arm64 patch arm64 2.7.6-7 [97.8 kB] Get:113 http://ftpmaster.internal/ubuntu hirsute/main arm64 libfakeroot arm64 1.25.3-1.1 [26.6 kB] Get:114 http://ftpmaster.internal/ubuntu hirsute/main arm64 fakeroot arm64 1.25.3-1.1 [62.4 kB] Get:115 http://ftpmaster.internal/ubuntu hirsute/main arm64 libnpth0 arm64 1.6-3 [7824 B] Get:116 http://ftpmaster.internal/ubuntu hirsute/main arm64 gpg arm64 2.2.20-1ubuntu2 [445 kB] Get:117 http://ftpmaster.internal/ubuntu hirsute/main arm64 gpgconf arm64 2.2.20-1ubuntu2 [117 kB] Get:118 http://ftpmaster.internal/ubuntu hirsute/main arm64 gpg-agent arm64 2.2.20-1ubuntu2 [216 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 85.2 MB in 4s (23.3 MB/s) (Reading database ... 12970 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.17-1ubuntu1_arm64.deb ... Unpacking libcrypt-dev:arm64 (1:4.4.17-1ubuntu1) over (1:4.4.16-1ubuntu1) ... Preparing to unpack .../libc6-dev_2.32-0ubuntu6_arm64.deb ... Unpacking libc6-dev:arm64 (2.32-0ubuntu6) over (2.32-0ubuntu3) ... Preparing to unpack .../libc-dev-bin_2.32-0ubuntu6_arm64.deb ... Unpacking libc-dev-bin (2.32-0ubuntu6) over (2.32-0ubuntu3) ... Preparing to unpack .../libcrypt1_1%3a4.4.17-1ubuntu1_arm64.deb ... Unpacking libcrypt1:arm64 (1:4.4.17-1ubuntu1) over (1:4.4.16-1ubuntu1) ... Setting up libcrypt1:arm64 (1:4.4.17-1ubuntu1) ... (Reading database ... 12969 files and directories currently installed.) Preparing to unpack .../00-linux-libc-dev_5.8.0-36.40+21.04.1_arm64.deb ... Unpacking linux-libc-dev:arm64 (5.8.0-36.40+21.04.1) over (5.8.0-25.26) ... Preparing to unpack .../01-libtirpc-common_1.3.1-1_all.deb ... Unpacking libtirpc-common (1.3.1-1) over (1.2.6-1build1) ... 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Setting up perl-modules-5.32 (5.32.0-6) ... Setting up libsqlite3-0:arm64 (3.34.0-1) ... Setting up binutils-common:arm64 (2.35.50.20210106-1ubuntu2) ... Setting up linux-libc-dev:arm64 (5.8.0-36.40+21.04.1) ... Setting up libctf-nobfd0:arm64 (2.35.50.20210106-1ubuntu2) ... Setting up libnpth0:arm64 (1.6-3) ... Setting up libgomp1:arm64 (10.2.1-6ubuntu1) ... Setting up libcap2:arm64 (1:2.44-1) ... Setting up libfakeroot:arm64 (1.25.3-1.1) ... Setting up libasan6:arm64 (10.2.1-6ubuntu1) ... Setting up libkrb5support0:arm64 (1.17-10ubuntu1) ... Setting up tzdata (2020f-1ubuntu2) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Jan 26 04:32:20 UTC 2021. Universal Time is now: Tue Jan 26 04:32:20 UTC 2021. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.25.3-1.1) ... Setting up libncurses6:arm64 (6.2+20201114-2) ... Setting up libmpc3:arm64 (1.2.0-1) ... Setting up libatomic1:arm64 (10.2.1-6ubuntu1) ... Setting up patch (2.7.6-7) ... 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-20599634 arm64 hirsute -c chroot:build-PACKAGEBUILD-20599634 --arch=arm64 --dist=hirsute --nolog vg_1.27.1+ds-1build1.dsc Initiating build PACKAGEBUILD-20599634 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-132-generic #136-Ubuntu SMP Tue Jan 12 15:01:53 UTC 2021 aarch64 sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-arm64-074.buildd +==============================================================================+ | vg 1.27.1+ds-1build1 (arm64) Tue, 26 Jan 2021 04:32:24 +0000 | +==============================================================================+ Package: vg Version: 1.27.1+ds-1build1 Source Version: 1.27.1+ds-1build1 Distribution: hirsute Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-20599634/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- vg_1.27.1+ds-1build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/vg-js9ESf/vg-1.27.1+ds' with '<>' I: NOTICE: Log filtering will replace 'build/vg-js9ESf' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-HUn1p1/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-HUn1p1/apt_archive ./ InRelease Get:2 copy:/<>/resolver-HUn1p1/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-HUn1p1/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-HUn1p1/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-HUn1p1/apt_archive ./ Packages [431 B] Fetched 1737 B in 0s (41.0 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libisl22 libperl5.30 perl-modules-5.30 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-HUn1p1/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (52.7 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14984 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in amd64 i386 arm64 ppc64el s390x riscv64 x32 all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), pv, bsdmainutils, zlib1g-dev, rs, libffi-dev, bwa, protobuf-compiler, libprotoc-dev, libprotobuf-dev, libjansson-dev, libbz2-dev, libncurses5-dev, automake, libtool, jq, samtools, unzip, librdf-dev, cmake, pkg-config, bc, gtk-doc-tools, raptor2-utils, rasqal-utils, bison, flex, gawk, liblz4-dev, liblzma-dev, libcairo2-dev, libpixman-1-dev, libssw-dev, librocksdb-dev, libdeflate-dev, libboost-program-options-dev, libjemalloc-dev, libbackward-cpp-dev, elfutils, libdw-dev, libelf-dev, libraptor2-dev, libsparsehash-dev, rapidjson-dev, libfml-dev, libfastahack-dev, fastahack, libsmithwaterman-dev, libdivsufsort-dev, libtsl-hopscotch-map-dev, libvcflib-dev (>= 1.0.1), libvcflib-tools, libhts-dev, help2man, python3:any, libsimde-dev Filtered Build-Depends: debhelper-compat (= 13), pv, bsdmainutils, zlib1g-dev, rs, libffi-dev, bwa, protobuf-compiler, libprotoc-dev, libprotobuf-dev, libjansson-dev, libbz2-dev, libncurses5-dev, automake, libtool, jq, samtools, unzip, librdf-dev, cmake, pkg-config, bc, gtk-doc-tools, raptor2-utils, rasqal-utils, bison, flex, gawk, liblz4-dev, liblzma-dev, libcairo2-dev, libpixman-1-dev, libssw-dev, librocksdb-dev, libdeflate-dev, libboost-program-options-dev, libjemalloc-dev, libbackward-cpp-dev, elfutils, libdw-dev, libelf-dev, libraptor2-dev, libsparsehash-dev, rapidjson-dev, libfml-dev, libfastahack-dev, fastahack, libsmithwaterman-dev, libdivsufsort-dev, libtsl-hopscotch-map-dev, libvcflib-dev (>= 1.0.1), libvcflib-tools, libhts-dev, help2man, python3:any, libsimde-dev dpkg-deb: building package 'sbuild-build-depends-vg-dummy' in '/<>/resolver-HUn1p1/apt_archive/sbuild-build-depends-vg-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-vg-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-HUn1p1/apt_archive ./ InRelease Get:2 copy:/<>/resolver-HUn1p1/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-HUn1p1/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-HUn1p1/apt_archive ./ Sources [860 B] Get:5 copy:/<>/resolver-HUn1p1/apt_archive ./ Packages [907 B] Fetched 2730 B in 0s (60.8 kB/s) Reading package lists... Reading package lists... Install vg build dependencies (apt-based resolver) -------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libisl22 libperl5.30 perl-modules-5.30 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bc bison bsdextrautils bsdmainutils bwa calendar cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism docbook docbook-to-man docbook-xml docbook-xsl dwz elfutils fastahack file flex fontconfig fontconfig-config fonts-dejavu-core gawk gettext gettext-base groff-base gtk-doc-tools help2man icu-devtools intltool-debian jq libarchive-zip-perl libarchive13 libasm1 libasn1-8-heimdal libbackward-cpp-dev libblas3 libblkid-dev libboost-program-options-dev libboost-program-options1.74-dev libboost-program-options1.74.0 libboost1.74-dev libbrotli-dev libbrotli1 libbsd0 libbz2-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdatrie1 libdebhelper-perl libdeflate-dev libdeflate0 libdisorder-dev libdisorder0 libdivsufsort-dev libdivsufsort3 libdw-dev libdw1 libelf-dev libelf1 libexpat1 libexpat1-dev libfastahack-dev libfastahack0 libffi-dev libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig-dev libfontconfig1 libfontconfig1-dev libfreetype-dev libfreetype6 libfreetype6-dev libfribidi0 libgflags2.2 libgfortran5 libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgmp-dev libgmpxx4ldbl libgraphite2-3 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libice-dev libice6 libicu-dev libicu67 libjansson-dev libjansson4 libjbig0 libjemalloc-dev libjemalloc2 libjpeg-turbo8 libjpeg8 libjq1 libjsoncpp24 libkrb5-26-heimdal liblapack3 libldap-2.4-2 liblocale-gettext-perl libltdl7 liblz4-dev liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmhash2 libmount-dev libmpdec3 libncurses-dev libncurses5-dev libnghttp2-14 libonig5 libosp5 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix2 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpixman-1-dev libpng-dev libprotobuf-dev libprotobuf-lite23 libprotobuf23 libprotoc-dev libprotoc23 libpsl5 libpthread-stubs0-dev libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libraptor2-0 libraptor2-dev librasqal3 librasqal3-dev librdf0 librdf0-dev librhash0 librocksdb-dev librocksdb5.17 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libselinux1-dev libsepol1-dev libsigsegv2 libsimde-dev libsm-dev libsm6 libsmithwaterman-dev libsmithwaterman0 libsnappy1v5 libsparsehash-dev libssh-4 libssw-dev libssw0 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libtsl-hopscotch-map-dev libuchardet0 libuv1 libvcflib-dev libvcflib-tools libvcflib1 libwebp6 libwind0-heimdal libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxcb-render0 libxcb-render0-dev libxcb-shm0 libxcb-shm0-dev libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxft2 libxml2 libxml2-dev libxrender-dev libxrender1 libxslt1-dev libxslt1.1 libxss1 libxt6 libyajl-dev libyajl2 littler m4 mailcap man-db media-types mime-support ncal opensp pkg-config po-debconf protobuf-compiler pv python3 python3-distutils python3-lib2to3 python3-lxml python3-minimal python3-pkg-resources python3-pygments python3.9 python3.9-minimal r-base-core r-cran-assertthat r-cran-callr r-cran-cli r-cran-colorspace r-cran-crayon r-cran-desc r-cran-digest r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plyr r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr rapidjson-dev raptor2-utils rasqal-utils rs samtools sgml-base sgml-data ucf unzip uuid-dev x11-common x11proto-core-dev x11proto-dev x11proto-xext-dev xdg-utils xml-core xorg-sgml-doctools xsltproc xtrans-dev zip zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc bison-doc whois vacation mailutils cmake-doc ninja-build dh-make docbook-defguide docbook-dsssl psgml dbtoepub docbook-xsl-doc-html | docbook-xsl-doc-pdf | docbook-xsl-doc-text | docbook-xsl-doc docbook-xsl-saxon fop libsaxon-java libxalan2-java libxslthl-java xalan flex-doc gawk-doc gettext-doc libasprintf-dev libgettextpo-dev groff dblatex lrzip binutils-dev libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-serialization1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev libcairo2-doc libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev freetype2-doc libgirepository1.0-dev libglib2.0-doc libgdk-pixbuf2.0-bin | libgdk-pixbuf2.0-dev libxml2-utils gmp-doc libgmp10-doc libmpfr-dev libice-doc icu-doc liblzma-doc ncurses-doc libraptor2-doc librasqal3-doc librdf-storage-postgresql librdf-storage-mysql librdf-storage-sqlite librdf-storage-virtuoso redland-utils librdf-perl python-librdf librdf-ruby libsm-doc tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk r-cran-pracma libx11-doc libxcb-doc libxext-doc m4-doc apparmor less www-browser doc-base libmail-box-perl protobuf-mode-el python3-doc python3-tk python3-venv python3-lxml-dbg python-lxml-doc python3-setuptools python-pygments-doc ttf-bitstream-vera python3.9-venv python3.9-doc binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-covr r-cran-htmlwidgets r-cran-knitr r-cran-rmarkdown r-cran-prettycode r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-dplyr r-cran-png r-cran-jpeg r-cran-viridis r-cran-unitizer r-cran-hmisc r-cran-maps r-cran-maptools r-cran-multcomp r-cran-rpart r-cran-sf r-cran-svglite r-cran-dbi r-cran-rsqlite r-cran-r.utils r-cran-forcats r-cran-stringr r-cran-magick r-cran-getopt r-cran-bit64 r-cran-bitops r-cran-doparallel r-cran-foreach r-cran-iterators r-cran-itertools r-cran-curl r-cran-inline r-cran-dichromat r-cran-devtools r-cran-usethis r-cran-blob r-cran-hms r-cran-htmltools r-cran-purrr r-cran-tidyr r-cran-zeallot rapidjson-doc cwltool sgml-base-doc perlsgml w3-recs Recommended packages: libfl-dev curl | wget | lynx bzip2-doc libarchive-cpio-perl shared-mime-info xdg-user-dirs libldap-common libpng-tools publicsuffix redland-utils libsasl2-modules libltdl-dev libmail-sendmail-perl python3-bs4 python3-html5lib r-recommended r-base-dev r-doc-html r-cran-cliapp r-cran-mockery r-cran-sp r-cran-mapproj r-cran-hexbin r-cran-vdiffr r-cran-quantreg r-cran-xml2 r-cran-lubridate r-cran-domc r-cran-abind r-cran-codetools r-cran-curl r-cran-rmarkdown r-cran-mockr r-cran-bit64 r-cran-hms r-cran-data.table r-cran-rsqlite r-cran-knitr r-cran-dplyr r-cran-generics r-cran-waldo r-cran-dbi libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bc bison bsdextrautils bsdmainutils bwa calendar cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism docbook docbook-to-man docbook-xml docbook-xsl dwz elfutils fastahack file flex fontconfig fontconfig-config fonts-dejavu-core gawk gettext gettext-base groff-base gtk-doc-tools help2man icu-devtools intltool-debian jq libarchive-zip-perl libarchive13 libasm1 libasn1-8-heimdal libbackward-cpp-dev libblas3 libblkid-dev libboost-program-options-dev libboost-program-options1.74-dev libboost-program-options1.74.0 libboost1.74-dev libbrotli-dev libbrotli1 libbsd0 libbz2-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdatrie1 libdebhelper-perl libdeflate-dev libdeflate0 libdisorder-dev libdisorder0 libdivsufsort-dev libdivsufsort3 libdw-dev libdw1 libelf-dev libelf1 libexpat1 libexpat1-dev libfastahack-dev libfastahack0 libffi-dev libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig-dev libfontconfig1 libfontconfig1-dev libfreetype-dev libfreetype6 libfreetype6-dev libfribidi0 libgflags2.2 libgfortran5 libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgmp-dev libgmpxx4ldbl libgraphite2-3 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libice-dev libice6 libicu-dev libicu67 libjansson-dev libjansson4 libjbig0 libjemalloc-dev libjemalloc2 libjpeg-turbo8 libjpeg8 libjq1 libjsoncpp24 libkrb5-26-heimdal liblapack3 libldap-2.4-2 liblocale-gettext-perl libltdl7 liblz4-dev liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmhash2 libmount-dev libmpdec3 libncurses-dev libncurses5-dev libnghttp2-14 libonig5 libosp5 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix2 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpixman-1-dev libpng-dev libprotobuf-dev libprotobuf-lite23 libprotobuf23 libprotoc-dev libprotoc23 libpsl5 libpthread-stubs0-dev libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libraptor2-0 libraptor2-dev librasqal3 librasqal3-dev librdf0 librdf0-dev librhash0 librocksdb-dev librocksdb5.17 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libselinux1-dev libsepol1-dev libsigsegv2 libsimde-dev libsm-dev libsm6 libsmithwaterman-dev libsmithwaterman0 libsnappy1v5 libsparsehash-dev libssh-4 libssw-dev libssw0 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libtsl-hopscotch-map-dev libuchardet0 libuv1 libvcflib-dev libvcflib-tools libvcflib1 libwebp6 libwind0-heimdal libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxcb-render0 libxcb-render0-dev libxcb-shm0 libxcb-shm0-dev libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxft2 libxml2 libxml2-dev libxrender-dev libxrender1 libxslt1-dev libxslt1.1 libxss1 libxt6 libyajl-dev libyajl2 littler m4 mailcap man-db media-types mime-support ncal opensp pkg-config po-debconf protobuf-compiler pv python3 python3-distutils python3-lib2to3 python3-lxml python3-minimal python3-pkg-resources python3-pygments python3.9 python3.9-minimal r-base-core r-cran-assertthat r-cran-callr r-cran-cli r-cran-colorspace r-cran-crayon r-cran-desc r-cran-digest r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plyr r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr rapidjson-dev raptor2-utils rasqal-utils rs samtools sbuild-build-depends-vg-dummy sgml-base sgml-data ucf unzip uuid-dev x11-common x11proto-core-dev x11proto-dev x11proto-xext-dev xdg-utils xml-core xorg-sgml-doctools xsltproc xtrans-dev zip zlib1g-dev 0 upgraded, 323 newly installed, 0 to remove and 0 not upgraded. Need to get 148 MB of archives. After this operation, 624 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu hirsute/main arm64 liblocale-gettext-perl arm64 1.07-4build1 [16.6 kB] Get:2 copy:/<>/resolver-HUn1p1/apt_archive ./ sbuild-build-depends-vg-dummy 0.invalid.0 [1196 B] Get:3 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpython3.9-minimal arm64 3.9.1-3 [750 kB] Get:4 http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu hirsute/main arm64 libdebhelper-perl all 13.3.1ubuntu2 [192 kB] Get:5 http://ppa.launchpad.net/ubuntu-toolchain-r/dpkg-lto/ubuntu hirsute/main arm64 debhelper all 13.3.1ubuntu2 [1015 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main arm64 libexpat1 arm64 2.2.10-1 [61.9 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/main arm64 python3.9-minimal arm64 3.9.1-3 [1835 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute/main arm64 python3-minimal arm64 3.9.0-3ubuntu1 [24.0 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute/main arm64 media-types all 4.0.0 [22.2 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute/main arm64 mailcap all 3.68ubuntu1 [24.1 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute/main arm64 mime-support all 3.66 [3696 B] Get:12 http://ftpmaster.internal/ubuntu hirsute/main arm64 libmpdec3 arm64 2.5.1~rc1-2 [79.4 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpython3.9-stdlib arm64 3.9.1-3 [1658 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute/main arm64 python3.9 arm64 3.9.1-3 [417 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpython3-stdlib arm64 3.9.0-3ubuntu1 [7292 B] Get:16 http://ftpmaster.internal/ubuntu hirsute/main arm64 python3 arm64 3.9.0-3ubuntu1 [48.8 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute/main arm64 bsdextrautils arm64 2.36.1-1ubuntu2 [73.8 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute/main arm64 libuchardet0 arm64 0.0.7-1 [68.0 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute/main arm64 groff-base arm64 1.22.4-5 [797 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpipeline1 arm64 1.5.3-1 [26.1 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute/main arm64 man-db arm64 2.9.3-2 [1100 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsigsegv2 arm64 2.12-3 [13.8 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute/main arm64 m4 arm64 1.4.18-5 [194 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute/main arm64 flex arm64 2.6.4-8 [287 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute/main arm64 gawk arm64 1:5.0.1+dfsg-1 [382 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute/main arm64 sgml-base all 1.30 [12.5 kB] Get:27 http://ftpmaster.internal/ubuntu hirsute/main arm64 libmagic-mgc arm64 1:5.39-3 [228 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute/main arm64 libmagic1 arm64 1:5.39-3 [75.1 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute/main arm64 file arm64 1:5.39-3 [23.6 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute/main arm64 libbsd0 arm64 0.10.0-1 [43.7 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute/main arm64 libelf1 arm64 0.182-3 [43.4 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute/main arm64 libfribidi0 arm64 1.0.8-2 [23.7 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute/main arm64 libglib2.0-0 arm64 2.66.4-1 [1217 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute/main arm64 libglib2.0-data all 2.66.4-1 [5756 B] Get:35 http://ftpmaster.internal/ubuntu hirsute/main arm64 libicu67 arm64 67.1-5 [8457 kB] Get:36 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxml2 arm64 2.9.10+dfsg-6.3build1 [558 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute/main arm64 python3-pkg-resources all 51.1.0-1 [143 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute/main arm64 ucf all 3.0043 [56.1 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute/main arm64 gettext-base arm64 0.21-3ubuntu2 [38.6 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpsl5 arm64 0.21.0-1.1ubuntu1 [52.0 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main arm64 libuv1 arm64 1.40.0-1 [75.4 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxau6 arm64 1:1.0.9-0ubuntu1 [7356 B] Get:43 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxdmcp6 arm64 1:1.1.3-0ubuntu1 [10.3 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxcb1 arm64 1.14-2.1 [43.5 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute/main arm64 libx11-data all 2:1.7.0-2 [112 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute/main arm64 libx11-6 arm64 2:1.7.0-2 [552 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxext6 arm64 2:1.3.4-0ubuntu1 [27.7 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/main arm64 autoconf all 2.69-14 [293 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main arm64 autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main arm64 automake all 1:1.16.3-2ubuntu1 [552 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main arm64 autopoint all 0.21-3ubuntu2 [422 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main arm64 bc arm64 1.07.1-2build2 [83.0 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/main arm64 bison arm64 2:3.7.4+dfsg-1 [696 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute/universe arm64 calendar arm64 12.1.7 [121 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute/universe arm64 ncal arm64 12.1.7 [18.9 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute/universe arm64 bsdmainutils all 12.1.7 [3296 B] Get:57 http://ftpmaster.internal/ubuntu hirsute/universe arm64 bwa arm64 0.7.17-5 [189 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/main arm64 cmake-data all 3.18.4-1ubuntu3 [1705 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute/main arm64 libarchive13 arm64 3.4.3-2 [311 kB] Get:60 http://ftpmaster.internal/ubuntu hirsute/main arm64 libbrotli1 arm64 1.0.9-2build2 [262 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute/main arm64 libroken18-heimdal arm64 7.7.0+dfsg-2 [39.4 kB] Get:62 http://ftpmaster.internal/ubuntu hirsute/main arm64 libasn1-8-heimdal arm64 7.7.0+dfsg-2 [150 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute/main arm64 libheimbase1-heimdal arm64 7.7.0+dfsg-2 [27.9 kB] Get:64 http://ftpmaster.internal/ubuntu hirsute/main arm64 libhcrypto4-heimdal arm64 7.7.0+dfsg-2 [84.8 kB] Get:65 http://ftpmaster.internal/ubuntu hirsute/main arm64 libwind0-heimdal arm64 7.7.0+dfsg-2 [47.2 kB] Get:66 http://ftpmaster.internal/ubuntu hirsute/main arm64 libhx509-5-heimdal arm64 7.7.0+dfsg-2 [98.6 kB] Get:67 http://ftpmaster.internal/ubuntu hirsute/main arm64 libkrb5-26-heimdal arm64 7.7.0+dfsg-2 [192 kB] Get:68 http://ftpmaster.internal/ubuntu hirsute/main arm64 libheimntlm0-heimdal arm64 7.7.0+dfsg-2 [14.8 kB] Get:69 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgssapi3-heimdal arm64 7.7.0+dfsg-2 [88.4 kB] Get:70 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2ubuntu1 [14.9 kB] Get:71 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2ubuntu1 [48.4 kB] Get:72 http://ftpmaster.internal/ubuntu hirsute/main arm64 libldap-2.4-2 arm64 2.4.56+dfsg-1ubuntu1 [145 kB] Get:73 http://ftpmaster.internal/ubuntu hirsute/main arm64 libnghttp2-14 arm64 1.42.0-1 [68.6 kB] Get:74 http://ftpmaster.internal/ubuntu hirsute/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2build2 [53.1 kB] Get:75 http://ftpmaster.internal/ubuntu hirsute/main arm64 libssh-4 arm64 0.9.5-1 [160 kB] Get:76 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcurl4 arm64 7.72.0-1ubuntu1 [218 kB] Get:77 http://ftpmaster.internal/ubuntu hirsute/main arm64 libjsoncpp24 arm64 1.9.4-4 [69.1 kB] Get:78 http://ftpmaster.internal/ubuntu hirsute/main arm64 librhash0 arm64 1.4.1-1 [116 kB] Get:79 http://ftpmaster.internal/ubuntu hirsute/main arm64 cmake arm64 3.18.4-1ubuntu3 [3652 kB] Get:80 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtool all 2.4.6-15 [161 kB] Get:81 http://ftpmaster.internal/ubuntu hirsute/main arm64 dh-autoreconf all 19 [16.1 kB] Get:82 http://ftpmaster.internal/ubuntu hirsute/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:83 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsub-override-perl all 0.09-2 [9532 B] Get:84 http://ftpmaster.internal/ubuntu hirsute/main arm64 libfile-stripnondeterminism-perl all 1.10.0-1 [17.0 kB] Get:85 http://ftpmaster.internal/ubuntu hirsute/main arm64 dh-strip-nondeterminism all 1.10.0-1 [5228 B] Get:86 http://ftpmaster.internal/ubuntu hirsute/main arm64 dwz arm64 0.13+20210118-1 [154 kB] Get:87 http://ftpmaster.internal/ubuntu hirsute/main arm64 gettext arm64 0.21-3ubuntu2 [775 kB] Get:88 http://ftpmaster.internal/ubuntu hirsute/main arm64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:89 http://ftpmaster.internal/ubuntu hirsute/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] Get:90 http://ftpmaster.internal/ubuntu hirsute/main arm64 xml-core all 0.18+nmu1 [21.6 kB] Get:91 http://ftpmaster.internal/ubuntu hirsute/main arm64 sgml-data all 2.0.11+nmu1 [171 kB] Get:92 http://ftpmaster.internal/ubuntu hirsute/universe arm64 docbook all 4.5-6 [122 kB] Get:93 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libosp5 arm64 1.5.2-13ubuntu3 [604 kB] Get:94 http://ftpmaster.internal/ubuntu hirsute/universe arm64 opensp arm64 1.5.2-13ubuntu3 [138 kB] Get:95 http://ftpmaster.internal/ubuntu hirsute/universe arm64 docbook-to-man arm64 1:2.0.0-45 [72.3 kB] Get:96 http://ftpmaster.internal/ubuntu hirsute/main arm64 docbook-xml all 4.5-9 [71.2 kB] Get:97 http://ftpmaster.internal/ubuntu hirsute/universe arm64 docbook-xsl all 1.79.2+dfsg-1 [1063 kB] Get:98 http://ftpmaster.internal/ubuntu hirsute/main arm64 libdw1 arm64 0.182-3 [202 kB] Get:99 http://ftpmaster.internal/ubuntu hirsute/main arm64 libasm1 arm64 0.182-3 [13.5 kB] Get:100 http://ftpmaster.internal/ubuntu hirsute/main arm64 elfutils arm64 0.182-3 [406 kB] Get:101 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libdisorder0 arm64 0.0.2+git20130809.8062ee1-2 [4320 B] Get:102 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libfastahack0 arm64 1.0.0+dfsg-7 [23.4 kB] Get:103 http://ftpmaster.internal/ubuntu hirsute/universe arm64 fastahack arm64 1.0.0+dfsg-7 [10.3 kB] Get:104 http://ftpmaster.internal/ubuntu hirsute/main arm64 libfreetype6 arm64 2.10.4+dfsg-1 [323 kB] Get:105 http://ftpmaster.internal/ubuntu hirsute/main arm64 fonts-dejavu-core all 2.37-2 [1041 kB] Get:106 http://ftpmaster.internal/ubuntu hirsute/main arm64 fontconfig-config all 2.13.1-4.2ubuntu2 [28.6 kB] Get:107 http://ftpmaster.internal/ubuntu hirsute/main arm64 libfontconfig1 arm64 2.13.1-4.2ubuntu2 [113 kB] Get:108 http://ftpmaster.internal/ubuntu hirsute/main arm64 fontconfig arm64 2.13.1-4.2ubuntu2 [181 kB] Get:109 http://ftpmaster.internal/ubuntu hirsute/main arm64 pkg-config arm64 0.29.2-1ubuntu1 [44.5 kB] Get:110 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxslt1.1 arm64 1.1.34-4 [141 kB] Get:111 http://ftpmaster.internal/ubuntu hirsute/main arm64 python3-lxml arm64 4.6.2-1 [948 kB] Get:112 http://ftpmaster.internal/ubuntu hirsute/main arm64 python3-pygments all 2.7.1+dfsg-1 [639 kB] Get:113 http://ftpmaster.internal/ubuntu hirsute/main arm64 xsltproc arm64 1.1.34-4 [13.9 kB] Get:114 http://ftpmaster.internal/ubuntu hirsute/universe arm64 gtk-doc-tools all 1.33.1-1 [159 kB] Get:115 http://ftpmaster.internal/ubuntu hirsute/universe arm64 help2man arm64 1.47.17 [181 kB] Get:116 http://ftpmaster.internal/ubuntu hirsute/main arm64 icu-devtools arm64 67.1-5 [178 kB] Get:117 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libonig5 arm64 6.9.5-2 [138 kB] Get:118 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libjq1 arm64 1.6-2.1ubuntu1 [109 kB] Get:119 http://ftpmaster.internal/ubuntu hirsute/universe arm64 jq arm64 1.6-2.1ubuntu1 [50.8 kB] Get:120 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libbackward-cpp-dev all 1.5-2 [31.8 kB] Get:121 http://ftpmaster.internal/ubuntu hirsute/main arm64 libblas3 arm64 3.9.0-3ubuntu1 [89.3 kB] Get:122 http://ftpmaster.internal/ubuntu hirsute/main arm64 libboost1.74-dev arm64 1.74.0-3ubuntu2 [9508 kB] Get:123 http://ftpmaster.internal/ubuntu hirsute/main arm64 libboost-program-options1.74.0 arm64 1.74.0-3ubuntu2 [317 kB] Get:124 http://ftpmaster.internal/ubuntu hirsute/main arm64 libboost-program-options1.74-dev arm64 1.74.0-3ubuntu2 [352 kB] Get:125 http://ftpmaster.internal/ubuntu hirsute/main arm64 libboost-program-options-dev arm64 1.74.0.3ubuntu2 [3188 B] Get:126 http://ftpmaster.internal/ubuntu hirsute/main arm64 libbrotli-dev arm64 1.0.9-2build2 [275 kB] Get:127 http://ftpmaster.internal/ubuntu hirsute/main arm64 libbz2-dev arm64 1.0.8-4ubuntu2 [31.6 kB] Get:128 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpixman-1-0 arm64 0.40.0-1 [137 kB] Get:129 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxcb-render0 arm64 1.14-2.1 [14.6 kB] Get:130 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxcb-shm0 arm64 1.14-2.1 [5592 B] Get:131 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxrender1 arm64 1:0.9.10-1 [16.1 kB] Get:132 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcairo2 arm64 1.16.0-5 [544 kB] Get:133 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcairo-gobject2 arm64 1.16.0-5 [17.1 kB] Get:134 http://ftpmaster.internal/ubuntu hirsute/main arm64 liblzo2-2 arm64 2.10-2 [45.5 kB] Get:135 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcairo-script-interpreter2 arm64 1.16.0-5 [52.6 kB] Get:136 http://ftpmaster.internal/ubuntu hirsute/main arm64 libexpat1-dev arm64 2.2.10-1 [104 kB] Get:137 http://ftpmaster.internal/ubuntu hirsute/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2ubuntu4 [154 kB] Get:138 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpng-dev arm64 1.6.37-3 [175 kB] Get:139 http://ftpmaster.internal/ubuntu hirsute/main arm64 libfreetype-dev arm64 2.10.4+dfsg-1 [481 kB] Get:140 http://ftpmaster.internal/ubuntu hirsute/main arm64 libfreetype6-dev arm64 2.10.4+dfsg-1 [9812 B] Get:141 http://ftpmaster.internal/ubuntu hirsute/main arm64 uuid-dev arm64 2.36.1-1ubuntu2 [35.7 kB] Get:142 http://ftpmaster.internal/ubuntu hirsute/main arm64 libfontconfig-dev arm64 2.13.1-4.2ubuntu2 [133 kB] Get:143 http://ftpmaster.internal/ubuntu hirsute/main arm64 libfontconfig1-dev arm64 2.13.1-4.2ubuntu2 [2028 B] Get:144 http://ftpmaster.internal/ubuntu hirsute/main arm64 xorg-sgml-doctools all 1:1.11-1.1 [10.9 kB] Get:145 http://ftpmaster.internal/ubuntu hirsute/main arm64 x11proto-dev all 2020.1-1 [594 kB] Get:146 http://ftpmaster.internal/ubuntu hirsute/main arm64 x11proto-core-dev all 2020.1-1 [2620 B] Get:147 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxau-dev arm64 1:1.0.9-0ubuntu1 [9728 B] Get:148 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxdmcp-dev arm64 1:1.1.3-0ubuntu1 [25.1 kB] Get:149 http://ftpmaster.internal/ubuntu hirsute/main arm64 xtrans-dev all 1.4.0-1 [68.9 kB] Get:150 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpthread-stubs0-dev arm64 0.4-1 [5376 B] Get:151 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxcb1-dev arm64 1.14-2.1 [81.6 kB] Get:152 http://ftpmaster.internal/ubuntu hirsute/main arm64 libx11-dev arm64 2:1.7.0-2 [635 kB] Get:153 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxrender-dev arm64 1:0.9.10-1 [22.9 kB] Get:154 http://ftpmaster.internal/ubuntu hirsute/main arm64 x11proto-xext-dev all 2020.1-1 [2620 B] Get:155 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxext-dev arm64 2:1.3.4-0ubuntu1 [82.1 kB] Get:156 http://ftpmaster.internal/ubuntu hirsute/main arm64 x11-common all 1:7.7+19ubuntu15 [22.2 kB] Get:157 http://ftpmaster.internal/ubuntu hirsute/main arm64 libice6 arm64 2:1.0.10-1 [37.2 kB] Get:158 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsm6 arm64 2:1.2.3-1 [15.1 kB] Get:159 http://ftpmaster.internal/ubuntu hirsute/main arm64 libice-dev arm64 2:1.0.10-1 [46.0 kB] Get:160 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsm-dev arm64 2:1.2.3-1 [16.4 kB] Get:161 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpixman-1-dev arm64 0.40.0-1 [154 kB] Get:162 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxcb-render0-dev arm64 1.14-2.1 [18.5 kB] Get:163 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxcb-shm0-dev arm64 1.14-2.1 [7036 B] Get:164 http://ftpmaster.internal/ubuntu hirsute/main arm64 libffi-dev arm64 3.4~20200819gead65ca871-0ubuntu3 [54.0 kB] Get:165 http://ftpmaster.internal/ubuntu hirsute/main arm64 libglib2.0-bin arm64 2.66.4-1 [68.9 kB] Get:166 http://ftpmaster.internal/ubuntu hirsute/main arm64 python3-lib2to3 all 3.9.0-1 [76.3 kB] Get:167 http://ftpmaster.internal/ubuntu hirsute/main arm64 python3-distutils all 3.9.0-1 [142 kB] Get:168 http://ftpmaster.internal/ubuntu hirsute/main arm64 libglib2.0-dev-bin arm64 2.66.4-1 [110 kB] Get:169 http://ftpmaster.internal/ubuntu hirsute/main arm64 libblkid-dev arm64 2.36.1-1ubuntu2 [165 kB] Get:170 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsepol1-dev arm64 3.1-1 [318 kB] Get:171 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpcre2-16-0 arm64 10.35-2ubuntu1 [159 kB] Get:172 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpcre2-32-0 arm64 10.35-2ubuntu1 [150 kB] Get:173 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpcre2-posix2 arm64 10.35-2ubuntu1 [5804 B] Get:174 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpcre2-dev arm64 10.35-2ubuntu1 [599 kB] Get:175 http://ftpmaster.internal/ubuntu hirsute/main arm64 libselinux1-dev arm64 3.1-2build2 [150 kB] Get:176 http://ftpmaster.internal/ubuntu hirsute/main arm64 libmount-dev arm64 2.36.1-1ubuntu2 [14.1 kB] Get:177 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpcre16-3 arm64 2:8.39-13 [126 kB] Get:178 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpcre32-3 arm64 2:8.39-13 [118 kB] Get:179 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpcrecpp0v5 arm64 2:8.39-13 [14.7 kB] Get:180 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpcre3-dev arm64 2:8.39-13 [467 kB] Get:181 http://ftpmaster.internal/ubuntu hirsute/main arm64 libglib2.0-dev arm64 2.66.4-1 [1526 kB] Get:182 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcairo2-dev arm64 1.16.0-5 [604 kB] Get:183 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcurl3-gnutls arm64 7.72.0-1ubuntu1 [215 kB] Get:184 http://ftpmaster.internal/ubuntu hirsute/main arm64 libcurl4-gnutls-dev arm64 7.72.0-1ubuntu1 [312 kB] Get:185 http://ftpmaster.internal/ubuntu hirsute/main arm64 libdatrie1 arm64 0.2.12-3 [17.9 kB] Get:186 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libdeflate0 arm64 1.7-1 [47.2 kB] Get:187 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libdeflate-dev arm64 1.7-1 [43.2 kB] Get:188 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libdisorder-dev arm64 0.0.2+git20130809.8062ee1-2 [3816 B] Get:189 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libdivsufsort3 arm64 2.0.1-5 [36.8 kB] Get:190 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libdivsufsort-dev arm64 2.0.1-5 [11.0 kB] Get:191 http://ftpmaster.internal/ubuntu hirsute/main arm64 libelf-dev arm64 0.182-3 [59.3 kB] Get:192 http://ftpmaster.internal/ubuntu hirsute/main arm64 liblzma-dev arm64 5.2.4-1ubuntu1 [144 kB] Get:193 http://ftpmaster.internal/ubuntu hirsute/main arm64 libdw-dev arm64 0.182-3 [281 kB] Get:194 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libfastahack-dev arm64 1.0.0+dfsg-7 [24.6 kB] Get:195 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libfml0 arm64 0.1+git20190320.b499514-1 [64.7 kB] Get:196 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libfml-dev arm64 0.1+git20190320.b499514-1 [77.8 kB] Get:197 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libgflags2.2 arm64 2.2.2-2 [67.0 kB] Get:198 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgfortran5 arm64 10.2.1-6ubuntu1 [345 kB] Get:199 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgmpxx4ldbl arm64 2:6.2.0+dfsg-6ubuntu1 [8816 B] Get:200 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgmp-dev arm64 2:6.2.0+dfsg-6ubuntu1 [299 kB] Get:201 http://ftpmaster.internal/ubuntu hirsute/main arm64 libgraphite2-3 arm64 1.3.14-1 [67.8 kB] Get:202 http://ftpmaster.internal/ubuntu hirsute/main arm64 libharfbuzz0b arm64 2.6.7-1ubuntu1 [313 kB] Get:203 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libhts3 arm64 1.11-4 [320 kB] Get:204 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libhts-dev arm64 1.11-4 [3833 kB] Get:205 http://ftpmaster.internal/ubuntu hirsute/main arm64 libicu-dev arm64 67.1-5 [9459 kB] Get:206 http://ftpmaster.internal/ubuntu hirsute/main arm64 libjansson4 arm64 2.13.1-1ubuntu1 [29.8 kB] Get:207 http://ftpmaster.internal/ubuntu hirsute/main arm64 libjansson-dev arm64 2.13.1-1ubuntu1 [32.5 kB] Get:208 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libjemalloc2 arm64 5.2.1-2 [166 kB] Get:209 http://ftpmaster.internal/ubuntu hirsute/main arm64 libjpeg-turbo8 arm64 2.0.3-0ubuntu2 [101 kB] Get:210 http://ftpmaster.internal/ubuntu hirsute/main arm64 libjpeg8 arm64 8c-2ubuntu8 [2198 B] Get:211 http://ftpmaster.internal/ubuntu hirsute/main arm64 liblapack3 arm64 3.9.0-3ubuntu1 [1528 kB] Get:212 http://ftpmaster.internal/ubuntu hirsute/main arm64 libltdl7 arm64 2.4.6-15 [37.7 kB] Get:213 http://ftpmaster.internal/ubuntu hirsute/main arm64 libmhash2 arm64 0.9.9.9-9 [94.4 kB] Get:214 http://ftpmaster.internal/ubuntu hirsute/main arm64 libncurses-dev arm64 6.2+20201114-2 [335 kB] Get:215 http://ftpmaster.internal/ubuntu hirsute/main arm64 libncurses5-dev arm64 6.2+20201114-2 [984 B] Get:216 http://ftpmaster.internal/ubuntu hirsute/main arm64 libthai-data all 0.1.28-3 [134 kB] Get:217 http://ftpmaster.internal/ubuntu hirsute/main arm64 libthai0 arm64 0.1.28-3 [16.8 kB] Get:218 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpango-1.0-0 arm64 1.46.2-3 [160 kB] Get:219 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpangoft2-1.0-0 arm64 1.46.2-3 [33.6 kB] Get:220 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpangocairo-1.0-0 arm64 1.46.2-3 [22.8 kB] Get:221 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpaper1 arm64 1.1.28 [12.7 kB] Get:222 http://ftpmaster.internal/ubuntu hirsute/main arm64 libpaper-utils arm64 1.1.28 [8328 B] Get:223 http://ftpmaster.internal/ubuntu hirsute/main arm64 libprotobuf-lite23 arm64 3.12.3-2ubuntu4 [169 kB] Get:224 http://ftpmaster.internal/ubuntu hirsute/main arm64 libprotobuf23 arm64 3.12.3-2ubuntu4 [736 kB] Get:225 http://ftpmaster.internal/ubuntu hirsute/main arm64 libprotoc23 arm64 3.12.3-2ubuntu4 [654 kB] Get:226 http://ftpmaster.internal/ubuntu hirsute/main arm64 libyajl2 arm64 2.1.0-3 [19.3 kB] Get:227 http://ftpmaster.internal/ubuntu hirsute/main arm64 libraptor2-0 arm64 2.0.15-0ubuntu2 [146 kB] Get:228 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxml2-dev arm64 2.9.10+dfsg-6.3build1 [682 kB] Get:229 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxslt1-dev arm64 1.1.34-4 [219 kB] Get:230 http://ftpmaster.internal/ubuntu hirsute/main arm64 libyajl-dev arm64 2.1.0-3 [25.0 kB] Get:231 http://ftpmaster.internal/ubuntu hirsute/main arm64 libraptor2-dev arm64 2.0.15-0ubuntu2 [196 kB] Get:232 http://ftpmaster.internal/ubuntu hirsute/main arm64 librasqal3 arm64 0.9.33-0.1 [160 kB] Get:233 http://ftpmaster.internal/ubuntu hirsute/main arm64 librasqal3-dev arm64 0.9.33-0.1 [207 kB] Get:234 http://ftpmaster.internal/ubuntu hirsute/main arm64 librdf0 arm64 1.0.17-1.1ubuntu1 [89.6 kB] Get:235 http://ftpmaster.internal/ubuntu hirsute/main arm64 librdf0-dev arm64 1.0.17-1.1ubuntu1 [230 kB] Get:236 http://ftpmaster.internal/ubuntu hirsute/main arm64 libsnappy1v5 arm64 1.1.8-1build1 [16.0 kB] Get:237 http://ftpmaster.internal/ubuntu hirsute/universe arm64 librocksdb5.17 arm64 5.17.2-3ubuntu1 [1508 kB] Get:238 http://ftpmaster.internal/ubuntu hirsute/universe arm64 librocksdb-dev arm64 5.17.2-3ubuntu1 [2582 kB] Get:239 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libsimde-dev all 0.0.0.git.20200424-1 [87.7 kB] Get:240 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libsmithwaterman0 arm64 0.0+git20160702.2610e25-11 [32.6 kB] Get:241 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libsmithwaterman-dev arm64 0.0+git20160702.2610e25-11 [36.0 kB] Get:242 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libsparsehash-dev all 2.0.3-2 [71.7 kB] Get:243 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libssw0 arm64 1.1-12 [17.8 kB] Get:244 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libssw-dev arm64 1.1-12 [20.1 kB] Get:245 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libtabixpp0 arm64 1.1.0-3 [8456 B] Get:246 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libtabixpp-dev arm64 1.1.0-3 [6920 B] Get:247 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtcl8.6 arm64 8.6.11+dfsg-1 [858 kB] Get:248 http://ftpmaster.internal/ubuntu hirsute/main arm64 libjbig0 arm64 2.1-3.1build1 [24.0 kB] Get:249 http://ftpmaster.internal/ubuntu hirsute/main arm64 libwebp6 arm64 0.6.1-2 [155 kB] Get:250 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtiff5 arm64 4.1.0+git201212-1ubuntu1 [155 kB] Get:251 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxft2 arm64 2.3.3-0ubuntu1 [35.9 kB] Get:252 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxss1 arm64 1:1.2.3-1 [8080 B] Get:253 http://ftpmaster.internal/ubuntu hirsute/main arm64 libtk8.6 arm64 8.6.11-1 [680 kB] Get:254 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libtsl-hopscotch-map-dev all 2.3.0-1 [36.5 kB] Get:255 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libvcflib1 arm64 1.0.1+dfsg-4 [133 kB] Get:256 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libvcflib-dev arm64 1.0.1+dfsg-4 [27.0 kB] Get:257 http://ftpmaster.internal/ubuntu hirsute/main arm64 zip arm64 3.0-11build1 [146 kB] Get:258 http://ftpmaster.internal/ubuntu hirsute/main arm64 unzip arm64 6.0-25ubuntu1 [163 kB] Get:259 http://ftpmaster.internal/ubuntu hirsute/main arm64 xdg-utils all 1.1.3-2ubuntu2 [61.5 kB] Get:260 http://ftpmaster.internal/ubuntu hirsute/main arm64 libxt6 arm64 1:1.2.0-1 [147 kB] Get:261 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-base-core arm64 4.0.3-1 [24.8 MB] Get:262 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-littler arm64 0.3.12-1 [81.9 kB] Get:263 http://ftpmaster.internal/ubuntu hirsute/universe arm64 littler all 0.3.12-1 [2380 B] Get:264 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-pkgkitten all 0.2.0-1 [23.6 kB] Get:265 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-rcpp arm64 1.0.5-1 [1945 kB] Get:266 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-plyr arm64 1.8.6-2build1 [830 kB] Get:267 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-digest arm64 0.6.27-1 [174 kB] Get:268 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-glue arm64 1.4.2-1 [134 kB] Get:269 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-gtable all 0.3.0+dfsg-2build1 [138 kB] Get:270 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-assertthat all 0.2.1-2build1 [56.5 kB] Get:271 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-crayon all 1.3.4-5 [498 kB] Get:272 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-fansi arm64 0.4.2-1 [340 kB] Get:273 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-cli all 2.2.0-1 [442 kB] Get:274 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-rlang arm64 0.4.8-1 [1130 kB] Get:275 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-ellipsis arm64 0.3.1-1build1 [31.8 kB] Get:276 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-evaluate all 0.14-2build1 [81.4 kB] Get:277 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-magrittr all 1.5-6build1 [154 kB] Get:278 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-r6 all 2.5.0-1 [98.5 kB] Get:279 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-rprojroot all 2.0.2-1 [114 kB] Get:280 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-desc all 1.2.0-3build1 [299 kB] Get:281 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-ps arm64 1.5.0-1 [276 kB] Get:282 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-processx arm64 3.4.5-1 [294 kB] Get:283 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-callr all 3.5.1-1 [386 kB] Get:284 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-prettyunits all 1.1.1-2build1 [39.6 kB] Get:285 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-withr all 2.3.0-1 [195 kB] Get:286 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-pkgbuild all 1.1.0-1 [145 kB] Get:287 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-rstudioapi all 0.13-1 [256 kB] Get:288 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-pkgload arm64 1.1.0-1 [168 kB] Get:289 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-praise all 1.0.0-4build1 [20.3 kB] Get:290 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-testthat arm64 2.3.2-2build1 [1047 kB] Get:291 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-isoband arm64 0.2.3-2 [1928 kB] Get:292 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-mass arm64 7.3-53-1 [1109 kB] Get:293 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-lattice arm64 0.20-41-1build1 [1120 kB] Get:294 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-nlme arm64 3.1.151-1 [2222 kB] Get:295 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-matrix arm64 1.2-18-1build1 [3408 kB] Get:296 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-mgcv arm64 1.8-33-1 [2912 kB] Get:297 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-farver arm64 2.0.3-1build2 [1323 kB] Get:298 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-labeling all 0.4.2-1 [62.6 kB] Get:299 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-lifecycle all 0.2.0-2build1 [93.3 kB] Get:300 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-colorspace arm64 2.0-0+dfsg-1 [1533 kB] Get:301 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-munsell all 0.5.0-2build1 [208 kB] Get:302 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-rcolorbrewer all 1.1-2-3 [54.6 kB] Get:303 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-viridislite all 0.3.0-4 [58.9 kB] Get:304 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-scales all 1.1.1-1build1 [486 kB] Get:305 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-utf8 arm64 1.1.4-2 [130 kB] Get:306 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-vctrs arm64 0.3.6-1 [1040 kB] Get:307 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-pillar all 1.4.7-1 [225 kB] Get:308 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] Get:309 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-tibble arm64 3.0.4-1 [422 kB] Get:310 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-ggplot2 all 3.3.2+dfsg-2 [3124 kB] Get:311 http://ftpmaster.internal/ubuntu hirsute/universe arm64 r-cran-gridbase all 0.4-7-5build1 [163 kB] Get:312 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libvcflib-tools arm64 1.0.1+dfsg-4 [583 kB] Get:313 http://ftpmaster.internal/ubuntu hirsute/main arm64 pv arm64 1.6.6-1 [50.5 kB] Get:314 http://ftpmaster.internal/ubuntu hirsute/universe arm64 rapidjson-dev all 1.1.0+dfsg2-7 [95.0 kB] Get:315 http://ftpmaster.internal/ubuntu hirsute/main arm64 raptor2-utils arm64 2.0.15-0ubuntu2 [13.4 kB] Get:316 http://ftpmaster.internal/ubuntu hirsute/main arm64 rasqal-utils arm64 0.9.33-0.1 [17.8 kB] Get:317 http://ftpmaster.internal/ubuntu hirsute/universe arm64 rs arm64 20200313-1 [15.6 kB] Get:318 http://ftpmaster.internal/ubuntu hirsute/universe arm64 samtools arm64 1.11-1 [495 kB] Get:319 http://ftpmaster.internal/ubuntu hirsute/universe arm64 libjemalloc-dev arm64 5.2.1-2 [294 kB] Get:320 http://ftpmaster.internal/ubuntu hirsute/main arm64 liblz4-dev arm64 1.9.3-0ubuntu1 [72.1 kB] Get:321 http://ftpmaster.internal/ubuntu hirsute/main arm64 libprotobuf-dev arm64 3.12.3-2ubuntu4 [1170 kB] Get:322 http://ftpmaster.internal/ubuntu hirsute/main arm64 libprotoc-dev arm64 3.12.3-2ubuntu4 [850 kB] Get:323 http://ftpmaster.internal/ubuntu hirsute/universe arm64 protobuf-compiler arm64 3.12.3-2ubuntu4 [28.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 148 MB in 10s (15.5 MB/s) Selecting previously unselected package liblocale-gettext-perl. 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Setting up libblas3:arm64 (3.9.0-3ubuntu1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libglib2.0-data (2.66.4-1) ... Setting up libgmpxx4ldbl:arm64 (2:6.2.0+dfsg-6ubuntu1) ... Setting up libuv1:arm64 (1.40.0-1) ... Setting up libexpat1-dev:arm64 (2.2.10-1) ... Setting up libfreetype6:arm64 (2.10.4+dfsg-1) ... Setting up libboost-program-options-dev:arm64 (1.74.0.3ubuntu2) ... Setting up libx11-data (2:1.7.0-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2build2) ... Setting up uuid-dev:arm64 (2.36.1-1ubuntu2) ... Setting up libprotoc23:arm64 (3.12.3-2ubuntu4) ... Setting up libtsl-hopscotch-map-dev (2.3.0-1) ... Setting up libfribidi0:arm64 (1.0.8-2) ... Setting up libpcre32-3:arm64 (2:8.39-13) ... Setting up libtcl8.6:arm64 (8.6.11+dfsg-1) ... Setting up autopoint (0.21-3ubuntu2) ... Setting up libwebp6:arm64 (0.6.1-2) ... Setting up icu-devtools (67.1-5) ... Setting up liblz4-dev:arm64 (1.9.3-0ubuntu1) ... Setting up pkg-config (0.29.2-1ubuntu1) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up ucf (3.0043) ... Setting up libpcre2-posix2:arm64 (10.35-2ubuntu1) ... Setting up libdisorder-dev:arm64 (0.0.2+git20130809.8062ee1-2) ... Setting up libjpeg-turbo8:arm64 (2.0.3-0ubuntu2) ... Setting up libltdl7:arm64 (2.4.6-15) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2ubuntu1) ... Setting up libssh-4:arm64 (0.9.5-1) ... Setting up libgfortran5:arm64 (10.2.1-6ubuntu1) ... Setting up libroken18-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up autoconf (2.69-14) ... Setting up libjsoncpp24:arm64 (1.9.4-4) ... Setting up libmhash2:arm64 (0.9.9.9-9) ... Setting up libyajl-dev:arm64 (2.1.0-3) ... Setting up liblzma-dev:arm64 (5.2.4-1ubuntu1) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2ubuntu4) ... Setting up pv (1.6.6-1) ... Setting up librhash0:arm64 (1.4.1-1) ... 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Setting up libxdmcp6:arm64 (1:1.1.3-0ubuntu1) ... Setting up flex (2.6.4-8) ... Setting up liblapack3:arm64 (3.9.0-3ubuntu1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.14-2.1) ... Setting up gettext (0.21-3ubuntu2) ... Setting up libfml-dev:arm64 (0.1+git20190320.b499514-1) ... Setting up libgmp-dev:arm64 (2:6.2.0+dfsg-6ubuntu1) ... Setting up mime-support (3.66) ... Setting up libxau-dev:arm64 (1:1.0.9-0ubuntu1) ... Setting up libpcre2-dev:arm64 (10.35-2ubuntu1) ... Setting up protobuf-compiler (3.12.3-2ubuntu4) ... Setting up libice-dev:arm64 (2:1.0.10-1) ... Setting up libssw-dev:arm64 (1.1-12) ... Setting up libtool (2.4.6-15) ... Setting up libarchive13:arm64 (3.4.3-2) ... Setting up libxcb-render0:arm64 (1.14-2.1) ... Setting up libselinux1-dev:arm64 (3.1-2build2) ... Setting up libjq1:arm64 (1.6-2.1ubuntu1) ... 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Setting up libsmithwaterman-dev (0.0+git20160702.2610e25-11) ... Setting up calendar (12.1.7) ... Setting up dh-strip-nondeterminism (1.10.0-1) ... Setting up x11proto-xext-dev (2020.1-1) ... Setting up dwz (0.13+20210118-1) ... Setting up libprotoc-dev:arm64 (3.12.3-2ubuntu4) ... Setting up groff-base (1.22.4-5) ... Setting up xml-core (0.18+nmu1) ... Setting up jq (1.6-2.1ubuntu1) ... Setting up libxslt1.1:arm64 (1.1.34-4) ... Setting up libx11-6:arm64 (2:1.7.0-2) ... Setting up libasm1:arm64 (0.182-3) ... Setting up libtiff5:arm64 (4.1.0+git201212-1ubuntu1) ... Setting up libfontconfig1:arm64 (2.13.1-4.2ubuntu2) ... Setting up librocksdb5.17 (5.17.2-3ubuntu1) ... Setting up libsm6:arm64 (2:1.2.3-1) ... Setting up libmount-dev:arm64 (2.36.1-1ubuntu2) ... Setting up python3.9 (3.9.1-3) ... Setting up librocksdb-dev (5.17.2-3ubuntu1) ... Setting up elfutils (0.182-3) ... Setting up fontconfig (2.13.1-4.2ubuntu2) ... Regenerating fonts cache... done. Setting up libxcb1-dev:arm64 (1.14-2.1) ... Setting up libxslt1-dev:arm64 (1.1.34-4) ... Setting up libxrender1:arm64 (1:0.9.10-1) ... Setting up libsm-dev:arm64 (2:1.2.3-1) ... Setting up libhx509-5-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:arm64 (1.46.2-3) ... Setting up xsltproc (1.1.34-4) ... Setting up libx11-dev:arm64 (2:1.7.0-2) ... Setting up libxext6:arm64 (2:1.3.4-0ubuntu1) ... Setting up python3 (3.9.0-3ubuntu1) ... Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libdw-dev:arm64 (0.182-3) ... Setting up libcairo2:arm64 (1.16.0-5) ... Setting up libfreetype6-dev:arm64 (2.10.4+dfsg-1) ... Setting up libxcb-shm0-dev:arm64 (1.14-2.1) ... Setting up bsdmainutils (12.1.7) ... Setting up libxcb-render0-dev:arm64 (1.14-2.1) ... Setting up libxt6:arm64 (1:1.2.0-1) ... Setting up libxext-dev:arm64 (2:1.3.4-0ubuntu1) ... Setting up python3-lxml:arm64 (4.6.2-1) ... Setting up libcairo-gobject2:arm64 (1.16.0-5) ... Setting up libxss1:arm64 (1:1.2.3-1) ... Setting up libpangoft2-1.0-0:arm64 (1.46.2-3) ... Setting up python3-lib2to3 (3.9.0-1) ... Setting up libxrender-dev:arm64 (1:0.9.10-1) ... Setting up libpangocairo-1.0-0:arm64 (1.46.2-3) ... Setting up libkrb5-26-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up python3-pkg-resources (51.1.0-1) ... Setting up python3-distutils (3.9.0-1) ... Setting up libcairo-script-interpreter2:arm64 (1.16.0-5) ... Setting up libglib2.0-dev-bin (2.66.4-1) ... Setting up libxft2:arm64 (2.3.3-0ubuntu1) ... Setting up libfontconfig-dev:arm64 (2.13.1-4.2ubuntu2) ... Setting up libtk8.6:arm64 (8.6.11-1) ... Setting up libheimntlm0-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up python3-pygments (2.7.1+dfsg-1) ... Setting up libglib2.0-dev:arm64 (2.66.4-1) ... Setting up libgssapi3-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up libcairo2-dev:arm64 (1.16.0-5) ... Setting up libfontconfig1-dev:arm64 (2.13.1-4.2ubuntu2) ... Setting up libldap-2.4-2:arm64 (2.4.56+dfsg-1ubuntu1) ... Setting up libcurl3-gnutls:arm64 (7.72.0-1ubuntu1) ... Setting up libcurl4-gnutls-dev:arm64 (7.72.0-1ubuntu1) ... Setting up libcurl4:arm64 (7.72.0-1ubuntu1) ... Setting up libhts3:arm64 (1.11-4) ... Setting up libraptor2-0:arm64 (2.0.15-0ubuntu2) ... Setting up raptor2-utils (2.0.15-0ubuntu2) ... Setting up libhts-dev:arm64 (1.11-4) ... Setting up samtools (1.11-1) ... Setting up r-base-core (4.0.3-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.3.4-5) ... Setting up r-cran-gtable (0.3.0+dfsg-2build1) ... Setting up r-cran-labeling (0.4.2-1) ... Setting up r-cran-lattice (0.20-41-1build1) ... Setting up r-cran-ps (1.5.0-1) ... Setting up r-cran-nlme (3.1.151-1) ... Setting up r-cran-farver (2.0.3-1build2) ... Setting up r-cran-viridislite (0.3.0-4) ... 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Setting up r-cran-vctrs (0.3.6-1) ... Setting up r-cran-pillar (1.4.7-1) ... Setting up r-cran-pkgload (1.1.0-1) ... Setting up r-cran-tibble (3.0.4-1) ... Setting up r-cran-testthat (2.3.2-2build1) ... Setting up r-cran-isoband (0.2.3-2) ... Setting up r-cran-ggplot2 (3.3.2+dfsg-2) ... Setting up libvcflib-tools (1.0.1+dfsg-4) ... Setting up debhelper (13.3.1ubuntu2) ... Setting up dh-autoreconf (19) ... Processing triggers for libc-bin (2.32-0ubuntu6) ... Processing triggers for sgml-base (1.30) ... Setting up docbook-xsl (1.79.2+dfsg-1) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.30) ... Setting up docbook-xml (4.5-9) ... Setting up docbook (4.5-6) ... Processing triggers for sgml-base (1.30) ... Setting up docbook-to-man (1:2.0.0-45) ... Setting up gtk-doc-tools (1.33.1-1) ... Setting up sbuild-build-depends-vg-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-132-generic arm64 (aarch64) Toolchain package versions: binutils_2.35.50.20210106-1ubuntu2 dpkg-dev_1.20.7.1ubuntu11 g++-10_10.2.1-6ubuntu1 gcc-10_10.2.1-6ubuntu1 libc6-dev_2.32-0ubuntu6 libstdc++-10-dev_10.2.1-6ubuntu1 libstdc++6_10.2.1-6ubuntu1 linux-libc-dev_5.8.0-36.40+21.04.1 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1build1 apt_2.1.18 autoconf_2.69-14 automake_1:1.16.3-2ubuntu1 autopoint_0.21-3ubuntu2 autotools-dev_20180224.1+nmu1 base-files_11ubuntu16 base-passwd_3.5.48 bash_5.1-1ubuntu1 bc_1.07.1-2build2 binutils_2.35.50.20210106-1ubuntu2 binutils-aarch64-linux-gnu_2.35.50.20210106-1ubuntu2 binutils-common_2.35.50.20210106-1ubuntu2 bison_2:3.7.4+dfsg-1 bsdextrautils_2.36.1-1ubuntu2 bsdmainutils_12.1.7 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python3_3.9.0-3ubuntu1 python3-distutils_3.9.0-1 python3-lib2to3_3.9.0-1 python3-lxml_4.6.2-1 python3-minimal_3.9.0-3ubuntu1 python3-pkg-resources_51.1.0-1 python3-pygments_2.7.1+dfsg-1 python3.9_3.9.1-3 python3.9-minimal_3.9.1-3 r-base-core_4.0.3-1 r-cran-assertthat_0.2.1-2build1 r-cran-callr_3.5.1-1 r-cran-cli_2.2.0-1 r-cran-colorspace_2.0-0+dfsg-1 r-cran-crayon_1.3.4-5 r-cran-desc_1.2.0-3build1 r-cran-digest_0.6.27-1 r-cran-ellipsis_0.3.1-1build1 r-cran-evaluate_0.14-2build1 r-cran-fansi_0.4.2-1 r-cran-farver_2.0.3-1build2 r-cran-ggplot2_3.3.2+dfsg-2 r-cran-glue_1.4.2-1 r-cran-gridbase_0.4-7-5build1 r-cran-gtable_0.3.0+dfsg-2build1 r-cran-isoband_0.2.3-2 r-cran-labeling_0.4.2-1 r-cran-lattice_0.20-41-1build1 r-cran-lifecycle_0.2.0-2build1 r-cran-littler_0.3.12-1 r-cran-magrittr_1.5-6build1 r-cran-mass_7.3-53-1 r-cran-matrix_1.2-18-1build1 r-cran-mgcv_1.8-33-1 r-cran-munsell_0.5.0-2build1 r-cran-nlme_3.1.151-1 r-cran-pillar_1.4.7-1 r-cran-pkgbuild_1.1.0-1 r-cran-pkgconfig_2.0.3-2build1 r-cran-pkgkitten_0.2.0-1 r-cran-pkgload_1.1.0-1 r-cran-plyr_1.8.6-2build1 r-cran-praise_1.0.0-4build1 r-cran-prettyunits_1.1.1-2build1 r-cran-processx_3.4.5-1 r-cran-ps_1.5.0-1 r-cran-r6_2.5.0-1 r-cran-rcolorbrewer_1.1-2-3 r-cran-rcpp_1.0.5-1 r-cran-rlang_0.4.8-1 r-cran-rprojroot_2.0.2-1 r-cran-rstudioapi_0.13-1 r-cran-scales_1.1.1-1build1 r-cran-testthat_2.3.2-2build1 r-cran-tibble_3.0.4-1 r-cran-utf8_1.1.4-2 r-cran-vctrs_0.3.6-1 r-cran-viridislite_0.3.0-4 r-cran-withr_2.3.0-1 rapidjson-dev_1.1.0+dfsg2-7 raptor2-utils_2.0.15-0ubuntu2 rasqal-utils_0.9.33-0.1 readline-common_8.1-1 rpcsvc-proto_1.4.2-0ubuntu4 rs_20200313-1 samtools_1.11-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-vg-dummy_0.invalid.0 sed_4.7-1ubuntu1 sensible-utils_0.0.14 sgml-base_1.30 sgml-data_2.0.11+nmu1 systemd_247.1-4ubuntu1 systemd-sysv_247.1-4ubuntu1 systemd-timesyncd_247.1-4ubuntu1 sysvinit-utils_2.96-5ubuntu1 tar_1.32+dfsg-1 tzdata_2020f-1ubuntu2 ubuntu-keyring_2020.06.17.1 ucf_3.0043 unzip_6.0-25ubuntu1 util-linux_2.36.1-1ubuntu2 uuid-dev_2.36.1-1ubuntu2 x11-common_1:7.7+19ubuntu15 x11proto-core-dev_2020.1-1 x11proto-dev_2020.1-1 x11proto-xext-dev_2020.1-1 xdg-utils_1.1.3-2ubuntu2 xml-core_0.18+nmu1 xorg-sgml-doctools_1:1.11-1.1 xsltproc_1.1.34-4 xtrans-dev_1.4.0-1 xz-utils_5.2.4-1ubuntu1 zip_3.0-11build1 zlib1g_1:1.2.11.dfsg-2ubuntu4 zlib1g-dev_1:1.2.11.dfsg-2ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sat Dec 12 12:18:23 2020 UTC gpgv: using RSA key D56571B88A8BBAF140BF63D6BD7EAA60778FA6F5 gpgv: issuer "doko@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./vg_1.27.1+ds-1build1.dsc dpkg-source: info: extracting vg in /<>/vg-1.27.1+ds dpkg-source: info: unpacking vg_1.27.1+ds.orig.tar.xz dpkg-source: info: unpacking vg_1.27.1+ds-1build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_packaged_libdeflate dpkg-source: info: applying use_packaged_boost dpkg-source: info: applying use_packaged_jemalloc dpkg-source: info: applying use_packaged_libbackward-cpp dpkg-source: info: applying use_packaged_rocksdb dpkg-source: info: applying use_packaged_elfutils dpkg-source: info: applying use_packaged_raptor2 dpkg-source: info: applying no_need_for_snappy dpkg-source: info: applying use_packaged_sparsehash dpkg-source: info: applying use_packaged_ssw dpkg-source: info: applying use_packaged_rapidjson dpkg-source: info: applying use_packaged_fermi-lite dpkg-source: info: applying spelling dpkg-source: info: applying no_rpath dpkg-source: info: applying no_pg dpkg-source: info: applying use_packaged_fastahack dpkg-source: info: applying hardening_flags dpkg-source: info: applying use_packaged_smithwaterman dpkg-source: info: applying static dpkg-source: info: applying use_packaged_lz4 dpkg-source: info: applying parallize_better dpkg-source: info: applying use_packaged_libtsl-hopscotch-map-dev dpkg-source: info: applying libVCFH_unneeded dpkg-source: info: applying better_clean dpkg-source: info: applying use_packaged_vcflib dpkg-source: info: applying use_packaged_htslib dpkg-source: info: applying simde dpkg-source: info: applying crossbuild dpkg-source: info: applying python3 Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-20599634 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-20599634 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-20599634 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package vg dpkg-buildpackage: info: source version 1.27.1+ds-1build1 dpkg-buildpackage: info: source distribution hirsute dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/vg-1.27.1+ds' dh_auto_clean || true make -j4 clean make[2]: Entering directory '/<>/vg-1.27.1+ds' rm -f -r lib rm -f -r obj/unittest rm -f -r obj/subcommand rm -f -r obj/io rm -f -r obj/algorithms rm -f -r obj rm -f -r share/ cd ./deps && cd sonLib && make clean make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/sonLib' cd C && make clean cd externalTools && make clean make[4]: Entering directory '/<>/vg-1.27.1+ds/deps/sonLib/C' make[4]: Entering directory '/<>/vg-1.27.1+ds/deps/sonLib/externalTools' cd cutest && make clean cd quicktree_1.1 && make clean rm -rf ../bin ../lib make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/sonLib/externalTools/cutest' make[4]: Leaving directory '/<>/vg-1.27.1+ds/deps/sonLib/C' make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/sonLib/externalTools/cutest' make[4]: Leaving directory '/<>/vg-1.27.1+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/gcsa2' Makefile:2: ../sdsl-lite/Make.helper: No such file or directory make[3]: *** No rule to make target '../sdsl-lite/Make.helper'. Stop. make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/gcsa2' make[2]: *** [Makefile:637: clean] Error 2 make[2]: Leaving directory '/<>/vg-1.27.1+ds' dh_auto_clean: error: make -j4 clean returned exit code 2 make[1]: Leaving directory '/<>/vg-1.27.1+ds' debian/rules override_dh_clean make[1]: Entering directory '/<>/vg-1.27.1+ds' rm -Rf ./deps/DYNAMIC/build/CMakeFiles dh_clean make[1]: Leaving directory '/<>/vg-1.27.1+ds' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a debian/rules override_dh_autoreconf make[1]: Entering directory '/<>/vg-1.27.1+ds' dh_autoreconf --sourcedirectory=/<>/vg-1.27.1+ds/deps/vowpal_wabbit libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' libtoolize: copying file 'acinclude.d/ltoptions.m4' libtoolize: copying file 'acinclude.d/ltsugar.m4' libtoolize: copying file 'acinclude.d/ltversion.m4' libtoolize: copying file 'acinclude.d/lt~obsolete.m4' configure.ac:15: installing './compile' configure.ac:13: installing './config.guess' configure.ac:13: installing './config.sub' configure.ac:3: installing './install-sh' configure.ac:3: installing './missing' cluster/Makefile.am: installing './depcomp' make[1]: Leaving directory '/<>/vg-1.27.1+ds' dh_auto_configure -a debian/rules override_dh_auto_build-arch make[1]: Entering directory '/<>/vg-1.27.1+ds' mkdir -p /<>/vg-1.27.1+ds/debian/help dh_auto_build -- all test/build_graph bin/shuf make -j4 "INSTALL=install --strip-program=true" all test/build_graph bin/shuf make[2]: Entering directory '/<>/vg-1.27.1+ds' . ./source_me.sh && cd deps/sdsl-lite && BUILD_PORTABLE=1 CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" ./install.sh /<>/vg-1.27.1+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /<>/vg-1.27.1+ds/lib && cp -r src/include/handlegraph /<>/vg-1.27.1+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /<>/vg-1.27.1+ds/lib/ && cp obj/* /<>/vg-1.27.1+ds/obj && cp src/*.h /<>/vg-1.27.1+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /<>/vg-1.27.1+ds/lib/libsonlib.a && mkdir -p /<>/vg-1.27.1+ds/include/sonLib && cp lib/*.h /<>/vg-1.27.1+ds/include/sonLib make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/gssw' gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c Library will be installed in '/<>/vg-1.27.1+ds' make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/sonLib' cd externalTools && make all WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. make[4]: Entering directory '/<>/vg-1.27.1+ds/deps/sonLib/externalTools' CMake Warning (dev) at /usr/share/cmake-3.18/Modules/GNUInstallDirs.cmake:225 (message): Unable to determine default CMAKE_INSTALL_LIBDIR directory because no target architecture is known. Please enable at least one language before including GNUInstallDirs. Call Stack (most recent call first): CMakeLists.txt:5 (include) This warning is for project developers. Use -Wno-dev to suppress it. cd cutest && make all make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/sonLib/externalTools/cutest' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make all CC="gcc -std=c99" make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- The C compiler identification is GNU 10.2.1 -- Detecting CXX compiler ABI info gcc -std=c99 -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done gcc -std=c99 -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c -- Detecting C compiler ABI info ./src/distancemat.c: In function ‘read_phylip_DistanceMatrix’: ./src/distancemat.c:390:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 390 | fscanf( handle, "%s", identifier ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/distancemat.c:397:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 397 | fscanf( handle, "%lf", &dist); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done -- Generating done -- Build files have been written to: /<>/vg-1.27.1+ds/deps/libhandlegraph make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/libhandlegraph' /usr/bin/cmake -S/<>/vg-1.27.1+ds/deps/libhandlegraph -B/<>/vg-1.27.1+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/vg-1.27.1+ds/deps/libhandlegraph/CMakeFiles /<>/vg-1.27.1+ds/deps/libhandlegraph//CMakeFiles/progress.marks gcc -std=c99 -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c -- Detecting C compiler ABI info - done make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/vg-1.27.1+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libhandlegraph' cd /<>/vg-1.27.1+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG Scanning dependencies of target handlegraph_objs make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libhandlegraph' [ 33%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/g++ -I/<>/vg-1.27.1+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o -c /<>/vg-1.27.1+ds/deps/libhandlegraph/src/handle.cpp gcc -std=c99 -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c gcc -std=c99 -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS gcc -std=c99 -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success gcc -std=c99 -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c ./src/tree.c: In function ‘read_newhampshire_Tnode’: ./src/tree.c:393:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 393 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:406:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 406 | fscanf( handle, "%1s", &c); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:417:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 417 | fscanf( handle, "%1s", &c); /* should be ) */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:420:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 420 | fscanf( handle, "%1s", &c); /* should be : */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c: In function ‘read_newhampshire_Tree’: ./src/tree.c:468:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 468 | fscanf( handle, "("); | ^~~~~~~~~~~~~~~~~~~~ ./src/tree.c:475:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 475 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:484:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fscanf( handle, "%1s", &c ); /* should be , */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:493:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 493 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ./src/tree.c:496:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 496 | fscanf( handle, "%1s", &c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -- Performing Test HAVE_CXA_DEMANGLE -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio -- Looking for C++ include cstdio - found In file included from /usr/include/string.h:519, from src/gssw.c:37: In function ‘strncpy’, inlined from ‘gssw_node_create’ at src/gssw.c:4958:5: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:91:10: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ gcc -std=c99 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -g -o bin/quicktree ./obj/align.o ./obj/cluster.o ./obj/distancemat.o ./obj/options.o ./obj/util.o ./obj/sequence.o ./obj/quicktree.o ./obj/buildtree.o ./obj/tree.o -lm -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libhandlegraph' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libhandlegraph' cd /<>/vg-1.27.1+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= Scanning dependencies of target handlegraph_static make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libhandlegraph' [ 66%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake -- Configuring done /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libhandlegraph' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libhandlegraph' cd /<>/vg-1.27.1+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= Scanning dependencies of target handlegraph_shared make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libhandlegraph' [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o -- Generating done -- Build files have been written to: /<>/vg-1.27.1+ds/deps/sdsl-lite/build make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/vg-1.27.1+ds/deps/sdsl-lite -B/<>/vg-1.27.1+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/<>/vg-1.27.1+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/vg-1.27.1+ds/deps/sdsl-lite -B/<>/vg-1.27.1+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/vg-1.27.1+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/<>/vg-1.27.1+ds/deps/sdsl-lite/build' cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/sdsl-lite /<>/vg-1.27.1+ds/deps/sdsl-lite/lib /<>/vg-1.27.1+ds/deps/sdsl-lite/build /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target sdsl make[6]: Leaving directory '/<>/vg-1.27.1+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/<>/vg-1.27.1+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/bits.cpp [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libhandlegraph' [100%] Built target handlegraph_shared make[4]: Leaving directory '/<>/vg-1.27.1+ds/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /<>/vg-1.27.1+ds/deps/libhandlegraph/CMakeFiles 0 make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/libhandlegraph' . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/<>/vg-1.27.1+ds/include" make libs && cp lib/libsublinearLS.a /<>/vg-1.27.1+ds/lib/ && mkdir -p /<>/vg-1.27.1+ds/include/sublinearLS && cp src/*.hpp /<>/vg-1.27.1+ds/include/sublinearLS/ make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens' rm -f /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/bin/* /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/*.o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/test/*.o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens' make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens' if [ ! -d /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj; fi if [ ! -d /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/test; fi if [ ! -d /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/bin; fi if [ ! -d /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/<>/vg-1.27.1+ds/include -L. -L/<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/math.o make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/<>/vg-1.27.1+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/<>/vg-1.27.1+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/<>/vg-1.27.1+ds/include -L. -L/<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/reference.o mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C # Make dest directory gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In function ‘strncpy’, inlined from ‘gssw_node_create.constprop’ at src/gssw.c:4958:5: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:91:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ src/gssw.c: In function ‘gssw_node_create.constprop’: src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:697:75: note: declared here 697 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:705:68: note: declared here 705 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:706:68: note: declared here 706 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp: In member function ‘sdsl::coder::elias_delta::impl::impl()’: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t[1]’ [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t[1]’ [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t[1]’ [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t[1]’ [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t[1]’ [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t[1]’ [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:82:35: note: while referencing ‘x’ 82 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In function ‘strncpy’, inlined from ‘gssw_node_create.constprop’ at src/gssw.c:4958:5: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:91:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ src/gssw.c: In function ‘gssw_node_create.constprop’: src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/<>/vg-1.27.1+ds/include -L. -L/<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/probability.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp: In member function ‘sdsl::coder::elias_gamma::impl::impl()’: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t[1]’ [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t[1]’ [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:51:31: note: while referencing ‘x’ 51 | for (uint64_t x=0; x < (1<<16); ++x) { | ^ In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t[1]’ [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t[1]’ [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:80:35: note: while referencing ‘x’ 80 | for (uint64_t x=0; x < (1<<8); ++x) { | ^ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/<>/vg-1.27.1+ds/include -L. -L/<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/config.cpp gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/gssw_test.c -o bin/gssw_test obj/gssw.o -lm -lz cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/<>/vg-1.27.1+ds/include -L. -L/<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In function ‘strncpy’, inlined from ‘gssw_node_create.constprop’ at src/gssw.c:4958:5: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:91:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ src/gssw.c: In function ‘gssw_node_create.constprop’: src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_config.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_isa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/<>/vg-1.27.1+ds/include -L. -L/<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/DP_map.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C ar rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/gssw' . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /<>/vg-1.27.1+ds/lib/ && cp -r src/include/structures /<>/vg-1.27.1+ds/include/ make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi find bin obj lib -type f -delete g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/<>/vg-1.27.1+ds/include -L. -L/<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/structures' make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/structures' if [ ! -d bin ]; then mkdir -p bin; fi if [ ! -d obj ]; then mkdir -p obj; fi if [ ! -d lib ]; then mkdir -p lib; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c src/union_find.cpp -o obj/union_find.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/<>/vg-1.27.1+ds/include -L. -L/<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/allele.o cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -I inc -I ../lib/ -c impl/*.cpp ar rc sonLib.a *.o ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o ranlib sonLib.a g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/<>/vg-1.27.1+ds/include -L. -L/<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/row_set.o rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -Wno-error=return-type -I/<>/vg-1.27.1+ds/include -L. -L/<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp: In member function ‘std::size_t haplotypeStateNode::node_to_child_index(const haplotypeStateNode*) const’: /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp:96:1: warning: control reaches end of non-void function [-Wreturn-type] 96 | } | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/<>/vg-1.27.1+ds/include -L. -L/<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c src/stable_double.cpp -o obj/stable_double.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/<>/vg-1.27.1+ds/include -L. -L/<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o rm -f lib/libstructures.a ar rs lib/libstructures.a obj/union_find.o obj/suffix_tree.o obj/stable_double.o ar: creating lib/libstructures.a make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/structures' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/<>/vg-1.27.1+ds/include -L. -L/<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_lcp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -g -I/<>/vg-1.27.1+ds/include -L. -L/<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rc /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/math.o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/reference.o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/probability.o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/allele.o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/row_set.o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o ranlib /<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/sublinear-Li-Stephens' . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.pc//g' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e 's/libvw_c_wrapper\.la//g' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper\.pc/d' configure.ac . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/vwdll/d' Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && sed -i -e '/libvw_c_wrapper/d' vowpalwabbit/Makefile.am . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3" ./autogen.sh || true ./autogen.sh: 22: [[: not found libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'acinclude.d'. libtoolize: copying file 'acinclude.d/libtool.m4' libtoolize: copying file 'acinclude.d/ltoptions.m4' libtoolize: copying file 'acinclude.d/ltsugar.m4' libtoolize: copying file 'acinclude.d/ltversion.m4' libtoolize: copying file 'acinclude.d/lt~obsolete.m4' [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_sa.cpp In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ configure.ac:15: installing './compile' configure.ac:3: installing './missing' cluster/Makefile.am: installing './depcomp' mv ../bin/sonLibTests.tmp ../bin/sonLibTests gcc -std=c99 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest gcc -std=c99 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest gcc -std=c99 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest make[4]: Leaving directory '/<>/vg-1.27.1+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/sonLib' rm -f lib/cleaned_old_protobuf* rm -f lib/libproto* lib/pkgconfig/protobuf* bin/protoc rm -Rf include/google/protobuf deps/protobuf touch lib/cleaned_old_protobuf_v003 cp deps/BBHash/BooPHF.h /<>/vg-1.27.1+ds/include cp -r deps/sparsepp/sparsepp include/ rm -Rf include/dynamic.hpp include/dynamic # annoyingly doesn't have an install option on the cmake, so we manually move their external dependency headers cd /<>/vg-1.27.1+ds/deps/DYNAMIC && rm -Rf build && mkdir -p build && cd build && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" && cmake -DCMAKE_VERBOSE_MAKEFILE=ON .. && make -- Setting build type to 'Debug' as none was specified. checking if gcc supports -fno-rtti -fno-exceptions... [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_sa_se.cpp no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... -- The C compiler identification is GNU 10.2.1 yes checking if gcc supports -c -o file.o... -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done Building in Debug mode -- Configuring done -- Generating done -- Build files have been written to: /<>/vg-1.27.1+ds/deps/DYNAMIC/build make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' /usr/bin/cmake -S/<>/vg-1.27.1+ds/deps/DYNAMIC -B/<>/vg-1.27.1+ds/deps/DYNAMIC/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/vg-1.27.1+ds/deps/DYNAMIC/build/CMakeFiles /<>/vg-1.27.1+ds/deps/DYNAMIC/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' checking for ld used by g++... make -f CMakeFiles/cw-bwt.dir/build.make CMakeFiles/cw-bwt.dir/depend make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... cd /<>/vg-1.27.1+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/DYNAMIC /<>/vg-1.27.1+ds/deps/DYNAMIC /<>/vg-1.27.1+ds/deps/DYNAMIC/build /<>/vg-1.27.1+ds/deps/DYNAMIC/build /<>/vg-1.27.1+ds/deps/DYNAMIC/build/CMakeFiles/cw-bwt.dir/DependInfo.cmake --color= yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes Scanning dependencies of target cw-bwt make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' make -f CMakeFiles/cw-bwt.dir/build.make CMakeFiles/cw-bwt.dir/build make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' [ 7%] Building CXX object CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o /usr/bin/c++ -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/internal -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -c /<>/vg-1.27.1+ds/deps/DYNAMIC/cw-bwt.cpp checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for ANSI C header files... (cached) yes checking for boostlib >= 1.0... In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking whether the Boost::Program_Options library is available... yes configure: error: Could not find a version of the library! . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3" ./configure --with-boost-program-options=boost_program_options checking for a BSD-compatible install... install --strip-program=true checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/io.cpp yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... yes checking for ANSI C header files... (cached) yes checking for boostlib >= 1.0... yes checking whether the Boost::Program_Options library is available... [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/louds_tree.cpp yes checking for main in -lboost_program_options... yes checking if zlib is wanted... yes checking for pthread_join in LIBS=-lpthread with CFLAGS=... In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ yes checking for joinable pthread attribute... [ 14%] Linking CXX executable cw-bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/cw-bwt.dir/link.txt --verbose=1 PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -rdynamic CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -o cw-bwt no checking for PTHREAD_PRIO_INHERIT... yes checking that generated files are newer than configure... done configure: creating ./config.status In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/memory_management.cpp config.status: creating Makefile config.status: creating vowpalwabbit/Makefile config.status: creating cluster/Makefile config.status: creating library/Makefile config.status: creating libvw.pc config.status: creating vowpalwabbit/config.h config.status: executing depfiles commands [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp config.status: executing libtool commands . ./source_me.sh && cd deps/vowpal_wabbit && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3" make make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/vowpal_wabbit' Making all in vowpalwabbit make[4]: Entering directory '/<>/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash '/<>/vg-1.27.1+ds/deps/vowpal_wabbit/missing' autoheader) rm -f stamp-h1 touch config.h.in cd .. && /bin/bash ./config.status vowpalwabbit/config.h config.status: creating vowpalwabbit/config.h config.status: vowpalwabbit/config.h is unchanged make all-am make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit' g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT vw-main.o -MD -MP -MF .deps/vw-main.Tpo -c -o vw-main.o `test -f 'main.cc' || echo './'`main.cc In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/ram_filebuf.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/ram_fs.cpp make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' [ 14%] Built target cw-bwt make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/depend make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' cd /<>/vg-1.27.1+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/DYNAMIC /<>/vg-1.27.1+ds/deps/DYNAMIC /<>/vg-1.27.1+ds/deps/DYNAMIC/build /<>/vg-1.27.1+ds/deps/DYNAMIC/build /<>/vg-1.27.1+ds/deps/DYNAMIC/build/CMakeFiles/rle_bwt.dir/DependInfo.cmake --color= Scanning dependencies of target rle_bwt make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/build make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' [ 21%] Building CXX object CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o /usr/bin/c++ -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/internal -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -c /<>/vg-1.27.1+ds/deps/DYNAMIC/rle_bwt.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_args.h:7, from main.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_args.h:7, from main.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_args.h:7, from main.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/sd_vector.cpp In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ mv -f .deps/vw-main.Tpo .deps/vw-main.Po depbase=`echo hash.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -fPIC -DPIC -o .libs/hash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 depbase=`echo parser_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parser_helper.lo -MD -MP -MF $depbase.Tpo -c -o parser_helper.lo parser_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -fPIC -DPIC -o .libs/parser_helper.o In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/structure_tree.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/uint128_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/uint256_t.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/util.cpp [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.27.1+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/wt_helper.cpp In file included from /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /<>/vg-1.27.1+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo global_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT global_data.lo -MD -MP -MF $depbase.Tpo -c -o global_data.lo global_data.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o [100%] Linking CXX static library libsdsl.a cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/sdsl.dir/link.txt --verbose=1 /usr/bin/ar qc libsdsl.a CMakeFiles/sdsl.dir/bits.cpp.o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o CMakeFiles/sdsl.dir/config.cpp.o CMakeFiles/sdsl.dir/construct_config.cpp.o CMakeFiles/sdsl.dir/construct_isa.cpp.o CMakeFiles/sdsl.dir/construct_lcp.cpp.o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o CMakeFiles/sdsl.dir/construct_sa.cpp.o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o CMakeFiles/sdsl.dir/io.cpp.o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o CMakeFiles/sdsl.dir/louds_tree.cpp.o CMakeFiles/sdsl.dir/memory_management.cpp.o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o CMakeFiles/sdsl.dir/ram_fs.cpp.o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o CMakeFiles/sdsl.dir/sd_vector.cpp.o CMakeFiles/sdsl.dir/sfstream.cpp.o CMakeFiles/sdsl.dir/structure_tree.cpp.o CMakeFiles/sdsl.dir/uint128_t.cpp.o CMakeFiles/sdsl.dir/uint256_t.cpp.o CMakeFiles/sdsl.dir/util.cpp.o CMakeFiles/sdsl.dir/wt_helper.cpp.o /usr/bin/ranlib libsdsl.a make[6]: Leaving directory '/<>/vg-1.27.1+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/vg-1.27.1+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/<>/vg-1.27.1+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/sdsl-lite/build' Removing old files rm -rf '/<>/vg-1.27.1+ds/include/sdsl/*' rm -f '/<>/vg-1.27.1+ds/lib/libsdsl*' make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/vg-1.27.1+ds/deps/sdsl-lite -B/<>/vg-1.27.1+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/vg-1.27.1+ds/deps/sdsl-lite/build/CMakeFiles /<>/vg-1.27.1+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/vg-1.27.1+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/sdsl-lite/build' cd /<>/vg-1.27.1+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/sdsl-lite /<>/vg-1.27.1+ds/deps/sdsl-lite/lib /<>/vg-1.27.1+ds/deps/sdsl-lite/build /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib /<>/vg-1.27.1+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/<>/vg-1.27.1+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/vg-1.27.1+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/<>/vg-1.27.1+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/<>/vg-1.27.1+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /<>/vg-1.27.1+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /<>/vg-1.27.1+ds/include/sdsl/bit_vector_il.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/bits.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/bp_support.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/bp_support_g.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/bp_support_gg.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/bp_support_sada.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/coder.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/coder_comma.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/config.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/construct.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/construct_bwt.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/construct_config.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/construct_isa.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/construct_lcp.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/construct_sa.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/construct_sa_se.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/csa_sada.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/csa_wt.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/cst_fully.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/cst_iterators.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/cst_sada.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/cst_sct3.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/dac_vector.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/enc_vector.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/fast_cache.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/hyb_vector.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/inv_perm_support.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/io.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/iterators.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/k2_treap.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/k2_tree.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/lcp.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/lcp_byte.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/lcp_dac.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/lcp_vlc.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/lcp_wt.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/louds_tree.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/memory_management.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/qsufsort.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/ram_filebuf.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/ram_fs.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/rank_support.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/rank_support_scan.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/rank_support_v.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/rank_support_v5.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/raster_img.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/rmq_support.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/rrr_helper.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/rrr_vector.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/sd_vector.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/select_support.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/select_support_mcl.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/select_support_scan.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/sfstream.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/structure_tree.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/suffix_arrays.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/suffix_trees.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/uint128_t.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/uint256_t.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/uintx_t.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/util.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/vectors.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/vlc_vector.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/wavelet_trees.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/wm_int.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/wt_algorithm.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/wt_ap.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/wt_blcd.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/wt_gmr.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/wt_helper.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/wt_huff.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/wt_hutu.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/wt_int.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/wt_pc.hpp -- Installing: /<>/vg-1.27.1+ds/include/sdsl/wt_rlmn.hpp -- Installing: /<>/vg-1.27.1+ds/lib/libsdsl.a make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/<>/vg-1.27.1+ds/include'. The library files are located in '/<>/vg-1.27.1+ds/lib'. Sample programs can be found in the examples-directory. Tests in the test-directory A cheat sheet in the extras/cheatsheet-directory. Have fun! . ./source_me.sh && cp deps/mmmultimap/src/mmmultimap.hpp deps/mmmultimap/src/mmmultiset.hpp /<>/vg-1.27.1+ds/include/ . ./source_me.sh && cp -r deps/ips4o/ips4o* /<>/vg-1.27.1+ds/include/ cp ./deps/gfakluge/src/*.hpp /<>/vg-1.27.1+ds/include/ && cp ./deps/gfakluge/src/tinyFA/*.hpp /<>/vg-1.27.1+ds/include/ cd ./deps/lru_cache && cp *.h* /<>/vg-1.27.1+ds/include/ cp deps/sha1/*.h* /<>/vg-1.27.1+ds/include/ cp deps/progress_bar/progress_bar.hpp /<>/vg-1.27.1+ds/include cp -r deps/dozeu/simde include depbase=`echo io_buf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT io_buf.lo -MD -MP -MF $depbase.Tpo -c -o io_buf.lo io_buf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.o [ 28%] Linking CXX executable rle_bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_bwt.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -rdynamic CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -o rle_bwt libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -o io_buf.o >/dev/null 2>&1 In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from global_data.cc:14: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from global_data.cc:14: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from global_data.cc:14: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo parse_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo parse_primitives.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parse_primitives.lo -MD -MP -MF $depbase.Tpo -c -o parse_primitives.lo parse_primitives.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.o >/dev/null 2>&1 diff: include/vg_environment_version.hpp: No such file or directory . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /<>/vg-1.27.1+ds/obj make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/progress_bar' g++ -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = sparse_parameters]’: parse_regressor.cc:129:57: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] 103 | catch (VW::vw_exception anExc) | ^~~~~ parse_regressor.cc: In instantiation of ‘void initialize_regressor(vw&, T&) [with T = dense_parameters]’: parse_regressor.cc:131:56: required from here parse_regressor.cc:103:27: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from parse_regressor.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' [ 28%] Built target rle_bwt make -f CMakeFiles/h0_lz77.dir/build.make CMakeFiles/h0_lz77.dir/depend make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' cd /<>/vg-1.27.1+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/DYNAMIC /<>/vg-1.27.1+ds/deps/DYNAMIC /<>/vg-1.27.1+ds/deps/DYNAMIC/build /<>/vg-1.27.1+ds/deps/DYNAMIC/build /<>/vg-1.27.1+ds/deps/DYNAMIC/build/CMakeFiles/h0_lz77.dir/DependInfo.cmake --color= g++ -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp Scanning dependencies of target h0_lz77 make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' make -f CMakeFiles/h0_lz77.dir/build.make CMakeFiles/h0_lz77.dir/build make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' [ 35%] Building CXX object CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o /usr/bin/c++ -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/internal -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -c /<>/vg-1.27.1+ds/deps/DYNAMIC/h0_lz77.cpp g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/progress_bar' g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp ln -s `which shuf` bin/shuf . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /<>/vg-1.27.1+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /<>/vg-1.27.1+ds/lib make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c algorithms.cpp In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/sdsl/wt_pc.hpp:25, from /<>/vg-1.27.1+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from algorithms.cpp:26: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo unique_sort.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT unique_sort.lo -MD -MP -MF $depbase.Tpo -c -o unique_sort.lo unique_sort.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -fPIC -DPIC -o .libs/unique_sort.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -o parse_regressor.o >/dev/null 2>&1 In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from unique_sort.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from unique_sort.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 depbase=`echo cache.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cache.lo -MD -MP -MF $depbase.Tpo -c -o cache.lo cache.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o [ 42%] Linking CXX executable h0_lz77 /usr/bin/cmake -E cmake_link_script CMakeFiles/h0_lz77.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -rdynamic CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -o h0_lz77 depbase=`echo rand48.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT rand48.lo -MD -MP -MF $depbase.Tpo -c -o rand48.lo rand48.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from cache.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from cache.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 depbase=`echo simple_label.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT simple_label.lo -MD -MP -MF $depbase.Tpo -c -o simple_label.lo simple_label.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -fPIC -DPIC -o .libs/simple_label.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c dbg.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/sdsl/wt_pc.hpp:25, from /<>/vg-1.27.1+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from dbg.cpp:26: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from cache.h:7, from simple_label.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from simple_label.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' [ 42%] Built target h0_lz77 make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.dir/depend make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' cd /<>/vg-1.27.1+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/DYNAMIC /<>/vg-1.27.1+ds/deps/DYNAMIC /<>/vg-1.27.1+ds/deps/DYNAMIC/build /<>/vg-1.27.1+ds/deps/DYNAMIC/build /<>/vg-1.27.1+ds/deps/DYNAMIC/build/CMakeFiles/benchmark.dir/DependInfo.cmake --color= Scanning dependencies of target benchmark make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.dir/build make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' [ 50%] Building CXX object CMakeFiles/benchmark.dir/benchmark.cpp.o /usr/bin/c++ -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/internal -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/benchmark.dir/benchmark.cpp.o -c /<>/vg-1.27.1+ds/deps/DYNAMIC/benchmark.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 depbase=`echo multiclass.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT multiclass.lo -MD -MP -MF $depbase.Tpo -c -o multiclass.lo multiclass.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from multiclass.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from multiclass.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from multiclass.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT oaa.lo -MD -MP -MF $depbase.Tpo -c -o oaa.lo oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c files.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/sdsl/wt_pc.hpp:25, from /<>/vg-1.27.1+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from files.cpp:26: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from oaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from oaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from oaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo multilabel_oaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT multilabel_oaa.lo -MD -MP -MF $depbase.Tpo -c -o multilabel_oaa.lo multilabel_oaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o [ 57%] Linking CXX executable benchmark /usr/bin/cmake -E cmake_link_script CMakeFiles/benchmark.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -rdynamic CMakeFiles/benchmark.dir/benchmark.cpp.o -o benchmark In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from multilabel_oaa.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from multilabel_oaa.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from multilabel_oaa.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c gcsa.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/sdsl/wt_pc.hpp:25, from /<>/vg-1.27.1+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/gcsa.h:28, from include/gcsa/algorithms.h:29, from gcsa.cpp:26: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' [ 57%] Built target benchmark make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/depend make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' cd /<>/vg-1.27.1+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/DYNAMIC /<>/vg-1.27.1+ds/deps/DYNAMIC /<>/vg-1.27.1+ds/deps/DYNAMIC/build /<>/vg-1.27.1+ds/deps/DYNAMIC/build /<>/vg-1.27.1+ds/deps/DYNAMIC/build/CMakeFiles/rle_lz77_v2.dir/DependInfo.cmake --color= Scanning dependencies of target rle_lz77_v2 make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/build make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' [ 64%] Building CXX object CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o /usr/bin/c++ -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/internal -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -c /<>/vg-1.27.1+ds/deps/DYNAMIC/rle_lz77_v2.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 depbase=`echo boosting.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT boosting.lo -MD -MP -MF $depbase.Tpo -c -o boosting.lo boosting.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o depbase=`echo ect.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT ect.lo -MD -MP -MF $depbase.Tpo -c -o ect.lo ect.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from boosting.cc:22: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from boosting.cc:22: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from boosting.cc:22: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 71%] Linking CXX executable rle_lz77_v2 /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v2.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -rdynamic CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -o rle_lz77_v2 In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from ect.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from ect.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from ect.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' [ 71%] Built target rle_lz77_v2 make -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/depend make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' cd /<>/vg-1.27.1+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/DYNAMIC /<>/vg-1.27.1+ds/deps/DYNAMIC /<>/vg-1.27.1+ds/deps/DYNAMIC/build /<>/vg-1.27.1+ds/deps/DYNAMIC/build /<>/vg-1.27.1+ds/deps/DYNAMIC/build/CMakeFiles/rle_lz77_v1.dir/DependInfo.cmake --color= Scanning dependencies of target rle_lz77_v1 make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/build make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' [ 78%] Building CXX object CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o /usr/bin/c++ -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/internal -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -c /<>/vg-1.27.1+ds/deps/DYNAMIC/rle_lz77_v1.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c internal.cpp In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/sdsl/wt_pc.hpp:25, from /<>/vg-1.27.1+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/internal.h:37, from internal.cpp:26: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c lcp.cpp depbase=`echo marginal.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT marginal.lo -MD -MP -MF $depbase.Tpo -c -o marginal.lo marginal.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/sdsl/wt_pc.hpp:25, from /<>/vg-1.27.1+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/files.h:29, from include/gcsa/lcp.h:29, from lcp.cpp:26: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo autolink.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT autolink.lo -MD -MP -MF $depbase.Tpo -c -o autolink.lo autolink.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o [ 85%] Linking CXX executable rle_lz77_v1 /usr/bin/cmake -E cmake_link_script CMakeFiles/rle_lz77_v1.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -rdynamic CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -o rle_lz77_v1 In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from marginal.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from marginal.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from marginal.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from autolink.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from autolink.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from autolink.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c path_graph.cpp make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' [ 85%] Built target rle_lz77_v1 make -f CMakeFiles/debug.dir/build.make CMakeFiles/debug.dir/depend make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' cd /<>/vg-1.27.1+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/DYNAMIC /<>/vg-1.27.1+ds/deps/DYNAMIC /<>/vg-1.27.1+ds/deps/DYNAMIC/build /<>/vg-1.27.1+ds/deps/DYNAMIC/build /<>/vg-1.27.1+ds/deps/DYNAMIC/build/CMakeFiles/debug.dir/DependInfo.cmake --color= Scanning dependencies of target debug make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' make -f CMakeFiles/debug.dir/build.make CMakeFiles/debug.dir/build make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' [ 92%] Building CXX object CMakeFiles/debug.dir/debug.cpp.o /usr/bin/c++ -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/internal -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms -I/<>/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/debug.dir/debug.cpp.o -c /<>/vg-1.27.1+ds/deps/DYNAMIC/debug.cpp In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/sdsl/wt_pc.hpp:25, from /<>/vg-1.27.1+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.o >/dev/null 2>&1 In file included from /<>/vg-1.27.1+ds/include/sdsl/wavelet_trees.hpp:33, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /<>/vg-1.27.1+ds/include/sdsl/wt_blcd.hpp: In instantiation of ‘static void sdsl::_balanced_shape::construct_tree(t_rac&, std::vector&) [with t_rac = const std::vector; t_wt = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’: /<>/vg-1.27.1+ds/include/sdsl/wt_pc.hpp:132:39: required from ‘sdsl::wt_pc::size_type sdsl::wt_pc::construct_tree_shape(const std::vector&) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; sdsl::wt_pc::size_type = long unsigned int]’ /<>/vg-1.27.1+ds/include/sdsl/wt_pc.hpp:216:35: required from ‘sdsl::wt_pc::wt_pc(sdsl::int_vector_buffer >::int_width>&, sdsl::wt_pc::size_type) [with t_shape = sdsl::balanced_shape; t_bitvector = sdsl::int_vector<1>; t_rank = sdsl::rank_support_v<1, 1>; t_select = sdsl::select_support_mcl<1, 1>; t_select_zero = sdsl::select_support_mcl<0, 1>; t_tree_strat = sdsl::byte_tree<>; typename t_tree_strat::type > = sdsl::_byte_tree, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> > >; sdsl::wt_pc::size_type = long unsigned int]’ include/gcsa/internal.h:105:10: required from ‘void gcsa::directConstruct(Type&, const sdsl::int_vector<8>&) [with Type = sdsl::wt_pc, sdsl::rank_support_v<1, 1>, sdsl::select_support_mcl<1, 1>, sdsl::select_support_mcl<0, 1>, sdsl::byte_tree<> >]’ path_graph.cpp:195:41: required from here /<>/vg-1.27.1+ds/include/sdsl/wt_blcd.hpp:85:21: warning: implicitly-declared ‘constexpr sdsl::pc_node::pc_node(const sdsl::pc_node&)’ is deprecated [-Wdeprecated-copy] 85 | pc_node root = temp_nodes[0]; | ^~~~ In file included from /<>/vg-1.27.1+ds/include/sdsl/wt_pc.hpp:28, from /<>/vg-1.27.1+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from include/gcsa/dbg.h:28, from include/gcsa/path_graph.h:29, from path_graph.cpp:26: /<>/vg-1.27.1+ds/include/sdsl/wt_helper.hpp:70:14: note: because ‘sdsl::pc_node’ has user-provided ‘sdsl::pc_node& sdsl::pc_node::operator=(const sdsl::pc_node&)’ 70 | pc_node& operator=(const pc_node& v); | ^~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.o >/dev/null 2>&1 [100%] Linking CXX executable debug /usr/bin/cmake -E cmake_link_script CMakeFiles/debug.dir/link.txt --verbose=1 /usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -rdynamic CMakeFiles/debug.dir/debug.cpp.o -o debug make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' [100%] Built target debug make[4]: Leaving directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' /usr/bin/cmake -E cmake_progress_start /<>/vg-1.27.1+ds/deps/DYNAMIC/build/CMakeFiles 0 make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/DYNAMIC/build' # Do the copy of the main file last so we can tell if this recipe failed and redo it. # Otherwise we get dynamic.hpp without its deps mkdir -p include/dynamic && cp -r /<>/vg-1.27.1+ds/deps/DYNAMIC/include/* include/dynamic . ./source_me.sh && cp -r deps/gbwt/include/gbwt /<>/vg-1.27.1+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /<>/vg-1.27.1+ds/lib make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/gbwt' rm -f build_gbwt build_ri merge_gbwt benchmark metadata_tool remove_seq algorithms.o benchmark.o build_gbwt.o build_ri.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o merge_gbwt.o metadata.o metadata_tool.o remove_seq.o support.o test.o utils.o variants.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/gbwt' make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/gbwt' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c algorithms.cpp In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c bwtmerge.cpp depbase=`echo binary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT binary.lo -MD -MP -MF $depbase.Tpo -c -o binary.lo binary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/internal.h:31, from /<>/vg-1.27.1+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from binary.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from binary.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from binary.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.o >/dev/null 2>&1 depbase=`echo lrq.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT lrq.lo -MD -MP -MF $depbase.Tpo -c -o lrq.lo lrq.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -fPIC -DPIC -o .libs/lrq.o In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrq.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrq.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrq.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cost_sensitive.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cost_sensitive.lo -MD -MP -MF $depbase.Tpo -c -o cost_sensitive.lo cost_sensitive.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c cached_gbwt.cpp In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from cost_sensitive.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from cost_sensitive.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.27.1+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.27.1+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c dynamic_gbwt.cpp In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.27.1+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.27.1+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c support.cpp depbase=`echo multilabel.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT multilabel.lo -MD -MP -MF $depbase.Tpo -c -o multilabel.lo multilabel.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/sdsl/wt_pc.hpp:25, from /<>/vg-1.27.1+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from support.cpp:26: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from multilabel.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from multilabel.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 depbase=`echo label_dictionary.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT label_dictionary.lo -MD -MP -MF $depbase.Tpo -c -o label_dictionary.lo label_dictionary.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.o depbase=`echo csoaa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT csoaa.lo -MD -MP -MF $depbase.Tpo -c -o csoaa.lo csoaa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c utils.cpp In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = long unsigned int; V = features]’: label_dictionary.cc:109:13: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from label_dictionary.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from label_dictionary.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from label_dictionary.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:149:15: required from ‘void v_hashmap::double_size() [with K = long unsigned int; V = features]’ v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = long unsigned int; V = features; uint64_t = long unsigned int]’ label_dictionary.cc:94:38: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from label_dictionary.cc:1: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from csoaa.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from csoaa.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from csoaa.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:57:15: required from ‘void v_hashmap::init(size_t, V, bool (*)(K&, K&)) [with K = long unsigned int; V = features; size_t = long unsigned int]’ csoaa.cc:895:56: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from reductions.h:14, from csoaa.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.o >/dev/null 2>&1 In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/sdsl/wt_pc.hpp:25, from /<>/vg-1.27.1+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from utils.cpp:26: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rcs libgcsa2.a algorithms.o dbg.o files.o gcsa.o internal.o lcp.o path_graph.o support.o utils.o make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/gcsa2' . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /<>/vg-1.27.1+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /<>/vg-1.27.1+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /<>/vg-1.27.1+ds/lib/lib3edgeconnected.a && mkdir -p /<>/vg-1.27.1+ds/include/sonLib && cp lib/*.h /<>/vg-1.27.1+ds/include/sonLib make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/<>/vg-1.27.1+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c ar rc 3EdgeConnected.a *.o ranlib 3EdgeConnected.a rm *.o mv 3EdgeConnected.a ../..//../sonLib/lib/ cp inc/*.h ../..//../sonLib/lib/ gcc -std=c99 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I../..//../sonLib/lib -o ../..//../sonLib/bin/3EdgeTests tests/*.c ../..//../sonLib/lib/3EdgeConnected.a ../..//../sonLib/lib/sonLib.a ../..//../sonLib/lib/cuTest.a -lz -lm /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c fast_locate.cpp depbase=`echo cb.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cb.lo -MD -MP -MF $depbase.Tpo -c -o cb.lo cb.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/<>/vg-1.27.1+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I .//../sonLib/lib/ -c impl/*.c In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.27.1+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.27.1+ds/include/gbwt/fast_locate.h:28, from fast_locate.cpp:25: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from example.h:10, from cb.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cb.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ ar rc stPinchesAndCacti.a *.o ranlib stPinchesAndCacti.a rm *.o mv stPinchesAndCacti.a .//../sonLib/lib/ cp inc/*.h .//../sonLib/lib/ gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /<>/vg-1.27.1+ds/include -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -I inc -I impl -I.//../sonLib/lib -o .//../sonLib/bin/stPinchesAndCactiTests tests/*.c impl/*.c .//../sonLib/lib/sonLib.a .//../sonLib/lib/cuTest.a -lz -lm .//../sonLib/lib/3EdgeConnected.a libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.o >/dev/null 2>&1 depbase=`echo cb_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cb_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_adf.lo cb_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_adf.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_adf.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_adf.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/pinchesAndCacti' rm -f /<>/vg-1.27.1+ds/include/vg.pb.h /<>/vg-1.27.1+ds/include/vg/vg.pb.h rm -Rf /<>/vg-1.27.1+ds/include/vg/io/ . ./source_me.sh && export CXXFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/<>/vg-1.27.1+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/<>/vg-1.27.1+ds -DCMAKE_LIBRARY_PATH=/<>/vg-1.27.1+ds/lib -DCMAKE_INSTALL_PREFIX=/<>/vg-1.27.1+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install -- The CXX compiler identification is GNU 10.2.1 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:321 ] Protobuf_USE_STATIC_LIBS = OFF /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c files.cpp -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:455 ] requested version of Google Protobuf is -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:463 ] location of common.h: /usr/include/google/protobuf/stubs/common.h -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:481 ] /usr/include/google/protobuf/stubs/common.h reveals protobuf 3.12.3 -- [ /usr/share/cmake-3.18/Modules/FindProtobuf.cmake:495 ] /usr/bin/protoc reveals version 3.12.3 -- Found Protobuf: /usr/lib/aarch64-linux-gnu/libprotobuf.so (found version "3.12.3") Protobuf will be /usr/lib/aarch64-linux-gnu/libprotobuf.so for PIC dynamic code and /usr/lib/aarch64-linux-gnu/libprotobuf.a for non-PIC static code -- Found Threads: TRUE -- Checking for module 'htslib' -- Found htslib, version 1.11-4 -- Checking for module 'jansson' -- Found jansson, version 2.13.1 -- Configuring done -- Generating done -- Build files have been written to: /<>/vg-1.27.1+ds/deps/libvgio make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' /usr/bin/cmake -P 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Scanning dependencies of target link_target make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' [ 0%] Built target link_target make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' cd /<>/vg-1.27.1+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= Dependee "/<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake" is newer than depender "/<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles/handlegraph.dir/depend.internal". 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Scanning dependencies of target handlegraph make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' [ 2%] Creating directories for 'handlegraph' /usr/bin/cmake -E make_directory /<>/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph /usr/bin/cmake -E make_directory /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /usr/bin/cmake -E make_directory /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix /usr/bin/cmake -E make_directory /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/tmp /usr/bin/cmake -E make_directory /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp /usr/bin/cmake -E make_directory /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src /usr/bin/cmake -E make_directory /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp /usr/bin/cmake -E touch /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-mkdir [ 4%] No download step for 'handlegraph' /usr/bin/cmake -E echo_append depbase=`echo cb_algs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.cc &&\ mv -f $depbase.Tpo $depbase.Plo /usr/bin/cmake -E touch /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-download [ 7%] No update step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-update libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.o [ 9%] No patch step for 'handlegraph' /usr/bin/cmake -E echo_append /usr/bin/cmake -E touch /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-patch [ 11%] Performing configure step for 'handlegraph' cd /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix "-GUnix Makefiles" /<>/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph Re-run cmake no build system arguments CMake Warning (dev) at /usr/share/cmake-3.18/Modules/GNUInstallDirs.cmake:225 (message): Unable to determine default CMAKE_INSTALL_LIBDIR directory because no target architecture is known. Please enable at least one language before including GNUInstallDirs. Call Stack (most recent call first): CMakeLists.txt:5 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- The C compiler identification is GNU 10.2.1 In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/files.h:29, from files.cpp:26: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done -- Generating done -- Build files have been written to: /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build cd /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-configure [ 14%] Performing build step for 'handlegraph' cd /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make make[6]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/<>/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph -B/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= Dependee "/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake" is newer than depender "/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/depend.internal". Dependee "/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/depend.internal". Scanning dependencies of target handlegraph_objs make[8]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/g++ -I/<>/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/handle.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c gbwt.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -o cb_adf.o >/dev/null 2>&1 In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from cb_algs.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from cb_algs.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from cb_algs.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ make[8]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= Dependee "/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake" is newer than depender "/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/depend.internal". Dependee "/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/depend.internal". Scanning dependencies of target handlegraph_static make[8]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Linking CXX static library libhandlegraph.a /usr/bin/cmake -P CMakeFiles/handlegraph_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_static.dir/link.txt --verbose=1 /usr/bin/ar qc libhandlegraph.a CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/ranlib libhandlegraph.a make[8]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= Dependee "/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake" is newer than depender "/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/depend.internal". Dependee "/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/depend.internal". Scanning dependencies of target handlegraph_shared make[8]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Linking CXX shared library libhandlegraph.so /usr/bin/cmake -E cmake_link_script CMakeFiles/handlegraph_shared.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -O3 -g -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.27.1+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ make[8]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_shared make[7]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make[6]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-build [ 16%] Performing install step for 'handlegraph' cd /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && make install make[6]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -S/<>/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph -B/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[7]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[8]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= make[8]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[8]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_objs.dir/build'. make[8]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 33%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[8]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= make[8]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[8]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_static.dir/build'. make[8]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [ 66%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[8]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= make[8]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[8]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[8]: Nothing to be done for 'CMakeFiles/handlegraph_shared.dir/build'. make[8]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' [100%] Built target handlegraph_shared make[7]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' /usr/bin/cmake -E cmake_progress_start /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[7]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' make[7]: Nothing to be done for 'preinstall'. make[7]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.so -- Installing: /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/lib/libhandlegraph.a -- Installing: /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include/handlegraph -- Installing: /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_handle_graph.hpp -- Installing: /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_handle_graph.hpp -- Installing: /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/handle_graph.hpp -- Installing: /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/serializable_handle_graph.hpp -- Installing: /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_deletable_handle_graph.hpp -- Installing: /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_handle_graph.hpp -- Installing: /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/util.hpp -- Installing: /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/path_position_handle_graph.hpp -- Installing: /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/deletable_handle_graph.hpp -- Installing: /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/types.hpp -- Installing: /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/expanding_overlay_graph.hpp -- Installing: /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/iteratee.hpp -- Installing: /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include/handlegraph/mutable_path_mutable_handle_graph.hpp make[6]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build' cd /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-build && /usr/bin/cmake -E touch /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-install [ 19%] Completed 'handlegraph' /usr/bin/cmake -E make_directory /<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles /usr/bin/cmake -E touch /<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles/handlegraph-complete /usr/bin/cmake -E touch /<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/src/handlegraph-stamp/handlegraph-done make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' [ 19%] Built target handlegraph make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' [ 21%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out /<>/vg-1.27.1+ds/deps/libvgio -I /<>/vg-1.27.1+ds/deps/libvgio/deps /<>/vg-1.27.1+ds/deps/libvgio/deps/vg.proto cd /<>/vg-1.27.1+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= Dependee "/<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake" is newer than depender "/<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Dependee "/<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Scanning dependencies of target vgio_static make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' [ 23%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /<>/vg-1.27.1+ds/deps/libvgio/vg.pb.cc /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c internal.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -o cb_algs.o >/dev/null 2>&1 depbase=`echo search.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/internal.h:31, from internal.cpp:26: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::clear() [with K = unsigned char*; V = Search::scored_action]’: search.cc:1265:29: required from here v_hashmap.h:94:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 94 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ search.cc: In instantiation of ‘void Search::push_at(v_array&, T, size_t) [with T = Search::action_repr; size_t = long unsigned int]’: search.cc:1537:22: required from here search.cc:945:13: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 945 | memset(v.end(), 0, sizeof(T) * (pos - v.size())); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from search.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_repr; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = Search::action_repr]’ search.cc:620:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_repr’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:98:8: note: ‘struct Search::action_repr’ declared here 98 | struct action_repr | ^~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::action_cache; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::action_cache]’ search.cc:1009:64: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::action_cache’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:115:8: note: ‘struct Search::action_cache’ declared here 115 | struct action_cache | ^~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = std::pair]’ search.cc:1084:94: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search.cc:1097:36: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = example; size_t = long unsigned int]’: search.cc:932:13: required from ‘void Search::ensure_size(v_array&, size_t) [with T = example; size_t = long unsigned int]’ search.cc:1517:47: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:24, from vw.h:15, from search.cc:9: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = Search::scored_action; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = Search::scored_action]’ search.cc:1695:65: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct Search::scored_action’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ search.cc:87:8: note: ‘struct Search::scored_action’ declared here 87 | struct scored_action | ^~~~~~~~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c metadata.cpp In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h: In instantiation of ‘void v_hashmap::double_size() [with K = unsigned char*; V = Search::scored_action]’: v_hashmap.h:236:9: required from ‘void v_hashmap::put_after_get(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ v_hashmap.h:247:5: required from ‘void v_hashmap::put(K&, uint64_t, V) [with K = unsigned char*; V = Search::scored_action; uint64_t = long unsigned int]’ search.cc:1295:65: required from here v_hashmap.h:157:11: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 157 | memset(dat.begin(), 0, base_size()*sizeof(hash_elem)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from search.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = v_hashmap::hash_elem; size_t = long unsigned int]’: v_hashmap.h:71:15: required from ‘void v_hashmap::init(size_t, bool (*)(K&, K&)) [with K = unsigned char*; V = Search::scored_action; size_t = long unsigned int]’ v_hashmap.h:83:21: required from ‘v_hashmap::v_hashmap() [with K = unsigned char*; V = Search::scored_action]’ search.cc:2266:71: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct v_hashmap::hash_elem’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from global_data.h:27, from vw.h:15, from search.cc:9: v_hashmap.h:17:10: note: ‘struct v_hashmap::hash_elem’ declared here 17 | struct hash_elem | ^~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c support.cpp depbase=`echo search_meta.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_meta.lo -MD -MP -MF $depbase.Tpo -c -o search_meta.lo search_meta.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/internal.h:31, from support.cpp:26: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 26%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/alignment_emitter.cpp search_meta.cc: In function ‘void SelectiveBranchingMT::run(Search::search&, std::vector&)’: search_meta.cc:247:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^~ search_meta.cc:247:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 247 | if (d.kbest_out) delete d.kbest_out; d.kbest_out = nullptr; | ^ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void push_many(v_array&, const T*, size_t) [with T = std::pair; size_t = long unsigned int]’: search_meta.cc:124:75: required from here v_array.h:193:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 193 | memcpy(v._end, _begin, num * sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from search_meta.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >]’ search_meta.cc:108:20: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair > >, std::__cxx11::basic_string*>; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair > >, std::__cxx11::basic_string*>]’ search_meta.cc:109:17: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair > >, std::__cxx11::basic_string*>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair > >, std::__cxx11::basic_string*>’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_meta.cc:110:22: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from search_meta.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/string:40, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from search_meta.cc:9: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 [ 28%] Building CXX object CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o /usr/bin/g++ -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/alignment_io.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c test.cpp In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/test.h:28, from test.cpp:29: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo search_sequencetask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_sequencetask.lo -MD -MP -MF $depbase.Tpo -c -o search_sequencetask.lo search_sequencetask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.o [ 30%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o /usr/bin/g++ -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/basic_stream.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c utils.cpp In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_sequencetask.h:7, from search_sequencetask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from utils.cpp:26: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from /<>/vg-1.27.1+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /<>/vg-1.27.1+ds/deps/libvgio/src/basic_stream.cpp:8: /<>/vg-1.27.1+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /<>/vg-1.27.1+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /<>/vg-1.27.1+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/deps/libvgio/vg/vg.pb.h:23, from /<>/vg-1.27.1+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /<>/vg-1.27.1+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 33%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c variants.cpp [ 35%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/variants.h:29, from variants.cpp:25: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 38%] Building CXX object CMakeFiles/vgio_static.dir/src/edit.cpp.o /usr/bin/g++ -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/edit.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/edit.cpp depbase=`echo search_dep_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_dep_parser.lo -MD -MP -MF $depbase.Tpo -c -o search_dep_parser.lo search_dep_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -fPIC -DPIC -o .libs/search_dep_parser.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 [ 40%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/hfile_cppstream.cpp In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 42%] Building CXX object CMakeFiles/vgio_static.dir/src/json2pb.cpp.o /usr/bin/g++ -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/json2pb.cpp In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::pair; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::pair]’ search_dep_parser.cc:442:28: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ In file included from global_data.h:19, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct std::pair’ with no trivial copy-assignment; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/bits/stl_algobase.h:64, from /usr/include/c++/10/bits/char_traits.h:39, from /usr/include/c++/10/ios:40, from /usr/include/c++/10/ostream:38, from /usr/include/c++/10/iostream:39, from global_data.h:8, from search.h:7, from search_dep_parser.h:7, from search_dep_parser.cc:6: /usr/include/c++/10/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ [ 45%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/message_emitter.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c build_gbwt.cpp [ 47%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o /usr/bin/g++ -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/message_iterator.cpp depbase=`echo search_hooktask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.27.1+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.27.1+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:31: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 /<>/vg-1.27.1+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /<>/vg-1.27.1+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /<>/vg-1.27.1+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /<>/vg-1.27.1+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /<>/vg-1.27.1+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /<>/vg-1.27.1+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /<>/vg-1.27.1+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 50%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/registry.cpp In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_hooktask.h:7, from search_hooktask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_multiclasstask.lo -MD -MP -MF $depbase.Tpo -c -o search_multiclasstask.lo search_multiclasstask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o [ 52%] Building CXX object CMakeFiles/vgio_static.dir/src/stream.cpp.o /usr/bin/g++ -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/stream.cpp In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_multiclasstask.h:7, from search_multiclasstask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 54%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/stream_multiplexer.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -o search_multiclasstask.o >/dev/null 2>&1 depbase=`echo search_entityrelationtask.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c build_ri.cpp [ 57%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/vpkg.cpp In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.27.1+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.27.1+ds/include/gbwt/fast_locate.h:28, from build_ri.cpp:29: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo search_graph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_graph.lo -MD -MP -MF $depbase.Tpo -c -o search_graph.lo search_graph.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -fPIC -DPIC -o .libs/search_graph.o In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_entityrelationtask.h:7, from search_entityrelationtask.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 59%] Linking CXX static library libvgio.a /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio_static.dir/link.txt --verbose=1 /usr/bin/ar qc libvgio.a CMakeFiles/vgio_static.dir/vg.pb.cc.o CMakeFiles/vgio_static.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio_static.dir/src/alignment_io.cpp.o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio_static.dir/src/edit.cpp.o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio_static.dir/src/json2pb.cpp.o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o CMakeFiles/vgio_static.dir/src/registry.cpp.o CMakeFiles/vgio_static.dir/src/stream.cpp.o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/ranlib libvgio.a make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' [ 59%] Built target vgio_static make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' cd /<>/vg-1.27.1+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= Dependee "/<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake" is newer than depender "/<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Dependee "/<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Scanning dependencies of target vgio make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' [ 61%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /<>/vg-1.27.1+ds/deps/libvgio/vg.pb.cc /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c merge_gbwt.cpp In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from search.h:7, from search_graph.h:7, from search_graph.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from search.h:7, from search_graph.h:7, from search_graph.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from search.h:7, from search_graph.h:7, from search_graph.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.27.1+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.27.1+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c benchmark.cpp In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.27.1+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.27.1+ds/include/gbwt/dynamic_gbwt.h:31, from benchmark.cpp:31: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT search_graph.lo -MD -MP -MF .deps/search_graph.Tpo -c search_graph.cc -o search_graph.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c metadata_tool.cpp In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.27.1+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c remove_seq.cpp depbase=`echo parse_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parse_example.lo -MD -MP -MF $depbase.Tpo -c -o parse_example.lo parse_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -fPIC -DPIC -o .libs/parse_example.o In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.27.1+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.27.1+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 64%] Building CXX object CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/alignment_emitter.cpp ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o fast_locate.o files.o gbwt.o internal.o metadata.o support.o test.o utils.o variants.o In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parse_example.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parse_example.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -o build_gbwt build_gbwt.o libgbwt.a -L/<>/vg-1.27.1+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 depbase=`echo scorer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from scorer.cc:3: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from scorer.cc:3: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from scorer.cc:3: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.o >/dev/null 2>&1 [ 66%] Building CXX object CMakeFiles/vgio.dir/src/alignment_io.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/alignment_io.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/alignment_io.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 /usr/bin/g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -o build_ri build_ri.o libgbwt.a -L/<>/vg-1.27.1+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 [ 69%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/basic_stream.cpp depbase=`echo network.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 /usr/bin/g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/<>/vg-1.27.1+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 In file included from /<>/vg-1.27.1+ds/deps/libvgio/include/vg/io/stream.hpp:17, from /<>/vg-1.27.1+ds/deps/libvgio/src/basic_stream.cpp:8: /<>/vg-1.27.1+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /<>/vg-1.27.1+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/deps/libvgio/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/deps/libvgio/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/deps/libvgio/src/basic_stream.cpp:69:31: required from here /<>/vg-1.27.1+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/deps/libvgio/vg/vg.pb.h:23, from /<>/vg-1.27.1+ds/deps/libvgio/include/vg/io/basic_stream.hpp:5, from /<>/vg-1.27.1+ds/deps/libvgio/src/basic_stream.cpp:7: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ depbase=`echo parse_args.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parse_args.lo -MD -MP -MF $depbase.Tpo -c -o parse_args.lo parse_args.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.o [ 71%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 73%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp /usr/bin/g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -o benchmark benchmark.o libgbwt.a -L/<>/vg-1.27.1+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from parse_args.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from parse_args.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from parse_args.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 76%] Building CXX object CMakeFiles/vgio.dir/src/edit.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/edit.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/edit.cpp [ 78%] Building CXX object CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/hfile_cppstream.cpp [ 80%] Building CXX object CMakeFiles/vgio.dir/src/json2pb.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/json2pb.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/json2pb.cpp depbase=`echo accumulate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT accumulate.lo -MD -MP -MF $depbase.Tpo -c -o accumulate.lo accumulate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o /usr/bin/g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -o metadata_tool metadata_tool.o libgbwt.a -L/<>/vg-1.27.1+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.cc:15: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.cc:15: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.cc:15: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ [ 83%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/message_emitter.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 [ 85%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/message_iterator.cpp /usr/bin/g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.27.1+ds/include -I/<>/vg-1.27.1+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -o remove_seq remove_seq.o libgbwt.a -L/<>/vg-1.27.1+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /<>/vg-1.27.1+ds/deps/libvgio/src/message_iterator.cpp: In member function ‘const vg::io::MessageIterator& vg::io::MessageIterator::operator++()’: /<>/vg-1.27.1+ds/deps/libvgio/src/message_iterator.cpp:192:79: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 192 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /<>/vg-1.27.1+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /<>/vg-1.27.1+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ /<>/vg-1.27.1+ds/deps/libvgio/src/message_iterator.cpp:328:75: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 328 | coded_in.SetTotalBytesLimit(MAX_MESSAGE_SIZE * 2, MAX_MESSAGE_SIZE * 2); | ^ In file included from /<>/vg-1.27.1+ds/deps/libvgio/include/vg/io/message_iterator.hpp:17, from /<>/vg-1.27.1+ds/deps/libvgio/src/message_iterator.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ [ 88%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/registry.cpp [ 90%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/stream.cpp [ 92%] Building CXX object CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/stream_multiplexer.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/gbwt' . ./source_me.sh && rm -Rf /<>/vg-1.27.1+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/<>/vg-1.27.1+ds/include:/<>/vg-1.27.1+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" make && cp lib/libbdsg.a /<>/vg-1.27.1+ds/lib && pwd && cp -r include/bdsg /<>/vg-1.27.1+ds/include make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/libbdsg' rm -r obj rm -r lib rm -r bin make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/libbdsg' make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/libbdsg' g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c src/eades_algorithm.cpp -o obj/eades_algorithm.o [ 95%] Building CXX object CMakeFiles/vgio.dir/src/vpkg.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.27.1+ds/deps/libvgio/include -I/<>/vg-1.27.1+ds/deps/libvgio -I/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/include -I/<>/vg-1.27.1+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/vpkg.cpp.o -c /<>/vg-1.27.1+ds/deps/libvgio/src/vpkg.cpp g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c src/hash_graph.cpp -o obj/hash_graph.o g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c src/is_single_stranded.cpp -o obj/is_single_stranded.o [ 97%] Linking CXX shared library libvgio.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vgio.dir/link.txt --verbose=1 /usr/bin/g++ -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.o CMakeFiles/vgio.dir/src/alignment_emitter.cpp.o CMakeFiles/vgio.dir/src/alignment_io.cpp.o CMakeFiles/vgio.dir/src/basic_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o CMakeFiles/vgio.dir/src/edit.cpp.o CMakeFiles/vgio.dir/src/hfile_cppstream.cpp.o CMakeFiles/vgio.dir/src/json2pb.cpp.o CMakeFiles/vgio.dir/src/message_emitter.cpp.o CMakeFiles/vgio.dir/src/message_iterator.cpp.o CMakeFiles/vgio.dir/src/registry.cpp.o CMakeFiles/vgio.dir/src/stream.cpp.o CMakeFiles/vgio.dir/src/stream_multiplexer.cpp.o CMakeFiles/vgio.dir/src/vpkg.cpp.o -L/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/lib -Wl,-rpath,/<>/vg-1.27.1+ds/deps/libvgio/handlegraph-prefix/lib: /usr/lib/aarch64-linux-gnu/libprotobuf.so -lhts -ljansson -lhandlegraph -ldl g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c src/node.cpp -o obj/node.o g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c src/odgi.cpp -o obj/odgi.o make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' [100%] Built target vgio make[4]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles 0 make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' /usr/bin/cmake -S/<>/vg-1.27.1+ds/deps/libvgio -B/<>/vg-1.27.1+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles /<>/vg-1.27.1+ds/deps/libvgio//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' cd /<>/vg-1.27.1+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' [ 0%] Built target link_target make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/depend make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' cd /<>/vg-1.27.1+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles/handlegraph.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' make -f CMakeFiles/handlegraph.dir/build.make CMakeFiles/handlegraph.dir/build make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/handlegraph.dir/build'. make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' [ 19%] Built target handlegraph make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' cd /<>/vg-1.27.1+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' [ 59%] Built target vgio_static make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' cd /<>/vg-1.27.1+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio /<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' [100%] Built target vgio make[4]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /<>/vg-1.27.1+ds/deps/libvgio/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/<>/vg-1.27.1+ds/deps/libvgio' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /<>/vg-1.27.1+ds/lib/libvgio.so -- Set runtime path of "/<>/vg-1.27.1+ds/lib/libvgio.so" to "" -- Installing: /<>/vg-1.27.1+ds/lib/libvgio.a -- Up-to-date: /<>/vg-1.27.1+ds/include -- Installing: /<>/vg-1.27.1+ds/include/vg -- Installing: /<>/vg-1.27.1+ds/include/vg/io -- Installing: /<>/vg-1.27.1+ds/include/vg/io/vpkg.hpp -- Installing: /<>/vg-1.27.1+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /<>/vg-1.27.1+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /<>/vg-1.27.1+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp -- Installing: /<>/vg-1.27.1+ds/include/vg/io/registry.hpp -- Installing: /<>/vg-1.27.1+ds/include/vg/io/hfile_internal.hpp -- Installing: /<>/vg-1.27.1+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /<>/vg-1.27.1+ds/include/vg/io/edit.hpp -- Installing: /<>/vg-1.27.1+ds/include/vg/io/gafkluge.hpp -- Installing: /<>/vg-1.27.1+ds/include/vg/io/fdstream.hpp -- Installing: /<>/vg-1.27.1+ds/include/vg/io/basic_stream.hpp -- Installing: /<>/vg-1.27.1+ds/include/vg/io/alignment_emitter.hpp -- Installing: /<>/vg-1.27.1+ds/include/vg/io/loader.hpp -- Installing: /<>/vg-1.27.1+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /<>/vg-1.27.1+ds/include/vg/io/message_emitter.hpp -- Installing: /<>/vg-1.27.1+ds/include/vg/io/json2pb.h -- Installing: /<>/vg-1.27.1+ds/include/vg/io/message_iterator.hpp -- Installing: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /<>/vg-1.27.1+ds/include/vg/io/alignment_io.hpp -- Installing: /<>/vg-1.27.1+ds/include/vg/vg.pb.h -- Installing: /<>/vg-1.27.1+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /<>/vg-1.27.1+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /<>/vg-1.27.1+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /<>/vg-1.27.1+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/libvgio' rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /<>/vg-1.27.1+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.cpp g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c src/packed_graph.cpp -o obj/packed_graph.o depbase=`echo gd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT gd.lo -MD -MP -MF $depbase.Tpo -c -o gd.lo gd.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -fPIC -DPIC -o .libs/gd.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd.cc:23: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd.cc:23: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c src/packed_structs.cpp -o obj/packed_structs.o g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c src/path_position_overlays.cpp -o obj/path_position_overlays.o g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c src/packed_path_position_overlay.cpp -o obj/packed_path_position_overlay.o g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c src/vectorizable_overlays.cpp -o obj/vectorizable_overlays.o g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c src/strand_split_overlay.cpp -o obj/strand_split_overlay.o g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -fopenmp -c src/utility.cpp -o obj/utility.o depbase=`echo learner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT learner.lo -MD -MP -MF $depbase.Tpo -c -o learner.lo learner.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from parser.h:7, from learner.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from parser.h:7, from learner.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parser.h:9, from learner.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 rm -f lib/libbdsg.a ar rs lib/libbdsg.a obj/eades_algorithm.o obj/hash_graph.o obj/is_single_stranded.o obj/node.o obj/odgi.o obj/packed_graph.o obj/packed_structs.o obj/path_position_overlays.o obj/packed_path_position_overlay.o obj/vectorizable_overlays.o obj/strand_split_overlay.o obj/utility.o ar: creating lib/libbdsg.a make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/libbdsg' /<>/vg-1.27.1+ds/deps/libbdsg mkdir -p /<>/vg-1.27.1+ds/include/dozeu && cp deps/dozeu/*.h /<>/vg-1.27.1+ds/include/dozeu/ . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /<>/vg-1.27.1+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /<>/vg-1.27.1+ds/lib make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/gbwtgraph' rm -f algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o gfa2gbwt.o minimizer.o path_cover.o utils.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/gbwtgraph' make[3]: Entering directory '/<>/vg-1.27.1+ds/deps/gbwtgraph' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c algorithms.cpp In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.27.1+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.27.1+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/algorithms.h:6, from algorithms.cpp:1: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ depbase=`echo mwt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from mwt.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from mwt.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from mwt.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c cached_gbwtgraph.cpp In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.27.1+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.27.1+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from include/gbwtgraph/cached_gbwtgraph.h:6, from cached_gbwtgraph.cpp:1: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c gbwtgraph.cpp In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.27.1+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.27.1+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c gfa.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.27.1+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.27.1+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c minimizer.cpp depbase=`echo lda_core.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT lda_core.lo -MD -MP -MF $depbase.Tpo -c -o lda_core.lo lda_core.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.o In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:13, from minimizer.cpp:1: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a depbase=`echo gd_mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c path_cover.cpp In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from lda_core.cc:17: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from lda_core.cc:17: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from lda_core.cc:17: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.27.1+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.27.1+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from gd_mf.cc:16: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from gd_mf.cc:16: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c utils.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -c gfa2gbwt.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 In file included from /<>/vg-1.27.1+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.27.1+ds/include/gbwt/utils.h:35, from /<>/vg-1.27.1+ds/include/gbwt/support.h:29, from /<>/vg-1.27.1+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.27.1+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.27.1+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.27.1+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ ar rcs libgbwtgraph.a algorithms.o cached_gbwtgraph.o gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o /usr/bin/g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.27.1+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/<>/vg-1.27.1+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 depbase=`echo mf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT mf.lo -MD -MP -MF $depbase.Tpo -c -o mf.lo mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from mf.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from mf.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from mf.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/gbwtgraph' depbase=`echo bfgs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT bfgs.lo -MD -MP -MF $depbase.Tpo -c -o bfgs.lo bfgs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -fPIC -DPIC -o .libs/bfgs.o bfgs.cc: In function ‘int process_pass(vw&, bfgs&)’: bfgs.cc:667:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 667 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/aarch64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:723:30: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 723 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/aarch64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:760:31: warning: catching polymorphic type ‘class curv_exception’ by value [-Wcatch-value=] 760 | catch (curv_exception e) | ^ bfgs.cc:774:32: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 774 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/aarch64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:816:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 816 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/aarch64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc:833:24: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 833 | ftime(&b.t_end_global); | ^ In file included from bfgs.cc:18: /usr/include/aarch64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ bfgs.cc: In function ‘void save_load(bfgs&, io_buf&, bool, bool)’: bfgs.cc:1042:28: warning: ‘int ftime(timeb*)’ is deprecated [-Wdeprecated-declarations] 1042 | ftime(&b.t_start_global); | ^ In file included from bfgs.cc:18: /usr/include/aarch64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb *__timebuf) | ^~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from accumulate.h:8, from bfgs.cc:19: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from accumulate.h:8, from bfgs.cc:19: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from accumulate.h:8, from bfgs.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.o >/dev/null 2>&1 depbase=`echo noop.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT noop.lo -MD -MP -MF $depbase.Tpo -c -o noop.lo noop.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.o In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from noop.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from noop.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from noop.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 depbase=`echo print.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT print.lo -MD -MP -MF $depbase.Tpo -c -o print.lo print.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.o depbase=`echo example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT example.lo -MD -MP -MF $depbase.Tpo -c -o example.lo example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/example.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from print.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from print.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from print.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parser.lo -MD -MP -MF $depbase.Tpo -c -o parser.lo parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from example.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from example.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from example.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 parser.cc: In function ‘void parse_cache(vw&, boost::program_options::variables_map&, std::string, bool)’: parser.cc:379:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 379 | catch (exception e) { f = -1; } | ^ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parser.cc:37: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from parser.cc:48: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from parser.cc:48: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 depbase=`echo loss_functions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.o depbase=`echo sender.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT sender.lo -MD -MP -MF $depbase.Tpo -c -o sender.lo sender.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.o In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from loss_functions.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from loss_functions.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from loss_functions.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.o >/dev/null 2>&1 depbase=`echo nn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from sender.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from cache.h:9, from sender.cc:19: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.o >/dev/null 2>&1 depbase=`echo confidence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT confidence.lo -MD -MP -MF $depbase.Tpo -c -o confidence.lo confidence.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -fPIC -DPIC -o .libs/confidence.o nn.cc: In function ‘void finish_setup(nn&, vw&)’: nn.cc:78:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 78 | memset (&n.output_layer, 0, sizeof (n.output_layer)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:106:50: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 106 | memset (&n.hiddenbias, 0, sizeof (n.hiddenbias)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ nn.cc:115:54: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct example’; use assignment or value-initialization instead [-Wclass-memaccess] 115 | memset (&n.outputweight, 0, sizeof (n.outputweight)); | ^ In file included from reductions.h:11, from nn.cc:11: example.h:57:8: note: ‘struct example’ declared here 57 | struct example : public example_predict // core example datatype. | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from nn.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from nn.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from nn.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from confidence.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from confidence.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from confidence.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.o >/dev/null 2>&1 depbase=`echo bs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from bs.cc:13: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from bs.cc:13: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from bs.cc:13: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo cbify.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cbify.lo -MD -MP -MF $depbase.Tpo -c -o cbify.lo cbify.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o depbase=`echo explore_eval.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT explore_eval.lo -MD -MP -MF $depbase.Tpo -c -o explore_eval.lo explore_eval.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.o In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cbify.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cbify.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cbify.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from explore_eval.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from explore_eval.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from explore_eval.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 depbase=`echo topk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT topk.lo -MD -MP -MF $depbase.Tpo -c -o topk.lo topk.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -o explore_eval.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from topk.cc:10: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from topk.cc:10: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from topk.cc:10: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo stagewise_poly.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT stagewise_poly.lo -MD -MP -MF $depbase.Tpo -c -o stagewise_poly.lo stagewise_poly.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -fPIC -DPIC -o .libs/stagewise_poly.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from stagewise_poly.cc:4: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from stagewise_poly.cc:4: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo log_multi.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT log_multi.lo -MD -MP -MF $depbase.Tpo -c -o log_multi.lo log_multi.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.o depbase=`echo recall_tree.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT recall_tree.lo -MD -MP -MF $depbase.Tpo -c -o recall_tree.lo recall_tree.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.o In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from log_multi.cc:11: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from log_multi.cc:11: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from log_multi.cc:11: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = node_pred; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = node_pred]’ log_multi.cc:93:17: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ log_multi.cc:16:7: note: ‘class node_pred’ declared here 16 | class node_pred | ^~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from recall_tree.cc:12: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from recall_tree.cc:12: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node]’ recall_tree.cc:94:31: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:29:8: note: ‘struct recall_tree_ns::node’ declared here 29 | struct node | ^~~~ In file included from io_buf.h:14, from reductions.h:10, from recall_tree.cc:12: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = recall_tree_ns::node_pred; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = recall_tree_ns::node_pred]’ recall_tree.cc:139:39: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct recall_tree_ns::node_pred’; use assignment instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ recall_tree.cc:21:8: note: ‘struct recall_tree_ns::node_pred’ declared here 21 | struct node_pred | ^~~~~~~~~ depbase=`echo active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT active.lo -MD -MP -MF $depbase.Tpo -c -o active.lo active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -fPIC -DPIC -o .libs/active.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT stagewise_poly.lo -MD -MP -MF .deps/stagewise_poly.Tpo -c stagewise_poly.cc -o stagewise_poly.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -o recall_tree.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT active.lo -MD -MP -MF .deps/active.Tpo -c active.cc -o active.o >/dev/null 2>&1 depbase=`echo active_cover.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o depbase=`echo cs_active.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -fPIC -DPIC -o .libs/cs_active.o In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from active_cover.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from active_cover.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from active_cover.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo kernel_svm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cs_active.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cs_active.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cs_active.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = lq_data; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = lq_data]’ cs_active.cc:216:32: required from ‘void predict_or_learn(cs_active&, LEARNER::base_learner&, example&) [with bool is_learn = true; bool is_simulation = true; LEARNER::base_learner = LEARNER::learner]’ cs_active.cc:347:151: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct lq_data’ with no trivial copy-assignment [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cs_active.cc:16:8: note: ‘struct lq_data’ declared here 16 | struct lq_data | ^~~~~~~ depbase=`echo best_constant.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT best_constant.lo -MD -MP -MF $depbase.Tpo -c -o best_constant.lo best_constant.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.o In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from memory.h:5, from v_array.h:21, from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from parse_primitives.h:10, from parse_example.h:8, from kernel_svm.cc:18: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from parse_example.h:9, from kernel_svm.cc:18: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from best_constant.h:3, from best_constant.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -o best_constant.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cs_active.lo -MD -MP -MF .deps/cs_active.Tpo -c cs_active.cc -o cs_active.o >/dev/null 2>&1 depbase=`echo ftrl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from ftrl.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from ftrl.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 depbase=`echo svrg.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT svrg.lo -MD -MP -MF $depbase.Tpo -c -o svrg.lo svrg.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -fPIC -DPIC -o .libs/svrg.o In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from svrg.cc:5: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from svrg.cc:5: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo lrqfa.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT lrqfa.lo -MD -MP -MF $depbase.Tpo -c -o lrqfa.lo lrqfa.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from lrqfa.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from lrqfa.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from lrqfa.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo interact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT interact.lo -MD -MP -MF $depbase.Tpo -c -o interact.lo interact.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT svrg.lo -MD -MP -MF .deps/svrg.Tpo -c svrg.cc -o svrg.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from interact.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from interact.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from interact.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1 depbase=`echo comp_io.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o depbase=`echo interactions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT interactions.lo -MD -MP -MF $depbase.Tpo -c -o interactions.lo interactions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -fPIC -DPIC -o .libs/interactions.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -o comp_io.o >/dev/null 2>&1 depbase=`echo vw_exception.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT vw_exception.lo -MD -MP -MF $depbase.Tpo -c -o vw_exception.lo vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -fPIC -DPIC -o .libs/vw_exception.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -o vw_exception.o >/dev/null 2>&1 In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from interactions.h:3, from interactions.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from interactions.h:3, from interactions.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from interactions.h:3, from interactions.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo vw_validate.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT vw_validate.lo -MD -MP -MF $depbase.Tpo -c -o vw_validate.lo vw_validate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT audit_regressor.lo -MD -MP -MF $depbase.Tpo -c -o audit_regressor.lo audit_regressor.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o depbase=`echo gen_cs_example.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT gen_cs_example.lo -MD -MP -MF $depbase.Tpo -c -o gen_cs_example.lo gen_cs_example.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -fPIC -DPIC -o .libs/gen_cs_example.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw_validate.cc:6: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw_validate.cc:6: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw_validate.cc:6: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from audit_regressor.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from audit_regressor.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from audit_regressor.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from global_data.h:16, from vw.h:15, from gen_cs_example.cc:8: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from vw.h:15, from gen_cs_example.cc:8: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from vw.h:15, from gen_cs_example.cc:8: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -o vw_validate.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1 depbase=`echo cb_explore.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o depbase=`echo action_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cb_explore_adf.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore_adf.lo cb_explore_adf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -fPIC -DPIC -o .libs/cb_explore_adf.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ depbase=`echo OjaNewton.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT OjaNewton.lo -MD -MP -MF $depbase.Tpo -c -o OjaNewton.lo OjaNewton.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from cb_explore_adf.cc:1: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from cb_explore_adf.cc:1: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from cb_explore_adf.cc:1: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from parse_regressor.h:8, from gd.h:11, from OjaNewton.cc:7: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from global_data.h:19, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from global_data.h:24, from parse_regressor.h:9, from gd.h:11, from OjaNewton.cc:7: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT cb_explore_adf.lo -MD -MP -MF .deps/cb_explore_adf.Tpo -c cb_explore_adf.cc -o cb_explore_adf.o >/dev/null 2>&1 depbase=`echo parse_example_json.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -o parse_example_json.o >/dev/null 2>&1 depbase=`echo baseline.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT baseline.lo -MD -MP -MF $depbase.Tpo -c -o baseline.lo baseline.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -fPIC -DPIC -o .libs/baseline.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.o >/dev/null 2>&1 In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from baseline.cc:9: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from baseline.cc:9: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from baseline.cc:9: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT baseline.lo -MD -MP -MF .deps/baseline.Tpo -c baseline.cc -o baseline.o >/dev/null 2>&1 depbase=`echo classweight.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT classweight.lo -MD -MP -MF $depbase.Tpo -c -o classweight.lo classweight.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o depbase=`echo allreduce_sockets.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT allreduce_sockets.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_sockets.lo allreduce_sockets.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -fPIC -DPIC -o .libs/allreduce_sockets.o In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = std::shared_ptr, std::__cxx11::basic_string > >; size_t = long unsigned int]’: v_array.h:77:7: required from ‘void v_array::erase() [with T = std::shared_ptr, std::__cxx11::basic_string > >]’ feature_group.h:272:23: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘class std::shared_ptr, std::__cxx11::basic_string > >’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘class std::shared_ptr, std::__cxx11::basic_string > >’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:84, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:22, from /usr/include/boost/function/function1.hpp:11, from /usr/include/boost/program_options/value_semantic.hpp:13, from /usr/include/boost/program_options/options_description.hpp:13, from /usr/include/boost/program_options.hpp:15, from reductions.h:7, from classweight.cc:2: /usr/include/c++/10/bits/shared_ptr.h:121:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 121 | class shared_ptr : public __shared_ptr<_Tp> | ^~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature_slice; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature_slice]’ feature_group.h:315:29: required from here v_array.h:62:29: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct feature_slice’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess] 62 | T* temp = (T *)realloc(_begin, sizeof(T) * length); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct feature_slice’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:26:8: note: ‘struct feature_slice’ declared here 26 | struct feature_slice //a helper struct for functions using the set {v,i,space_name} | ^~~~~~~~~~~~~ In file included from io_buf.h:14, from reductions.h:10, from classweight.cc:2: v_array.h: In instantiation of ‘void v_array::resize(size_t) [with T = feature; size_t = long unsigned int]’: v_array.h:94:7: required from ‘void v_array::push_back(const T&) [with T = feature]’ feature_group.h:329:29: required from here v_array.h:69:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct feature’; use assignment or value-initialization instead [-Wclass-memaccess] 69 | memset(_begin+old_len, 0, (length-old_len)*sizeof(T)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from example.h:17, from reductions.h:11, from classweight.cc:2: feature_group.h:19:8: note: ‘struct feature’ declared here 19 | struct feature //sparse feature definition for the library interface | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT allreduce_sockets.lo -MD -MP -MF .deps/allreduce_sockets.Tpo -c allreduce_sockets.cc -o allreduce_sockets.o >/dev/null 2>&1 depbase=`echo allreduce_threads.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o depbase=`echo active_interactor.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT active_interactor.o -MD -MP -MF $depbase.Tpo -c -o active_interactor.o active_interactor.cc &&\ mv -f $depbase.Tpo $depbase.Po libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -o allreduce_threads.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -o active_interactor active_interactor.o -L/usr/lib -lboost_program_options -L/lib -lz -lpthread /bin/bash ../libtool --tag=CXX --mode=link g++ -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -o liballreduce.la -rpath /usr/local/lib allreduce_sockets.lo allreduce_threads.lo vw_exception.lo -L/usr/lib -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/10/crtbeginS.o .libs/allreduce_sockets.o .libs/allreduce_threads.o .libs/vw_exception.o -L/usr/lib -lboost_program_options -L/lib -lz -lpthread -L/<>/vg-1.27.1+ds/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/10 -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/<>/vg-1.27.1+ds/lib -L. -L/usr/lib/gcc/aarch64-linux-gnu/10/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/10/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -flto=auto -O3 -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -flto=auto -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 libtool: link: g++ -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -flto=auto -ffat-lto-objects -o active_interactor active_interactor.o -L/usr/lib -lboost_program_options -L/lib -lz -lpthread libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.o >/dev/null 2>&1 libtool: link: (cd ".libs" && rm -f "liballreduce.so.0" && ln -s "liballreduce.so.0.0.0" "liballreduce.so.0") libtool: link: (cd ".libs" && rm -f "liballreduce.so" && ln -s "liballreduce.so.0.0.0" "liballreduce.so") libtool: link: ar cr .libs/liballreduce.a allreduce_sockets.o allreduce_threads.o vw_exception.o libtool: link: ranlib .libs/liballreduce.a libtool: link: ( cd ".libs" && rm -f "liballreduce.la" && ln -s "../liballreduce.la" "liballreduce.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -o libvw.la -rpath /usr/local/lib hash.lo parser_helper.lo global_data.lo io_buf.lo parse_regressor.lo parse_primitives.lo unique_sort.lo cache.lo rand48.lo simple_label.lo multiclass.lo oaa.lo multilabel_oaa.lo boosting.lo ect.lo marginal.lo autolink.lo binary.lo lrq.lo cost_sensitive.lo multilabel.lo label_dictionary.lo csoaa.lo cb.lo cb_adf.lo cb_algs.lo search.lo search_meta.lo search_sequencetask.lo search_dep_parser.lo search_hooktask.lo search_multiclasstask.lo search_entityrelationtask.lo search_graph.lo parse_example.lo scorer.lo network.lo parse_args.lo accumulate.lo gd.lo learner.lo mwt.lo lda_core.lo gd_mf.lo mf.lo bfgs.lo noop.lo print.lo example.lo parser.lo loss_functions.lo sender.lo nn.lo confidence.lo bs.lo cbify.lo explore_eval.lo topk.lo stagewise_poly.lo log_multi.lo recall_tree.lo active.lo active_cover.lo cs_active.lo kernel_svm.lo best_constant.lo ftrl.lo svrg.lo lrqfa.lo interact.lo comp_io.lo interactions.lo vw_exception.lo vw_validate.lo audit_regressor.lo gen_cs_example.lo cb_explore.lo action_score.lo cb_explore_adf.lo OjaNewton.lo parse_example_json.lo baseline.lo classweight.lo liballreduce.la -L/usr/lib -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/10/crtbeginS.o .libs/hash.o .libs/parser_helper.o .libs/global_data.o .libs/io_buf.o .libs/parse_regressor.o .libs/parse_primitives.o .libs/unique_sort.o .libs/cache.o .libs/rand48.o .libs/simple_label.o .libs/multiclass.o .libs/oaa.o .libs/multilabel_oaa.o .libs/boosting.o .libs/ect.o .libs/marginal.o .libs/autolink.o .libs/binary.o .libs/lrq.o .libs/cost_sensitive.o .libs/multilabel.o .libs/label_dictionary.o .libs/csoaa.o .libs/cb.o .libs/cb_adf.o .libs/cb_algs.o .libs/search.o .libs/search_meta.o .libs/search_sequencetask.o .libs/search_dep_parser.o .libs/search_hooktask.o .libs/search_multiclasstask.o .libs/search_entityrelationtask.o .libs/search_graph.o .libs/parse_example.o .libs/scorer.o .libs/network.o .libs/parse_args.o .libs/accumulate.o .libs/gd.o .libs/learner.o .libs/mwt.o .libs/lda_core.o .libs/gd_mf.o .libs/mf.o .libs/bfgs.o .libs/noop.o .libs/print.o .libs/example.o .libs/parser.o .libs/loss_functions.o .libs/sender.o .libs/nn.o .libs/confidence.o .libs/bs.o .libs/cbify.o .libs/explore_eval.o .libs/topk.o .libs/stagewise_poly.o .libs/log_multi.o .libs/recall_tree.o .libs/active.o .libs/active_cover.o .libs/cs_active.o .libs/kernel_svm.o .libs/best_constant.o .libs/ftrl.o .libs/svrg.o .libs/lrqfa.o .libs/interact.o .libs/comp_io.o .libs/interactions.o .libs/vw_exception.o .libs/vw_validate.o .libs/audit_regressor.o .libs/gen_cs_example.o .libs/cb_explore.o .libs/action_score.o .libs/cb_explore_adf.o .libs/OjaNewton.o .libs/parse_example_json.o .libs/baseline.o .libs/classweight.o -Wl,-rpath -Wl,/<>/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/.libs ./.libs/liballreduce.so -L/usr/lib -lboost_program_options -L/lib -lz -lpthread -L/<>/vg-1.27.1+ds/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/10 -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/<>/vg-1.27.1+ds/lib -L. -L/usr/lib/gcc/aarch64-linux-gnu/10/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/10/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -flto=auto -O3 -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -flto=auto -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 comp_io.h:19:7: warning: type 'struct comp_io_buf' violates the C++ One Definition Rule [-Wodr] 19 | class comp_io_buf : public io_buf | ^ comp_io.h:19:7: note: a different type is defined in another translation unit 19 | class comp_io_buf : public io_buf | ^ comp_io.h:22:23: note: the first difference of corresponding definitions is field 'gz_files' 22 | std::vector gz_files; | ^ comp_io.h:22:23: note: a field of same name but different type is defined in another translation unit 22 | std::vector gz_files; | ^ /usr/include/c++/10/bits/stl_vector.h:389:11: note: type name 'std::vector >' should match type name 'std::vector >' 389 | class vector : protected _Vector_base<_Tp, _Alloc> | ^ ftrl.cc:19:8: warning: type 'struct update_data' violates the C++ One Definition Rule [-Wodr] 19 | struct update_data | ^ OjaNewton.cc:18:8: note: a different type is defined in another translation unit 18 | struct update_data | ^ ftrl.cc:21:9: note: the first difference of corresponding definitions is field 'update' 21 | float update; | ^ OjaNewton.cc:20:21: note: a field with different name is defined in another translation unit 20 | struct OjaNewton *ON; | ^ libtool: link: (cd ".libs" && rm -f "libvw.so.0" && ln -s "libvw.so.0.0.0" "libvw.so.0") libtool: link: (cd ".libs" && rm -f "libvw.so" && ln -s "libvw.so.0.0.0" "libvw.so") libtool: link: ar cr .libs/libvw.a hash.o parser_helper.o global_data.o io_buf.o parse_regressor.o parse_primitives.o unique_sort.o cache.o rand48.o simple_label.o multiclass.o oaa.o multilabel_oaa.o boosting.o ect.o marginal.o autolink.o binary.o lrq.o cost_sensitive.o multilabel.o label_dictionary.o csoaa.o cb.o cb_adf.o cb_algs.o search.o search_meta.o search_sequencetask.o search_dep_parser.o search_hooktask.o search_multiclasstask.o search_entityrelationtask.o search_graph.o parse_example.o scorer.o network.o parse_args.o accumulate.o gd.o learner.o mwt.o lda_core.o gd_mf.o mf.o bfgs.o noop.o print.o example.o parser.o loss_functions.o sender.o nn.o confidence.o bs.o cbify.o explore_eval.o topk.o stagewise_poly.o log_multi.o recall_tree.o active.o active_cover.o cs_active.o kernel_svm.o best_constant.o ftrl.o svrg.o lrqfa.o interact.o comp_io.o interactions.o vw_exception.o vw_validate.o audit_regressor.o gen_cs_example.o cb_explore.o action_score.o cb_explore_adf.o OjaNewton.o parse_example_json.o baseline.o classweight.o libtool: link: ranlib .libs/libvw.a libtool: link: ( cd ".libs" && rm -f "libvw.la" && ln -s "../libvw.la" "libvw.la" ) /bin/bash ../libtool --tag=CXX --mode=link g++ -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -o vw vw-main.o libvw.la liballreduce.la -L/usr/lib -lboost_program_options -L/lib -lz -lpthread libtool: link: g++ -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -flto=auto -ffat-lto-objects -o .libs/vw vw-main.o ./.libs/libvw.so ./.libs/liballreduce.so -L/usr/lib -lboost_program_options -L/lib -lz -lpthread make[5]: Leaving directory '/<>/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/<>/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/<>/vg-1.27.1+ds/deps/vowpal_wabbit/cluster' depbase=`echo spanning_tree_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT spanning_tree_main.o -MD -MP -MF $depbase.Tpo -c -o spanning_tree_main.o spanning_tree_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/spanning_tree.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT ../vowpalwabbit/spanning_tree.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/spanning_tree.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ../vowpalwabbit/vw_exception.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT ../vowpalwabbit/vw_exception.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/usr/include -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -L/usr/lib -lboost_program_options -L/lib -lz -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/usr/include -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -flto=auto -ffat-lto-objects -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -L/usr/lib -lboost_program_options -L/lib -lz -lpthread ../vowpalwabbit/.libs/liballreduce.so make[4]: Leaving directory '/<>/vg-1.27.1+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/<>/vg-1.27.1+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT library_example.o -MD -MP -MF $depbase.Tpo -c -o library_example.o library_example.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_train.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT ezexample_train.o -MD -MP -MF $depbase.Tpo -c -o ezexample_train.o ezexample_train.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo ezexample_predict.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -I../vowpalwabbit -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -MT ezexample_predict.o -MD -MP -MF $depbase.Tpo -c -o ezexample_predict.o ezexample_predict.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/usr/include -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -L/usr/lib -lboost_program_options -L/lib -lz -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -o library_example library_example.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/usr/include -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -flto=auto -ffat-lto-objects -o .libs/library_example library_example.o -L/usr/lib -lboost_program_options -L/lib -lz -lpthread ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so /bin/bash ../libtool --tag=CXX --mode=link g++ -I/usr/include -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -L/usr/lib -lboost_program_options -L/lib -lz -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -o ezexample_predict ezexample_predict.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/usr/include -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -flto=auto -ffat-lto-objects -o .libs/ezexample_predict ezexample_predict.o -L/usr/lib -lboost_program_options -L/lib -lz -lpthread ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so /bin/bash ../libtool --tag=CXX --mode=link g++ -I/usr/include -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -L/usr/lib -lboost_program_options -L/lib -lz -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -o ezexample_train ezexample_train.o ../vowpalwabbit/libvw.la ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/usr/include -I/include -I /usr/include/rapidjson/ -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -flto=auto -ffat-lto-objects -o .libs/ezexample_train ezexample_train.o -L/usr/lib -lboost_program_options -L/lib -lz -lpthread ../vowpalwabbit/.libs/libvw.so ../vowpalwabbit/.libs/liballreduce.so make[4]: Leaving directory '/<>/vg-1.27.1+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/<>/vg-1.27.1+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/<>/vg-1.27.1+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/<>/vg-1.27.1+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /<>/vg-1.27.1+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /<>/vg-1.27.1+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /<>/vg-1.27.1+ds/include/vowpalwabbit/ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/vg.hpp:29, from src/augment.cpp:1: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:208:74: required from ‘void vg::io::for_each_parallel_impl(std::istream&, const std::function&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:314:27: required from ‘void vg::io::for_each_parallel(std::istream&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ src/augment.cpp:46:124: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/aligner.hpp:12, from src/vg.hpp:20, from src/augment.cpp:1: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/cactus_snarl_finder.o src/cactus_snarl_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/dinucleotide_machine.o src/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/dozeu_interface.o src/dozeu_interface.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/dozeu_pinning_overlay.o src/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/gapless_extender.o src/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/gfa.o src/gfa.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/vg.hpp:29, from src/genotypekit.hpp:19, from src/genotypekit.cpp:1: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Translation; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Translation]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Translation; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Translation; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Translation; std::istream = std::basic_istream]’ src/genotypekit.cpp:291:37: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/genotypekit.hpp:18, from src/genotypekit.cpp:1: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/vg.hpp:29, from src/genotypekit.hpp:19, from src/genotypekit.cpp:1: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::LocationSupport; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::LocationSupport]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::LocationSupport; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::LocationSupport; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::LocationSupport; std::istream = std::basic_istream]’ src/genotypekit.cpp:334:37: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/genotypekit.hpp:18, from src/genotypekit.cpp:1: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/haplotype_indexer.o src/haplotype_indexer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/haplotypes.o src/haplotypes.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/haplotype_indexer.cpp:10: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Alignment]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Alignment; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Alignment; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Alignment; std::istream = std::basic_istream]’ src/haplotype_indexer.cpp:455:44: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/google/protobuf/type.pb.h:23, from /usr/include/google/protobuf/util/type_resolver.h:39, from /<>/vg-1.27.1+ds/include/vg/io/registry.hpp:23, from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:15, from src/haplotype_indexer.cpp:10: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/homogenizer.o src/homogenizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/hts_alignment_emitter.o src/hts_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/incremental_subgraph.o src/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/index.o src/index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/index_manager.o src/index_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/integrated_snarl_finder.o src/integrated_snarl_finder.cpp In file included from src/stream_index.hpp:17, from src/indexed_vg.hpp:15, from src/indexed_vg.cpp:6: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:198:9: required from ‘bool vg::io::ProtobufIterator::seek_group(int64_t) [with T = vg::Graph; int64_t = long int]’ src/indexed_vg.cpp:41:13: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/stream_index.hpp:16, from src/indexed_vg.hpp:15, from src/indexed_vg.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/mcmc_caller.o src/mcmc_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/min_distance.o src/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/multipath_alignment_emitter.o src/multipath_alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/packer.o src/packer.cpp In file included from src/packer.cpp:2: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Edit; std::string = std::__cxx11::basic_string]’: src/packer.cpp:899:41: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:18, from src/packer.cpp:2: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/path.o src/path.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/path.cpp:2: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Path; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Path]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Path; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Path; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Path; std::istream = std::basic_istream]’ src/path.cpp:118:32: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/path.hpp:11, from src/path.cpp:1: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/prune.o src/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/qual_adj_xdrop_aligner.o src/qual_adj_xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/sampler.o src/sampler.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/vg.hpp:29, from src/readfilter.hpp:9, from src/readfilter.cpp:1: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:208:74: required from ‘void vg::io::for_each_parallel_impl(std::istream&, const std::function&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:293:27: required from ‘void vg::io::for_each_interleaved_pair_parallel(std::istream&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ src/readfilter.cpp:755:82: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/aligner.hpp:12, from src/vg.hpp:20, from src/readfilter.hpp:9, from src/readfilter.cpp:1: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/seed_clusterer.o src/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp In file included from src/snarls.hpp:18, from src/snarls.cpp:10: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Snarl; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Snarl]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Snarl; std::istream = std::basic_istream]’ src/snarls.cpp:502:49: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/message_emitter.hpp:18, from /<>/vg-1.27.1+ds/include/vg/io/protobuf_emitter.hpp:18, from src/snarls.cpp:8: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/splicing.o src/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/srpe.o src/srpe.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/traversal_finder.o src/traversal_finder.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/vg.hpp:29, from src/translator.hpp:16, from src/translator.cpp:1: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Translation; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Translation]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Translation; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Translation; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Translation; std::istream = std::basic_istream]’ src/translator.cpp:14:32: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/translator.hpp:15, from src/translator.cpp:1: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/version.o src/version.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/vg.hpp:29, from src/variant_recall.hpp:16, from src/variant_recall.cpp:2: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:208:74: required from ‘void vg::io::for_each_parallel_impl(std::istream&, const std::function&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:293:27: required from ‘void vg::io::for_each_interleaved_pair_parallel(std::istream&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ src/variant_recall.cpp:71:67: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/variant_recall.hpp:15, from src/variant_recall.cpp:2: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/viz.o src/viz.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/vg.hpp:29, from src/vg.cpp:1: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ src/vg.cpp:80:32: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/aligner.hpp:12, from src/vg.hpp:20, from src/vg.cpp:1: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/alignment_path_offsets.o src/algorithms/alignment_path_offsets.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/append_graph.o src/algorithms/append_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/apply_bulk_modifications.o src/algorithms/apply_bulk_modifications.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/approx_path_distance.o src/algorithms/approx_path_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/are_equivalent.o src/algorithms/are_equivalent.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/copy_graph.o src/algorithms/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/count_walks.o src/algorithms/count_walks.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/dagify.o src/algorithms/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/dijkstra.o src/algorithms/dijkstra.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/algorithms/coverage_depth.cpp:4: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:208:74: required from ‘void vg::io::for_each_parallel_impl(std::istream&, const std::function&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:314:27: required from ‘void vg::io::for_each_parallel(std::istream&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ src/algorithms/coverage_depth.cpp:268:67: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from /<>/vg-1.27.1+ds/src/handle.hpp:21, from src/algorithms/coverage_depth.hpp:11, from src/algorithms/coverage_depth.cpp:1: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/distance_to_head.o src/algorithms/distance_to_head.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/distance_to_tail.o src/algorithms/distance_to_tail.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/eades_algorithm.o src/algorithms/eades_algorithm.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/extend.o src/algorithms/extend.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/extract_connecting_graph.o src/algorithms/extract_connecting_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/extract_containing_graph.o src/algorithms/extract_containing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/extract_extending_graph.o src/algorithms/extract_extending_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/find_shortest_paths.o src/algorithms/find_shortest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/find_tips.o src/algorithms/find_tips.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/gfa_to_handle.o src/algorithms/gfa_to_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/is_acyclic.o src/algorithms/is_acyclic.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/is_single_stranded.o src/algorithms/is_single_stranded.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/jump_along_path.o src/algorithms/jump_along_path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/k_widest_paths.o src/algorithms/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/nearest_offsets_in_paths.o src/algorithms/nearest_offsets_in_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/next_pos_chars.o src/algorithms/next_pos_chars.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/remove_high_degree.o src/algorithms/remove_high_degree.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/reverse_complement.o src/algorithms/reverse_complement.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/sorted_id_ranges.o src/algorithms/sorted_id_ranges.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/split_strands.o src/algorithms/split_strands.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/strongly_connected_components.o src/algorithms/strongly_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/three_edge_connected_components.o src/algorithms/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/to_gfa.o src/algorithms/to_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/topological_sort.o src/algorithms/topological_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/unchop.o src/algorithms/unchop.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/algorithms/weakly_connected_components.o src/algorithms/weakly_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/io/load_proto_to_graph.o src/io/load_proto_to_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/io/register_libvg_io.o src/io/register_libvg_io.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/io/register_loader_saver_distance_index.o src/io/register_loader_saver_distance_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/io/register_loader_saver_gbwt.o src/io/register_loader_saver_gbwt.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp In file included from src/io/load_proto_to_graph.cpp:15: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: src/io/load_proto_to_graph.cpp:35:43: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/io/../handle.hpp:21, from src/io/load_proto_to_graph.hpp:10, from src/io/load_proto_to_graph.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/io/register_loader_saver_gcsa.o src/io/register_loader_saver_gcsa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/io/register_loader_saver_hash_graph.o src/io/register_loader_saver_hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/io/register_loader_saver_lcp.o src/io/register_loader_saver_lcp.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/io/register_loader_saver_minimizer.o src/io/register_loader_saver_minimizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/io/register_loader_saver_odgi.o src/io/register_loader_saver_odgi.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/io/register_loader_saver_packed_graph.o src/io/register_loader_saver_packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/io/register_loader_saver_r_index.o src/io/register_loader_saver_r_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/io/register_loader_saver_snarl_manager.o src/io/register_loader_saver_snarl_manager.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/io/register_loader_saver_vg.o src/io/register_loader_saver_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/io/register_loader_saver_xg.o src/io/register_loader_saver_xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/aligner.o src/unittest/aligner.cpp In file included from src/io/register_loader_saver_snarl_manager.cpp:7: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Snarl; std::string = std::__cxx11::basic_string]’: src/io/register_loader_saver_snarl_manager.cpp:26:47: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/google/protobuf/type.pb.h:23, from /usr/include/google/protobuf/util/type_resolver.h:39, from /<>/vg-1.27.1+ds/include/vg/io/registry.hpp:23, from src/io/register_loader_saver_snarl_manager.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from src/io/register_loader_saver_vg.cpp:7: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: src/io/register_loader_saver_vg.cpp:35:47: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/google/protobuf/type.pb.h:23, from /usr/include/google/protobuf/util/type_resolver.h:39, from /<>/vg-1.27.1+ds/include/vg/io/registry.hpp:23, from src/io/register_loader_saver_vg.cpp:6: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/banded_global_aligner.o src/unittest/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/blocked_gzip_input_stream.o src/unittest/blocked_gzip_input_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/blocked_gzip_output_stream.o src/unittest/blocked_gzip_output_stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/copy_graph.o src/unittest/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/dinucleotide_machine.o src/unittest/dinucleotide_machine.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/dozeu_pinning_overlay.o src/unittest/dozeu_pinning_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/driver.o src/unittest/driver.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/flow_sort_test.o src/unittest/flow_sort_test.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/gapless_extender.o src/unittest/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/incremental_subgraph.o src/unittest/incremental_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/k_widest_paths.o src/unittest/k_widest_paths.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/min_distance.o src/unittest/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/multipath_alignment_graph.o src/unittest/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/path_component_index.o src/unittest/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/seed_clusterer.o src/unittest/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/source_sink_overlay.o src/unittest/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/splicing.o src/unittest/splicing.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/srpe_filter.o src/unittest/srpe_filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/stream.o src/unittest/stream.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/unittest/stream.cpp:5: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Position; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Position]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Position; std::istream = std::basic_istream]’ src/unittest/stream.cpp:171:62: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/google/protobuf/type.pb.h:23, from /usr/include/google/protobuf/util/type_resolver.h:39, from /<>/vg-1.27.1+ds/include/vg/io/registry.hpp:23, from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:15, from src/unittest/stream.cpp:5: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/unittest/stream.cpp:5: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:208:74: required from ‘void vg::io::for_each_parallel_impl(std::istream&, const std::function&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:314:27: required from ‘void vg::io::for_each_parallel(std::istream&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ src/unittest/stream.cpp:235:6: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/google/protobuf/type.pb.h:23, from /usr/include/google/protobuf/util/type_resolver.h:39, from /<>/vg-1.27.1+ds/include/vg/io/registry.hpp:23, from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:15, from src/unittest/stream.cpp:5: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/unittest/stream.cpp:5: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ src/unittest/stream.cpp:37:10: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/google/protobuf/type.pb.h:23, from /usr/include/google/protobuf/util/type_resolver.h:39, from /<>/vg-1.27.1+ds/include/vg/io/registry.hpp:23, from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:15, from src/unittest/stream.cpp:5: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/surject.o src/unittest/surject.cpp In file included from src/unittest/../stream_index.hpp:17, from src/unittest/stream_index.cpp:9: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Alignment]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Alignment; std::istream = std::basic_istream]’ src/unittest/stream_index.cpp:352:35: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/unittest/../stream_index.hpp:16, from src/unittest/stream_index.cpp:9: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/three_edge_connected_components.o src/unittest/three_edge_connected_components.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/traversal_support.o src/unittest/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/annotate_main.cpp:2: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:208:74: required from ‘void vg::io::for_each_parallel_impl(std::istream&, const std::function&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:314:27: required from ‘void vg::io::for_each_parallel(std::istream&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ src/subcommand/annotate_main.cpp:366:18: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../aligner.hpp:12, from src/subcommand/../vg.hpp:20, from src/subcommand/annotate_main.cpp:2: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/augment_main.cpp:26: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Alignment]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Alignment; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Alignment; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Alignment; std::istream = std::basic_istream]’ src/subcommand/augment_main.cpp:313:73: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../aligner.hpp:12, from src/subcommand/../vg.hpp:20, from src/subcommand/augment_main.cpp:26: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/augment_main.cpp:26: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Locus; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Locus]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Locus; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Locus; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Locus; std::istream = std::basic_istream]’ src/subcommand/augment_main.cpp:375:61: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../aligner.hpp:12, from src/subcommand/../vg.hpp:20, from src/subcommand/augment_main.cpp:26: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/bugs_main.o src/subcommand/bugs_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/chunk_main.cpp:15: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:208:74: required from ‘void vg::io::for_each_parallel_impl(std::istream&, const std::function&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:314:27: required from ‘void vg::io::for_each_parallel(std::istream&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ src/subcommand/chunk_main.cpp:815:77: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../aligner.hpp:12, from src/subcommand/../vg.hpp:20, from src/subcommand/chunk_main.cpp:15: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/compare_main.o src/subcommand/compare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp In file included from src/subcommand/../snarls.hpp:18, from src/subcommand/../seed_clusterer.hpp:4, from src/subcommand/cluster_main.cpp:16: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:208:74: required from ‘void vg::io::for_each_parallel_impl(std::istream&, const std::function&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:314:27: required from ‘void vg::io::for_each_parallel(std::istream&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ src/subcommand/cluster_main.cpp:395:10: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/message_emitter.hpp:18, from /<>/vg-1.27.1+ds/include/vg/io/protobuf_emitter.hpp:18, from src/subcommand/../snarls.hpp:17, from src/subcommand/../seed_clusterer.hpp:4, from src/subcommand/cluster_main.cpp:16: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/crash_main.o src/subcommand/crash_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/convert_main.cpp:2: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:208:74: required from ‘void vg::io::for_each_parallel_impl(std::istream&, const std::function&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:314:27: required from ‘void vg::io::for_each_parallel(std::istream&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ src/subcommand/convert_main.cpp:147:57: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../aligner.hpp:12, from src/subcommand/../vg.hpp:20, from src/subcommand/convert_main.cpp:2: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/gampcompare_main.o src/subcommand/gampcompare_main.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/gamcompare_main.cpp:14: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:208:74: required from ‘void vg::io::for_each_parallel_impl(std::istream&, const std::function&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:314:27: required from ‘void vg::io::for_each_parallel(std::istream&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ src/subcommand/gamcompare_main.cpp:123:57: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../utility.hpp:19, from src/subcommand/../alignment.hpp:7, from src/subcommand/gamcompare_main.cpp:13: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/find_main.cpp:2: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Alignment]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Alignment; std::istream = std::basic_istream]’ src/subcommand/find_main.cpp:473:62: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../aligner.hpp:12, from src/subcommand/../vg.hpp:20, from src/subcommand/find_main.cpp:2: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/gampcompare_main.cpp:16: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:208:74: required from ‘void vg::io::for_each_parallel_impl(std::istream&, const std::function&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:314:27: required from ‘void vg::io::for_each_parallel(std::istream&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ src/subcommand/gampcompare_main.cpp:147:57: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../algorithms/../handle.hpp:21, from src/subcommand/../algorithms/alignment_path_offsets.hpp:3, from src/subcommand/gampcompare_main.cpp:13: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/gampcompare_main.cpp:16: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::MultipathAlignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:208:74: required from ‘void vg::io::for_each_parallel_impl(std::istream&, const std::function&, const std::function&, const std::function&, size_t) [with T = vg::MultipathAlignment; std::istream = std::basic_istream; size_t = long unsigned int]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:314:27: required from ‘void vg::io::for_each_parallel(std::istream&, const std::function&, size_t) [with T = vg::MultipathAlignment; std::istream = std::basic_istream; size_t = long unsigned int]’ src/subcommand/gampcompare_main.cpp:263:69: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../algorithms/../handle.hpp:21, from src/subcommand/../algorithms/alignment_path_offsets.hpp:3, from src/subcommand/gampcompare_main.cpp:13: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp In file included from src/subcommand/gamsort_main.cpp:1: src/subcommand/../stream_sorter.hpp: In instantiation of ‘void vg::StreamSorter::stream_sort(std::istream&, std::ostream&, vg::StreamIndex*) [with Message = vg::Alignment; std::istream = std::basic_istream; std::ostream = std::basic_ostream]’: src/subcommand/gamsort_main.cpp:174:57: required from here src/subcommand/../stream_sorter.hpp:275:76: warning: ‘int google::protobuf::MessageLite::ByteSize() const’ is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations] 275 | buffered_message_bytes += thread_buffer.back().ByteSize(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/google/protobuf/generated_enum_util.h:36, from /usr/include/google/protobuf/map.h:55, from /usr/include/google/protobuf/generated_message_table_driven.h:34, from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:26, from src/subcommand/../stream_sorter.hpp:4, from src/subcommand/gamsort_main.cpp:1: /usr/include/google/protobuf/message_lite.h:420:7: note: declared here 420 | int ByteSize() const { return internal::ToIntSize(ByteSizeLong()); } | ^~~~~~~~ In file included from src/subcommand/../stream_sorter.hpp:6, from src/subcommand/gamsort_main.cpp:1: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:208:74: required from ‘void vg::io::for_each_parallel_impl(std::istream&, const std::function&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:314:27: required from ‘void vg::io::for_each_parallel(std::istream&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ src/subcommand/gamsort_main.cpp:120:60: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../stream_sorter.hpp:4, from src/subcommand/gamsort_main.cpp:1: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/giraffe_main.o src/subcommand/giraffe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/../index.hpp:21, from src/subcommand/genotype_main.cpp:4: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Alignment]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Alignment; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Alignment; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Alignment; std::istream = std::basic_istream]’ src/subcommand/genotype_main.cpp:324:14: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../aligner.hpp:12, from src/subcommand/../vg.hpp:20, from src/subcommand/../index.hpp:21, from src/subcommand/genotype_main.cpp:4: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from src/subcommand/../snarls.hpp:18, from src/subcommand/../seed_clusterer.hpp:4, from src/subcommand/giraffe_main.cpp:19: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:208:74: required from ‘void vg::io::for_each_parallel_impl(std::istream&, const std::function&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:304:27: required from ‘void vg::io::for_each_interleaved_pair_parallel_after_wait(std::istream&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ src/subcommand/giraffe_main.cpp:1241:130: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/message_emitter.hpp:18, from /<>/vg-1.27.1+ds/include/vg/io/protobuf_emitter.hpp:18, from src/subcommand/../snarls.hpp:17, from src/subcommand/../seed_clusterer.hpp:4, from src/subcommand/giraffe_main.cpp:19: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/index_main.cpp:13: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Alignment]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Alignment; std::istream = std::basic_istream]’ src/subcommand/index_main.cpp:712:58: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../aligner.hpp:12, from src/subcommand/../vg.hpp:20, from src/subcommand/index_main.cpp:13: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/index_main.cpp:13: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ src/subcommand/index_main.cpp:733:54: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../aligner.hpp:12, from src/subcommand/../vg.hpp:20, from src/subcommand/index_main.cpp:13: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/locify_main.o src/subcommand/locify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/locify_main.cpp:15: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Locus; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Locus]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Locus; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Locus; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Locus; std::istream = std::basic_istream]’ src/subcommand/locify_main.cpp:237:37: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../aligner.hpp:12, from src/subcommand/../vg.hpp:20, from src/subcommand/locify_main.cpp:15: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/../phased_genome.hpp:18, from src/subcommand/../mcmc_genotyper.hpp:12, from src/subcommand/mcmc_main.cpp:14: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::MultipathAlignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::MultipathAlignment]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::MultipathAlignment; std::istream = std::basic_istream]’ src/subcommand/mcmc_main.cpp:181:65: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/google/protobuf/type.pb.h:23, from /usr/include/google/protobuf/util/type_resolver.h:39, from /<>/vg-1.27.1+ds/include/vg/io/registry.hpp:23, from /<>/vg-1.27.1+ds/include/vg/io/vpkg.hpp:8, from src/subcommand/mcmc_main.cpp:13: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/map_main.cpp:2: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:208:74: required from ‘void vg::io::for_each_parallel_impl(std::istream&, const std::function&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:293:27: required from ‘void vg::io::for_each_interleaved_pair_parallel(std::istream&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ src/subcommand/map_main.cpp:1185:70: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../aligner.hpp:12, from src/subcommand/../vg.hpp:20, from src/subcommand/map_main.cpp:2: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/mod_main.cpp:13: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Locus; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Locus]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Locus; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Locus; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Locus; std::istream = std::basic_istream]’ src/subcommand/mod_main.cpp:570:43: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../aligner.hpp:12, from src/subcommand/../vg.hpp:20, from src/subcommand/mod_main.cpp:13: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/../mapper.hpp:9, from src/subcommand/../multipath_mapper.hpp:11, from src/subcommand/mpmap_main.cpp:13: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:208:74: required from ‘void vg::io::for_each_parallel_impl(std::istream&, const std::function&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:304:27: required from ‘void vg::io::for_each_interleaved_pair_parallel_after_wait(std::istream&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ src/subcommand/mpmap_main.cpp:2032:95: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/google/protobuf/type.pb.h:23, from /usr/include/google/protobuf/util/type_resolver.h:39, from /<>/vg-1.27.1+ds/include/vg/io/registry.hpp:23, from /<>/vg-1.27.1+ds/include/vg/io/vpkg.hpp:8, from src/subcommand/mpmap_main.cpp:12: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/pack_main.cpp:2: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:208:74: required from ‘void vg::io::for_each_parallel_impl(std::istream&, const std::function&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:314:27: required from ‘void vg::io::for_each_parallel(std::istream&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ src/subcommand/pack_main.cpp:228:65: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../aligner.hpp:12, from src/subcommand/../vg.hpp:20, from src/subcommand/pack_main.cpp:2: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/recalibrate_main.o src/subcommand/recalibrate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/recalibrate_main.cpp:13: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Alignment]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Alignment; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Alignment; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Alignment; std::istream = std::basic_istream]’ src/subcommand/recalibrate_main.cpp:185:50: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../utility.hpp:19, from src/subcommand/../alignment.hpp:7, from src/subcommand/recalibrate_main.cpp:12: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/sift_main.cpp:10: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:208:74: required from ‘void vg::io::for_each_parallel_impl(std::istream&, const std::function&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:293:27: required from ‘void vg::io::for_each_interleaved_pair_parallel(std::istream&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ src/subcommand/sift_main.cpp:544:65: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/google/protobuf/type.pb.h:23, from /usr/include/google/protobuf/util/type_resolver.h:39, from /<>/vg-1.27.1+ds/include/vg/io/registry.hpp:23, from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:15, from src/subcommand/sift_main.cpp:10: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/srpe_main.o src/subcommand/srpe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/stats_main.cpp:15: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:208:74: required from ‘void vg::io::for_each_parallel_impl(std::istream&, const std::function&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:314:27: required from ‘void vg::io::for_each_parallel(std::istream&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ src/subcommand/stats_main.cpp:810:59: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/google/protobuf/type.pb.h:23, from /usr/include/google/protobuf/util/type_resolver.h:39, from /<>/vg-1.27.1+ds/include/vg/io/registry.hpp:23, from /<>/vg-1.27.1+ds/include/vg/io/vpkg.hpp:8, from src/subcommand/stats_main.cpp:14: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/surject_main.cpp:17: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:208:74: required from ‘void vg::io::for_each_parallel_impl(std::istream&, const std::function&, const std::function&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:293:27: required from ‘void vg::io::for_each_interleaved_pair_parallel(std::istream&, const std::function&, size_t) [with T = vg::Alignment; std::istream = std::basic_istream; size_t = long unsigned int]’ src/subcommand/surject_main.cpp:293:18: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../aligner.hpp:12, from src/subcommand/../vg.hpp:20, from src/subcommand/surject_main.cpp:17: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/translate_main.cpp:15: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Path; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Path]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Path; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Path; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Path; std::istream = std::basic_istream]’ src/subcommand/translate_main.cpp:136:41: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../aligner.hpp:12, from src/subcommand/../vg.hpp:20, from src/subcommand/translate_main.cpp:15: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/translate_main.cpp:15: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Alignment]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Alignment; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Alignment; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Alignment; std::istream = std::basic_istream]’ src/subcommand/translate_main.cpp:145:40: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../aligner.hpp:12, from src/subcommand/../vg.hpp:20, from src/subcommand/translate_main.cpp:15: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/translate_main.cpp:15: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Locus; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Locus]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Locus; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Locus; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Locus; std::istream = std::basic_istream]’ src/subcommand/translate_main.cpp:154:41: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../aligner.hpp:12, from src/subcommand/../vg.hpp:20, from src/subcommand/translate_main.cpp:15: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/translate_main.cpp:15: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Translation; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Translation]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Translation; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Translation; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Translation; std::istream = std::basic_istream]’ src/subcommand/translate_main.cpp:165:44: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../aligner.hpp:12, from src/subcommand/../vg.hpp:20, from src/subcommand/translate_main.cpp:15: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/validate_main.cpp:15: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Alignment]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Alignment; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Alignment; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Alignment; std::istream = std::basic_istream]’ src/subcommand/validate_main.cpp:137:22: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../aligner.hpp:12, from src/subcommand/../vg.hpp:20, from src/subcommand/validate_main.cpp:15: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/aligner.o obj/alignment.o obj/augment.o obj/banded_global_aligner.o obj/benchmark.o obj/build_index.o obj/cactus.o obj/cactus_snarl_finder.o obj/chunker.o obj/cluster.o obj/constructor.o obj/crash.o obj/dagified_graph.o obj/deconstructor.o obj/dinucleotide_machine.o obj/dozeu_interface.o obj/dozeu_pinning_overlay.o obj/entropy.o obj/extra_node_graph.o obj/feature_set.o obj/filter.o obj/flow_sort.o obj/funnel.o obj/gapless_extender.o obj/gbwt_helper.o obj/genome_state.o obj/genotypekit.o obj/genotyper.o obj/gfa.o obj/gff_reader.o obj/graph.o obj/graph_caller.o obj/graph_synchronizer.o obj/haplotype_extracter.o obj/haplotype_indexer.o obj/haplotypes.o obj/homogenizer.o obj/hts_alignment_emitter.o obj/identity_overlay.o obj/incremental_subgraph.o obj/index.o obj/index_manager.o obj/indexed_vg.o obj/integrated_snarl_finder.o obj/kmer.o obj/mapper.o obj/mcmc_caller.o obj/mcmc_genotyper.o obj/mem.o obj/memoizing_graph.o obj/memusage.o obj/min_distance.o obj/minimizer_mapper.o obj/msa_converter.o obj/multipath_alignment.o obj/multipath_alignment_emitter.o obj/multipath_alignment_graph.o obj/multipath_mapper.o obj/name_mapper.o obj/nested_traversal_finder.o obj/null_masking_graph.o obj/option.o obj/packer.o obj/path.o obj/path_component_index.o obj/path_index.o obj/path_subgraph.o obj/phase_unfolder.o obj/phased_genome.o obj/position.o obj/preflight.o obj/progressive.o obj/prune.o obj/qual_adj_xdrop_aligner.o obj/rare_variant_simplifier.o obj/readfilter.o obj/region.o obj/region_expander.o obj/reverse_graph.o obj/sampler.o obj/scanner.o obj/seed_clusterer.o obj/small_snarl_simplifier.o obj/snarl_caller.o obj/snarls.o obj/source_sink_overlay.o obj/splicing.o obj/split_strand_graph.o obj/srpe.o obj/ssw_aligner.o obj/statistics.o obj/stream_index.o obj/stream_sorter.o obj/subgraph.o obj/subgraph_overlay.o obj/surjector.o obj/transcriptome.o obj/translator.o obj/traversal_finder.o obj/traversal_support.o obj/tree_subgraph.o obj/utility.o obj/variant_adder.o obj/variant_recall.o obj/vcf_buffer.o obj/vectorizer.o obj/version.o obj/vg.o obj/vg_set.o obj/viz.o obj/watchdog.o obj/xdrop_aligner.o obj/algorithms/alignment_path_offsets.o obj/algorithms/append_graph.o obj/algorithms/apply_bulk_modifications.o obj/algorithms/approx_path_distance.o obj/algorithms/are_equivalent.o obj/algorithms/copy_graph.o obj/algorithms/count_walks.o obj/algorithms/coverage_depth.o obj/algorithms/dagify.o obj/algorithms/dfs.o obj/algorithms/dijkstra.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/eades_algorithm.o obj/algorithms/expand_context.o obj/algorithms/extend.o obj/algorithms/extract_connecting_graph.o obj/algorithms/extract_containing_graph.o obj/algorithms/extract_extending_graph.o obj/algorithms/find_shortest_paths.o obj/algorithms/find_tips.o obj/algorithms/gfa_to_handle.o obj/algorithms/id_sort.o obj/algorithms/is_acyclic.o obj/algorithms/is_single_stranded.o obj/algorithms/jump_along_path.o obj/algorithms/k_widest_paths.o obj/algorithms/kmer.o obj/algorithms/merge.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/next_pos_chars.o obj/algorithms/normalize.o obj/algorithms/path_string.o obj/algorithms/remove_high_degree.o obj/algorithms/reverse_complement.o obj/algorithms/shortest_cycle.o obj/algorithms/simplify_siblings.o obj/algorithms/sorted_id_ranges.o obj/algorithms/split_strands.o obj/algorithms/strongly_connected_components.o obj/algorithms/subgraph.o obj/algorithms/three_edge_connected_components.o obj/algorithms/to_gfa.o obj/algorithms/topological_sort.o obj/algorithms/unchop.o obj/algorithms/walk.o obj/algorithms/weakly_connected_components.o obj/io/load_proto_to_graph.o obj/io/register_libvg_io.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_gcsa.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_r_index.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_xg.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/vectorize_main.cpp:16: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Alignment]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Alignment; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Alignment; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Alignment; std::istream = std::basic_istream]’ src/subcommand/vectorize_main.cpp:304:36: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../aligner.hpp:12, from src/subcommand/../vg.hpp:20, from src/subcommand/vectorize_main.cpp:16: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/view_main.cpp:17: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Alignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Alignment]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Alignment; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Alignment; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Alignment; std::istream = std::basic_istream]’ src/subcommand/view_main.cpp:456:36: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../multipath_alignment.hpp:15, from src/subcommand/view_main.cpp:16: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/view_main.cpp:17: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Locus; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Locus]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Locus; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Locus; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Locus; std::istream = std::basic_istream]’ src/subcommand/view_main.cpp:463:36: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../multipath_alignment.hpp:15, from src/subcommand/view_main.cpp:16: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/view_main.cpp:17: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Graph; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Graph]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Graph; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Graph; std::istream = std::basic_istream]’ src/subcommand/view_main.cpp:497:44: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../multipath_alignment.hpp:15, from src/subcommand/view_main.cpp:16: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/view_main.cpp:17: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::MultipathAlignment; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::MultipathAlignment]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::MultipathAlignment; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::MultipathAlignment; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::MultipathAlignment; std::istream = std::basic_istream]’ src/subcommand/view_main.cpp:705:48: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../multipath_alignment.hpp:15, from src/subcommand/view_main.cpp:16: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/view_main.cpp:17: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Pileup; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Pileup]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Pileup; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Pileup; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Pileup; std::istream = std::basic_istream]’ src/subcommand/view_main.cpp:795:48: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../multipath_alignment.hpp:15, from src/subcommand/view_main.cpp:16: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/view_main.cpp:17: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Translation; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Translation]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Translation; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Translation; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Translation; std::istream = std::basic_istream]’ src/subcommand/view_main.cpp:819:44: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../multipath_alignment.hpp:15, from src/subcommand/view_main.cpp:16: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/view_main.cpp:17: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::Snarl; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::Snarl]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::Snarl; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Snarl; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::Snarl; std::istream = std::basic_istream]’ src/subcommand/view_main.cpp:869:44: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../multipath_alignment.hpp:15, from src/subcommand/view_main.cpp:16: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:17, from src/subcommand/../vg.hpp:29, from src/subcommand/view_main.cpp:17: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp: In instantiation of ‘static bool vg::io::ProtobufIterator::parse_from_string(T&, const string&) [with T = vg::SnarlTraversal; std::string = std::__cxx11::basic_string]’: /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:240:31: required from ‘void vg::io::ProtobufIterator::fill_value() [with T = vg::SnarlTraversal]’ /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:137:5: required from ‘vg::io::ProtobufIterator::ProtobufIterator(std::istream&) [with T = vg::SnarlTraversal; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:108:29: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::SnarlTraversal; std::istream = std::basic_istream]’ /<>/vg-1.27.1+ds/include/vg/io/stream.hpp:117:13: required from ‘void vg::io::for_each(std::istream&, const std::function&) [with T = vg::SnarlTraversal; std::istream = std::basic_istream]’ src/subcommand/view_main.cpp:882:44: required from here /<>/vg-1.27.1+ds/include/vg/io/protobuf_iterator.hpp:274:36: warning: ‘void google::protobuf::io::CodedInputStream::SetTotalBytesLimit(int, int)’ is deprecated: Please use the single parameter version of SetTotalBytesLimit(). The second parameter is ignored. [-Wdeprecated-declarations] 274 | coded_stream.SetTotalBytesLimit(MessageIterator::MAX_MESSAGE_SIZE * 2, MessageIterator::MAX_MESSAGE_SIZE * 2); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.27.1+ds/include/vg/vg.pb.h:23, from src/subcommand/../multipath_alignment.hpp:15, from src/subcommand/view_main.cpp:16: /usr/include/google/protobuf/io/coded_stream.h:397:8: note: declared here 397 | void SetTotalBytesLimit(int total_bytes_limit, int) { | ^~~~~~~~~~~~~~~~~~ . ./source_me.sh && g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -flto=auto -ffat-lto-objects -I/usr/include/fastahack -I/<>/vg-1.27.1+ds/include -I. -I/<>/vg-1.27.1+ds/src -I/<>/vg-1.27.1+ds/src/unittest -I/<>/vg-1.27.1+ds/src/subcommand -I/<>/vg-1.27.1+ds/include/dynamic -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -ffile-prefix-map=/<>/vg-1.27.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -flto=auto -ffat-lto-objects -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/<>/vg-1.27.1+ds/lib /<>/vg-1.27.1+ds/lib/libvgio.a -lz -lgssw -lssw -lprotobuf -lsublinearLS -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -ljansson -latomic -rdynamic -ldw -lelf -ldl -llzma -lrocksdb -lbz2 -ljemalloc lto1: fatal error: multiple prevailing defs for ‘_ZTIN4sdsl14rank_support_vILh1ELh1EEE’ compilation terminated. lto-wrapper: fatal error: g++ returned 1 exit status compilation terminated. /usr/bin/ld: error: lto-wrapper failed collect2: error: ld returned 1 exit status make[2]: *** [Makefile:336: test/build_graph] Error 1 make[2]: *** Waiting for unfinished jobs.... make[2]: Leaving directory '/<>/vg-1.27.1+ds' dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true" all test/build_graph bin/shuf returned exit code 2 make[1]: *** [debian/rules:34: override_dh_auto_build-arch] Error 25 make[1]: Leaving directory '/<>/vg-1.27.1+ds' make: *** [debian/rules:19: binary-arch] Error 2 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2021-01-26T05:57:55Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Type: any Build-Space: n/a Build-Time: 4988 Distribution: hirsute Fail-Stage: build Host Architecture: arm64 Install-Time: 126 Job: vg_1.27.1+ds-1build1.dsc Machine Architecture: arm64 Package: vg Package-Time: 5131 Source-Version: 1.27.1+ds-1build1 Space: n/a Status: attempted Version: 1.27.1+ds-1build1 -------------------------------------------------------------------------------- Finished at 2021-01-26T05:57:55Z Build needed 01:25:31, no disk space E: Build failure (dpkg-buildpackage died) RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=hirsute --arch=arm64 PACKAGEBUILD-20599634 Scanning for processes to kill in build PACKAGEBUILD-20599634