https://launchpad.net/ubuntu/+archive/test-rebuild-20200327-focal/+build/18984357 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-071 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:17:51 UTC 2020 aarch64 Buildd toolchain package versions: launchpad-buildd_189 python-lpbuildd_189 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 12 Apr 07:28:55 ntpdate[1904]: adjust time server 10.211.37.1 offset -0.001246 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-18984357 --image-type chroot /home/buildd/filecache-default/18e2e531223b07f48186d9b3ceb0e5fa09966f01 Creating target for build PACKAGEBUILD-18984357 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-18984357 Starting target for build PACKAGEBUILD-18984357 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-18984357 'deb http://ftpmaster.internal/ubuntu focal main universe' Overriding sources.list in build-PACKAGEBUILD-18984357 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-18984357 Updating target for build PACKAGEBUILD-18984357 Get:1 http://ftpmaster.internal/ubuntu focal InRelease [265 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main arm64 Packages [943 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main Translation-en [503 kB] Get:4 http://ftpmaster.internal/ubuntu focal/universe arm64 Packages [8440 kB] Get:5 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5131 kB] Fetched 15.3 MB in 6s (2377 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: systemd-timesyncd The following packages will be upgraded: apt binutils binutils-aarch64-linux-gnu binutils-common bsdutils fdisk gcc-10-base libapparmor1 libapt-pkg6.0 libatomic1 libbinutils libblkid1 libcc1-0 libctf-nobfd0 libctf0 libfdisk1 libgcc-s1 libgomp1 libitm1 liblsan0 libmount1 libsmartcols1 libstdc++6 libsystemd0 libtsan0 libubsan1 libudev1 libuuid1 login mount passwd pinentry-curses systemd systemd-sysv util-linux 35 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 12.7 MB of archives. After this operation, 160 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main arm64 bsdutils arm64 1:2.34-0.1ubuntu9 [60.3 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main arm64 login arm64 1:4.8.1-1ubuntu4 [219 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main arm64 libblkid1 arm64 2.34-0.1ubuntu9 [129 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main arm64 libuuid1 arm64 2.34-0.1ubuntu9 [19.5 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main arm64 libfdisk1 arm64 2.34-0.1ubuntu9 [160 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main arm64 libmount1 arm64 2.34-0.1ubuntu9 [140 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main arm64 libsmartcols1 arm64 2.34-0.1ubuntu9 [93.1 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main arm64 fdisk arm64 2.34-0.1ubuntu9 [114 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main arm64 util-linux arm64 2.34-0.1ubuntu9 [982 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main arm64 libatomic1 arm64 10-20200405-0ubuntu1 [9220 B] Get:11 http://ftpmaster.internal/ubuntu focal/main arm64 libubsan1 arm64 10-20200405-0ubuntu1 [126 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main arm64 libtsan0 arm64 10-20200405-0ubuntu1 [302 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main arm64 liblsan0 arm64 10-20200405-0ubuntu1 [130 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main arm64 libitm1 arm64 10-20200405-0ubuntu1 [23.8 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main arm64 libgomp1 arm64 10-20200405-0ubuntu1 [92.0 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main arm64 gcc-10-base arm64 10-20200405-0ubuntu1 [18.5 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main arm64 libgcc-s1 arm64 10-20200405-0ubuntu1 [34.8 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main arm64 libcc1-0 arm64 10-20200405-0ubuntu1 [37.1 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main arm64 libstdc++6 arm64 10-20200405-0ubuntu1 [463 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main arm64 systemd-sysv arm64 245.4-2ubuntu1 [10.3 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main arm64 systemd arm64 245.4-2ubuntu1 [3485 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main arm64 systemd-timesyncd arm64 245.4-2ubuntu1 [26.2 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main arm64 libapparmor1 arm64 2.13.3-7ubuntu4 [32.8 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main arm64 mount arm64 2.34-0.1ubuntu9 [112 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main arm64 libsystemd0 arm64 245.4-2ubuntu1 [249 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main arm64 libudev1 arm64 245.4-2ubuntu1 [71.8 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main arm64 libapt-pkg6.0 arm64 2.0.1ubuntu1 [760 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main arm64 apt arm64 2.0.1ubuntu1 [1238 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main arm64 passwd arm64 1:4.8.1-1ubuntu4 [771 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main arm64 libctf0 arm64 2.34-6ubuntu1 [43.0 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main arm64 binutils arm64 2.34-6ubuntu1 [3348 B] Get:32 http://ftpmaster.internal/ubuntu focal/main arm64 binutils-aarch64-linux-gnu arm64 2.34-6ubuntu1 [1989 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main arm64 libbinutils arm64 2.34-6ubuntu1 [473 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main arm64 binutils-common arm64 2.34-6ubuntu1 [207 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main arm64 libctf-nobfd0 arm64 2.34-6ubuntu1 [43.7 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main arm64 pinentry-curses arm64 1.1.0-3build1 [34.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 12.7 MB in 1s (10.2 MB/s) (Reading database ... 12807 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.34-0.1ubuntu9_arm64.deb ... Unpacking bsdutils (1:2.34-0.1ubuntu9) over (1:2.34-0.1ubuntu8) ... Setting up bsdutils (1:2.34-0.1ubuntu9) ... (Reading database ... 12807 files and directories currently installed.) Preparing to unpack .../login_1%3a4.8.1-1ubuntu4_arm64.deb ... Unpacking login (1:4.8.1-1ubuntu4) over (1:4.8.1-1ubuntu3) ... Setting up login (1:4.8.1-1ubuntu4) ... (Reading database ... 12807 files and directories currently installed.) Preparing to unpack .../libblkid1_2.34-0.1ubuntu9_arm64.deb ... Unpacking libblkid1:arm64 (2.34-0.1ubuntu9) over (2.34-0.1ubuntu8) ... Setting up libblkid1:arm64 (2.34-0.1ubuntu9) ... (Reading database ... 12807 files and directories currently installed.) Preparing to unpack .../libuuid1_2.34-0.1ubuntu9_arm64.deb ... Unpacking libuuid1:arm64 (2.34-0.1ubuntu9) over (2.34-0.1ubuntu8) ... Setting up libuuid1:arm64 (2.34-0.1ubuntu9) ... (Reading database ... 12807 files and directories currently installed.) Preparing to unpack .../libfdisk1_2.34-0.1ubuntu9_arm64.deb ... Unpacking libfdisk1:arm64 (2.34-0.1ubuntu9) over (2.34-0.1ubuntu8) ... Preparing to unpack .../libmount1_2.34-0.1ubuntu9_arm64.deb ... Unpacking libmount1:arm64 (2.34-0.1ubuntu9) over (2.34-0.1ubuntu8) ... Setting up libmount1:arm64 (2.34-0.1ubuntu9) ... (Reading database ... 12807 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.34-0.1ubuntu9_arm64.deb ... Unpacking libsmartcols1:arm64 (2.34-0.1ubuntu9) over (2.34-0.1ubuntu8) ... Setting up libsmartcols1:arm64 (2.34-0.1ubuntu9) ... (Reading database ... 12807 files and directories currently installed.) Preparing to unpack .../fdisk_2.34-0.1ubuntu9_arm64.deb ... Unpacking fdisk (2.34-0.1ubuntu9) over (2.34-0.1ubuntu8) ... Preparing to unpack .../util-linux_2.34-0.1ubuntu9_arm64.deb ... Unpacking util-linux (2.34-0.1ubuntu9) over (2.34-0.1ubuntu8) ... Setting up util-linux (2.34-0.1ubuntu9) ... (Reading database ... 12807 files and directories currently installed.) Preparing to unpack .../0-libatomic1_10-20200405-0ubuntu1_arm64.deb ... Unpacking libatomic1:arm64 (10-20200405-0ubuntu1) over (10-20200324-1ubuntu1) ... Preparing to unpack .../1-libubsan1_10-20200405-0ubuntu1_arm64.deb ... Unpacking libubsan1:arm64 (10-20200405-0ubuntu1) over (10-20200324-1ubuntu1) ... Preparing to unpack .../2-libtsan0_10-20200405-0ubuntu1_arm64.deb ... Unpacking libtsan0:arm64 (10-20200405-0ubuntu1) over (10-20200324-1ubuntu1) ... Preparing to unpack .../3-liblsan0_10-20200405-0ubuntu1_arm64.deb ... Unpacking liblsan0:arm64 (10-20200405-0ubuntu1) over (10-20200324-1ubuntu1) ... Preparing to unpack .../4-libitm1_10-20200405-0ubuntu1_arm64.deb ... Unpacking libitm1:arm64 (10-20200405-0ubuntu1) over (10-20200324-1ubuntu1) ... Preparing to unpack .../5-libgomp1_10-20200405-0ubuntu1_arm64.deb ... Unpacking libgomp1:arm64 (10-20200405-0ubuntu1) over (10-20200324-1ubuntu1) ... Preparing to unpack .../6-gcc-10-base_10-20200405-0ubuntu1_arm64.deb ... Unpacking gcc-10-base:arm64 (10-20200405-0ubuntu1) over (10-20200324-1ubuntu1) ... Setting up gcc-10-base:arm64 (10-20200405-0ubuntu1) ... (Reading database ... 12807 files and directories currently installed.) Preparing to unpack .../libgcc-s1_10-20200405-0ubuntu1_arm64.deb ... Unpacking libgcc-s1:arm64 (10-20200405-0ubuntu1) over (10-20200324-1ubuntu1) ... Setting up libgcc-s1:arm64 (10-20200405-0ubuntu1) ... (Reading database ... 12807 files and directories currently installed.) Preparing to unpack .../libcc1-0_10-20200405-0ubuntu1_arm64.deb ... Unpacking libcc1-0:arm64 (10-20200405-0ubuntu1) over (10-20200324-1ubuntu1) ... Preparing to unpack .../libstdc++6_10-20200405-0ubuntu1_arm64.deb ... Unpacking libstdc++6:arm64 (10-20200405-0ubuntu1) over (10-20200324-1ubuntu1) ... Setting up libstdc++6:arm64 (10-20200405-0ubuntu1) ... (Reading database ... 12807 files and directories currently installed.) Preparing to unpack .../0-systemd-sysv_245.4-2ubuntu1_arm64.deb ... Unpacking systemd-sysv (245.4-2ubuntu1) over (245.2-1ubuntu2) ... Preparing to unpack .../1-systemd_245.4-2ubuntu1_arm64.deb ... Unpacking systemd (245.4-2ubuntu1) over (245.2-1ubuntu2) ... dpkg: warning: unable to delete old directory '/etc/dhcp/dhclient-exit-hooks.d': Directory not empty Selecting previously unselected package systemd-timesyncd. Preparing to unpack .../2-systemd-timesyncd_245.4-2ubuntu1_arm64.deb ... Unpacking systemd-timesyncd (245.4-2ubuntu1) ... Preparing to unpack .../3-libapparmor1_2.13.3-7ubuntu4_arm64.deb ... Unpacking libapparmor1:arm64 (2.13.3-7ubuntu4) over (2.13.3-7ubuntu3) ... Preparing to unpack .../4-mount_2.34-0.1ubuntu9_arm64.deb ... Unpacking mount (2.34-0.1ubuntu9) over (2.34-0.1ubuntu8) ... Preparing to unpack .../5-libsystemd0_245.4-2ubuntu1_arm64.deb ... Unpacking libsystemd0:arm64 (245.4-2ubuntu1) over (245.2-1ubuntu2) ... Setting up libsystemd0:arm64 (245.4-2ubuntu1) ... (Reading database ... 12808 files and directories currently installed.) Preparing to unpack .../libudev1_245.4-2ubuntu1_arm64.deb ... Unpacking libudev1:arm64 (245.4-2ubuntu1) over (245.2-1ubuntu2) ... Setting up libudev1:arm64 (245.4-2ubuntu1) ... (Reading database ... 12808 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.0.1ubuntu1_arm64.deb ... Unpacking libapt-pkg6.0:arm64 (2.0.1ubuntu1) over (2.0.1) ... Setting up libapt-pkg6.0:arm64 (2.0.1ubuntu1) ... (Reading database ... 12808 files and directories currently installed.) Preparing to unpack .../apt_2.0.1ubuntu1_arm64.deb ... Unpacking apt (2.0.1ubuntu1) over (2.0.1) ... Setting up apt (2.0.1ubuntu1) ... (Reading database ... 12808 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.8.1-1ubuntu4_arm64.deb ... Unpacking passwd (1:4.8.1-1ubuntu4) over (1:4.8.1-1ubuntu3) ... Setting up passwd (1:4.8.1-1ubuntu4) ... (Reading database ... 12808 files and directories currently installed.) Preparing to unpack .../0-libctf0_2.34-6ubuntu1_arm64.deb ... Unpacking libctf0:arm64 (2.34-6ubuntu1) over (2.34-5ubuntu1) ... Preparing to unpack .../1-binutils_2.34-6ubuntu1_arm64.deb ... Unpacking binutils (2.34-6ubuntu1) over (2.34-5ubuntu1) ... Preparing to unpack .../2-binutils-aarch64-linux-gnu_2.34-6ubuntu1_arm64.deb ... Unpacking binutils-aarch64-linux-gnu (2.34-6ubuntu1) over (2.34-5ubuntu1) ... Preparing to unpack .../3-libbinutils_2.34-6ubuntu1_arm64.deb ... Unpacking libbinutils:arm64 (2.34-6ubuntu1) over (2.34-5ubuntu1) ... Preparing to unpack .../4-binutils-common_2.34-6ubuntu1_arm64.deb ... Unpacking binutils-common:arm64 (2.34-6ubuntu1) over (2.34-5ubuntu1) ... Preparing to unpack .../5-libctf-nobfd0_2.34-6ubuntu1_arm64.deb ... Unpacking libctf-nobfd0:arm64 (2.34-6ubuntu1) over (2.34-5ubuntu1) ... Preparing to unpack .../6-pinentry-curses_1.1.0-3build1_arm64.deb ... Unpacking pinentry-curses (1.1.0-3build1) over (1.1.0-3) ... Setting up pinentry-curses (1.1.0-3build1) ... Setting up libapparmor1:arm64 (2.13.3-7ubuntu4) ... Setting up binutils-common:arm64 (2.34-6ubuntu1) ... Setting up libctf-nobfd0:arm64 (2.34-6ubuntu1) ... Setting up libgomp1:arm64 (10-20200405-0ubuntu1) ... Setting up libatomic1:arm64 (10-20200405-0ubuntu1) ... Setting up libfdisk1:arm64 (2.34-0.1ubuntu9) ... Setting up libubsan1:arm64 (10-20200405-0ubuntu1) ... Setting up mount (2.34-0.1ubuntu9) ... Setting up libbinutils:arm64 (2.34-6ubuntu1) ... Setting up libcc1-0:arm64 (10-20200405-0ubuntu1) ... Setting up liblsan0:arm64 (10-20200405-0ubuntu1) ... Setting up libitm1:arm64 (10-20200405-0ubuntu1) ... Setting up libtsan0:arm64 (10-20200405-0ubuntu1) ... Setting up libctf0:arm64 (2.34-6ubuntu1) ... Setting up binutils-aarch64-linux-gnu (2.34-6ubuntu1) ... Setting up binutils (2.34-6ubuntu1) ... Setting up fdisk (2.34-0.1ubuntu9) ... Setting up systemd (245.4-2ubuntu1) ... Created symlink /etc/systemd/system/systemd-remount-fs.service.wants/systemd-pstore.service -> /lib/systemd/system/systemd-pstore.service. Initializing machine ID from KVM UUID. Removing obsolete conffile /etc/dhcp/dhclient-exit-hooks.d/timesyncd ... Removing obsolete conffile /etc/systemd/timesyncd.conf ... Setting up systemd-timesyncd (245.4-2ubuntu1) ... Created symlink /etc/systemd/system/sysinit.target.wants/systemd-timesyncd.service -> /lib/systemd/system/systemd-timesyncd.service. Setting up systemd-sysv (245.4-2ubuntu1) ... Processing triggers for libc-bin (2.31-0ubuntu7) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-18984357 arm64 focal -c chroot:build-PACKAGEBUILD-18984357 --arch=arm64 --dist=focal --nolog vg_1.22.0+ds-1.dsc Initiating build PACKAGEBUILD-18984357 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:17:51 UTC 2020 aarch64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-071.buildd +==============================================================================+ | vg 1.22.0+ds-1 (arm64) 12 Apr 2020 07:29 | +==============================================================================+ Package: vg Version: 1.22.0+ds-1 Source Version: 1.22.0+ds-1 Distribution: focal Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 I: NOTICE: Log filtering will replace 'build/vg-gBC0Ug/vg-1.22.0+ds' with '<>' I: NOTICE: Log filtering will replace 'build/vg-gBC0Ug' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-18984357/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- vg_1.22.0+ds-1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-j7JmlL/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-j7JmlL/apt_archive ./ InRelease Get:2 copy:/<>/resolver-j7JmlL/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-j7JmlL/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-j7JmlL/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-j7JmlL/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (40.8 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 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-j7JmlL/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 (65.0 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12808 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) ... Merged Build-Depends: debhelper-compat (= 12), 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 Filtered Build-Depends: debhelper-compat (= 12), 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 dpkg-deb: building package 'sbuild-build-depends-vg-dummy' in '/<>/resolver-Ce5cNf/apt_archive/sbuild-build-depends-vg-dummy.deb'. Ign:1 copy:/<>/resolver-Ce5cNf/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Ce5cNf/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-Ce5cNf/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Ce5cNf/apt_archive ./ Sources [559 B] Get:5 copy:/<>/resolver-Ce5cNf/apt_archive ./ Packages [864 B] Fetched 3542 B in 0s (48.9 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 additional packages will be installed: autoconf automake autopoint autotools-dev bc bison bsdmainutils bwa 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-options1.71-dev libboost-program-options1.71.0 libboost1.71-dev libbrotli1 libbsd0 libbz2-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev libcroco3 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 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 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libice-dev libice6 libicu-dev libicu66 libjansson-dev libjansson4 libjbig0 libjemalloc-dev libjemalloc2 libjpeg-turbo8 libjpeg8 libjq1 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common liblocale-gettext-perl libltdl7 liblz4-dev liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmhash2 libmount-dev libmpdec2 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-lite17 libprotobuf17 libprotoc-dev libprotoc17 libpsl5 libpthread-stubs0-dev libpython3-stdlib libpython3.8-minimal libpython3.8-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 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 man-db mime-support opensp pkg-config po-debconf protobuf-compiler pv python3 python3-distutils python3-lib2to3 python3-lxml python3-minimal python3-pygments python3.8 python3.8-minimal r-base-core r-cran-assertthat r-cran-cli r-cran-colorspace r-cran-crayon r-cran-digest r-cran-ellipsis r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-labeling r-cran-lattice r-cran-lazyeval 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-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr 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 wamerican | wordlist whois vacation 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 libboost1.71-doc libboost-atomic1.71-dev libboost-chrono1.71-dev libboost-container1.71-dev libboost-context1.71-dev libboost-contract1.71-dev libboost-coroutine1.71-dev libboost-date-time1.71-dev libboost-exception1.71-dev libboost-fiber1.71-dev libboost-filesystem1.71-dev libboost-graph1.71-dev libboost-graph-parallel1.71-dev libboost-iostreams1.71-dev libboost-locale1.71-dev libboost-log1.71-dev libboost-math1.71-dev libboost-mpi1.71-dev libboost-mpi-python1.71-dev libboost-numpy1.71-dev libboost-python1.71-dev libboost-random1.71-dev libboost-regex1.71-dev libboost-serialization1.71-dev libboost-stacktrace1.71-dev libboost-system1.71-dev libboost-test1.71-dev libboost-thread1.71-dev libboost-timer1.71-dev libboost-type-erasure1.71-dev libboost-wave1.71-dev libboost1.71-tools-dev libmpfrc++-dev libntl-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 krb5-doc krb5-user 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 python3-doc python3-tk python3-venv python3-lxml-dbg python-lxml-doc python-pygments-doc ttf-bitstream-vera python3.8-venv python3.8-doc binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-callr r-cran-covr r-cran-htmlwidgets r-cran-knitr r-cran-rmarkdown r-cran-rstudioapi 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-hmisc r-cran-maps r-cran-maptools r-cran-multcomp r-cran-quantreg r-cran-rpart r-cran-sf r-cran-svglite r-cran-dbi r-cran-rsqlite r-cran-r.utils r-cran-forcats r-cran-getopt r-cran-testthat r-cran-doparallel r-cran-foreach r-cran-iterators r-cran-inline r-cran-dichromat r-cran-htmltools r-cran-xml2 r-cran-zeallot libgdal-dev sgml-base-doc perlsgml w3-recs Recommended packages: libfl-dev curl | wget | lynx bzip2-doc libarchive-cpio-perl shared-mime-info xdg-user-dirs krb5-locales libpng-tools publicsuffix redland-utils libsasl2-modules libltdl-dev libmail-sendmail-perl python3-bs4 python3-html5lib python3-pkg-resources r-recommended r-base-dev r-doc-html r-cran-testthat r-cran-mockery r-cran-sp r-cran-mapproj r-cran-hexbin r-cran-vdiffr r-cran-lubridate r-cran-domc r-cran-abind r-cran-rmarkdown r-cran-bit64 r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-data.table r-cran-rsqlite r-cran-knitr r-cran-dplyr r-cran-mockr r-cran-generics r-cran-dbi cwltool 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 bsdmainutils bwa 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-options1.71-dev libboost-program-options1.71.0 libboost1.71-dev libbrotli1 libbsd0 libbz2-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev libcroco3 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 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 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libice-dev libice6 libicu-dev libicu66 libjansson-dev libjansson4 libjbig0 libjemalloc-dev libjemalloc2 libjpeg-turbo8 libjpeg8 libjq1 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common liblocale-gettext-perl libltdl7 liblz4-dev liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmhash2 libmount-dev libmpdec2 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-lite17 libprotobuf17 libprotoc-dev libprotoc17 libpsl5 libpthread-stubs0-dev libpython3-stdlib libpython3.8-minimal libpython3.8-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 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 man-db mime-support opensp pkg-config po-debconf protobuf-compiler pv python3 python3-distutils python3-lib2to3 python3-lxml python3-minimal python3-pygments python3.8 python3.8-minimal r-base-core r-cran-assertthat r-cran-cli r-cran-colorspace r-cran-crayon r-cran-digest r-cran-ellipsis r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-labeling r-cran-lattice r-cran-lazyeval 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-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr 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, 312 newly installed, 0 to remove and 0 not upgraded. Need to get 137 MB of archives. After this operation, 601 MB of additional disk space will be used. Get:1 copy:/<>/resolver-Ce5cNf/apt_archive ./ sbuild-build-depends-vg-dummy 0.invalid.0 [1192 B] Get:2 http://ftpmaster.internal/ubuntu focal/main arm64 liblocale-gettext-perl arm64 1.07-4 [16.7 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main arm64 libpython3.8-minimal arm64 3.8.2-1ubuntu1 [702 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main arm64 libexpat1 arm64 2.2.9-1build1 [61.3 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main arm64 python3.8-minimal arm64 3.8.2-1ubuntu1 [1828 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main arm64 python3-minimal arm64 3.8.2-0ubuntu2 [23.6 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main arm64 mime-support all 3.64ubuntu1 [30.6 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main arm64 libmpdec2 arm64 2.4.2-3 [79.6 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main arm64 libpython3.8-stdlib arm64 3.8.2-1ubuntu1 [1641 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main arm64 python3.8 arm64 3.8.2-1ubuntu1 [364 kB] 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focal/main arm64 flex arm64 2.6.4-6.2 [307 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main arm64 gawk arm64 1:5.0.1+dfsg-1 [382 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main arm64 sgml-base all 1.29.1 [12.4 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main arm64 libmagic-mgc arm64 1:5.38-4 [218 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main arm64 libmagic1 arm64 1:5.38-4 [71.7 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main arm64 file arm64 1:5.38-4 [23.3 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main arm64 libelf1 arm64 0.176-1.1build1 [44.2 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main arm64 libfribidi0 arm64 1.0.8-2 [23.7 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main arm64 libglib2.0-0 arm64 2.64.1-1 [1197 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main arm64 libglib2.0-data all 2.64.1-1 [6540 B] Get:31 http://ftpmaster.internal/ubuntu focal/main arm64 libicu66 arm64 66.1-2ubuntu2 [8357 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main arm64 libxml2 arm64 2.9.10+dfsg-4build1 [569 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main arm64 ucf all 3.0038+nmu1 [51.6 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main arm64 gettext-base arm64 0.19.8.1-10build1 [48.2 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main arm64 libkrb5support0 arm64 1.17-6ubuntu4 [30.4 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main arm64 libk5crypto3 arm64 1.17-6ubuntu4 [80.5 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main arm64 libkeyutils1 arm64 1.6-6ubuntu1 [10.1 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main arm64 libkrb5-3 arm64 1.17-6ubuntu4 [312 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main arm64 libgssapi-krb5-2 arm64 1.17-6ubuntu4 [113 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main arm64 libpsl5 arm64 0.21.0-1ubuntu1 [51.3 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main arm64 libxau6 arm64 1:1.0.9-0ubuntu1 [7356 B] Get:42 http://ftpmaster.internal/ubuntu focal/main arm64 libxdmcp6 arm64 1:1.1.3-0ubuntu1 [10.3 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main arm64 libxcb1 arm64 1.14-2 [43.0 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main arm64 libx11-data all 2:1.6.9-2ubuntu1 [113 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main arm64 libx11-6 arm64 2:1.6.9-2ubuntu1 [553 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main arm64 libxext6 arm64 2:1.3.4-0ubuntu1 [27.7 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main arm64 autoconf all 2.69-11.1 [321 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main arm64 autotools-dev all 20180224.1 [39.6 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main arm64 automake all 1:1.16.1-4ubuntu6 [522 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main arm64 autopoint all 0.19.8.1-10build1 [412 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main arm64 bc arm64 1.07.1-2build1 [84.1 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main arm64 bison arm64 2:3.5.1+dfsg-1 [640 kB] Get:53 http://ftpmaster.internal/ubuntu focal/universe arm64 bwa arm64 0.7.17-4 [190 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main arm64 cmake-data all 3.16.3-1ubuntu1 [1612 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main arm64 libarchive13 arm64 3.4.0-2ubuntu1 [304 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main arm64 libbrotli1 arm64 1.0.7-6build1 [261 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main arm64 libroken18-heimdal arm64 7.7.0+dfsg-1ubuntu1 [39.4 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main arm64 libasn1-8-heimdal arm64 7.7.0+dfsg-1ubuntu1 [150 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main arm64 libheimbase1-heimdal arm64 7.7.0+dfsg-1ubuntu1 [27.9 kB] Get:60 http://ftpmaster.internal/ubuntu focal/main arm64 libhcrypto4-heimdal arm64 7.7.0+dfsg-1ubuntu1 [86.4 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main arm64 libwind0-heimdal arm64 7.7.0+dfsg-1ubuntu1 [47.3 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main arm64 libhx509-5-heimdal arm64 7.7.0+dfsg-1ubuntu1 [98.7 kB] Get:63 http://ftpmaster.internal/ubuntu focal/main arm64 libkrb5-26-heimdal arm64 7.7.0+dfsg-1ubuntu1 [191 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main arm64 libheimntlm0-heimdal arm64 7.7.0+dfsg-1ubuntu1 [14.7 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main arm64 libgssapi3-heimdal arm64 7.7.0+dfsg-1ubuntu1 [88.3 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2 [15.1 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2 [48.4 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main arm64 libldap-common all 2.4.49+dfsg-2ubuntu1 [17.3 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main arm64 libldap-2.4-2 arm64 2.4.49+dfsg-2ubuntu1 [146 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main arm64 libnghttp2-14 arm64 1.40.0-1build1 [74.7 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2build1 [53.3 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main arm64 libssh-4 arm64 0.9.3-2ubuntu2 [159 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main arm64 libcurl4 arm64 7.68.0-1ubuntu1 [213 kB] Get:74 http://ftpmaster.internal/ubuntu focal/main arm64 libjsoncpp1 arm64 1.7.4-3.1ubuntu2 [69.8 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main arm64 librhash0 arm64 1.3.9-1 [111 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main arm64 libuv1 arm64 1.34.2-1ubuntu1 [75.0 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main arm64 cmake arm64 3.16.3-1ubuntu1 [3115 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main arm64 libtool all 2.4.6-14 [161 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main arm64 dh-autoreconf all 19 [16.1 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main arm64 libdebhelper-perl all 12.10ubuntu1 [62.1 kB] Get:81 http://ftpmaster.internal/ubuntu focal/main arm64 libarchive-zip-perl all 1.67-2 [90.5 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main arm64 libsub-override-perl all 0.09-2 [9532 B] Get:83 http://ftpmaster.internal/ubuntu focal/main arm64 libfile-stripnondeterminism-perl all 1.6.3-2 [16.0 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main arm64 dh-strip-nondeterminism all 1.6.3-2 [5228 B] Get:85 http://ftpmaster.internal/ubuntu focal/main arm64 dwz arm64 0.13-5 [134 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main arm64 libcroco3 arm64 0.6.13-1 [77.1 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main arm64 gettext arm64 0.19.8.1-10build1 [850 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main arm64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main arm64 po-debconf all 1.0.21 [233 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main arm64 debhelper all 12.10ubuntu1 [877 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main arm64 xml-core all 0.18+nmu1 [21.6 kB] Get:92 http://ftpmaster.internal/ubuntu focal/universe arm64 sgml-data all 2.0.11 [171 kB] Get:93 http://ftpmaster.internal/ubuntu focal/universe arm64 docbook all 4.5-6 [122 kB] Get:94 http://ftpmaster.internal/ubuntu focal/universe arm64 libosp5 arm64 1.5.2-13ubuntu3 [604 kB] Get:95 http://ftpmaster.internal/ubuntu focal/universe arm64 opensp arm64 1.5.2-13ubuntu3 [138 kB] Get:96 http://ftpmaster.internal/ubuntu focal/universe arm64 docbook-to-man arm64 1:2.0.0-42 [68.6 kB] Get:97 http://ftpmaster.internal/ubuntu focal/universe arm64 docbook-xml all 4.5-9 [71.2 kB] Get:98 http://ftpmaster.internal/ubuntu focal/universe arm64 docbook-xsl all 1.79.1+dfsg-2 [1075 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main arm64 libdw1 arm64 0.176-1.1build1 [212 kB] Get:100 http://ftpmaster.internal/ubuntu focal/main arm64 libasm1 arm64 0.176-1.1build1 [13.5 kB] Get:101 http://ftpmaster.internal/ubuntu focal/main arm64 elfutils arm64 0.176-1.1build1 [248 kB] Get:102 http://ftpmaster.internal/ubuntu focal/universe arm64 libdisorder0 arm64 0.0.2+git20130809.8062ee1-1 [4056 B] Get:103 http://ftpmaster.internal/ubuntu focal/universe arm64 libfastahack0 arm64 1.0.0+dfsg-5build1 [22.1 kB] Get:104 http://ftpmaster.internal/ubuntu focal/universe arm64 fastahack arm64 1.0.0+dfsg-5build1 [10.5 kB] Get:105 http://ftpmaster.internal/ubuntu focal/main arm64 libfreetype6 arm64 2.10.1-2 [316 kB] Get:106 http://ftpmaster.internal/ubuntu focal/main arm64 fonts-dejavu-core all 2.37-1 [1041 kB] Get:107 http://ftpmaster.internal/ubuntu focal/main arm64 fontconfig-config all 2.13.1-2ubuntu3 [28.8 kB] Get:108 http://ftpmaster.internal/ubuntu focal/main arm64 libfontconfig1 arm64 2.13.1-2ubuntu3 [111 kB] Get:109 http://ftpmaster.internal/ubuntu focal/main arm64 fontconfig arm64 2.13.1-2ubuntu3 [170 kB] Get:110 http://ftpmaster.internal/ubuntu focal/main arm64 pkg-config arm64 0.29.1-0ubuntu4 [43.8 kB] Get:111 http://ftpmaster.internal/ubuntu focal/main arm64 libxslt1.1 arm64 1.1.34-4 [141 kB] Get:112 http://ftpmaster.internal/ubuntu focal/main arm64 python3-lxml arm64 4.5.0-1 [1163 kB] Get:113 http://ftpmaster.internal/ubuntu focal/main arm64 python3-pygments all 2.3.1+dfsg-1ubuntu2 [579 kB] Get:114 http://ftpmaster.internal/ubuntu focal/main arm64 xsltproc arm64 1.1.34-4 [13.9 kB] Get:115 http://ftpmaster.internal/ubuntu focal/universe arm64 gtk-doc-tools all 1.32-4 [321 kB] Get:116 http://ftpmaster.internal/ubuntu focal/universe arm64 help2man arm64 1.47.13 [173 kB] Get:117 http://ftpmaster.internal/ubuntu focal/main arm64 icu-devtools arm64 66.1-2ubuntu2 [175 kB] Get:118 http://ftpmaster.internal/ubuntu focal/universe arm64 libonig5 arm64 6.9.4-1 [134 kB] Get:119 http://ftpmaster.internal/ubuntu focal/universe arm64 libjq1 arm64 1.6-1 [107 kB] Get:120 http://ftpmaster.internal/ubuntu focal/universe arm64 jq arm64 1.6-1 [49.6 kB] Get:121 http://ftpmaster.internal/ubuntu focal/universe arm64 libbackward-cpp-dev all 1.4-5 [27.7 kB] Get:122 http://ftpmaster.internal/ubuntu focal/main arm64 libblas3 arm64 3.9.0-1build1 [89.1 kB] Get:123 http://ftpmaster.internal/ubuntu focal/main arm64 libboost1.71-dev arm64 1.71.0-6ubuntu6 [9068 kB] Get:124 http://ftpmaster.internal/ubuntu focal/main arm64 libboost-program-options1.71.0 arm64 1.71.0-6ubuntu6 [326 kB] Get:125 http://ftpmaster.internal/ubuntu focal/main arm64 libboost-program-options1.71-dev arm64 1.71.0-6ubuntu6 [372 kB] Get:126 http://ftpmaster.internal/ubuntu focal/main arm64 libboost-program-options-dev arm64 1.71.0.0ubuntu1 [3408 B] Get:127 http://ftpmaster.internal/ubuntu focal/main arm64 libbz2-dev arm64 1.0.8-2 [31.6 kB] Get:128 http://ftpmaster.internal/ubuntu focal/main arm64 libpixman-1-0 arm64 0.38.4-0ubuntu1 [130 kB] Get:129 http://ftpmaster.internal/ubuntu focal/main arm64 libxcb-render0 arm64 1.14-2 [14.7 kB] Get:130 http://ftpmaster.internal/ubuntu focal/main arm64 libxcb-shm0 arm64 1.14-2 [5560 B] Get:131 http://ftpmaster.internal/ubuntu focal/main arm64 libxrender1 arm64 1:0.9.10-1 [16.1 kB] Get:132 http://ftpmaster.internal/ubuntu focal/main arm64 libcairo2 arm64 1.16.0-4ubuntu1 [538 kB] Get:133 http://ftpmaster.internal/ubuntu focal/main arm64 libcairo-gobject2 arm64 1.16.0-4ubuntu1 [17.0 kB] Get:134 http://ftpmaster.internal/ubuntu focal/main arm64 liblzo2-2 arm64 2.10-2 [45.5 kB] Get:135 http://ftpmaster.internal/ubuntu focal/main arm64 libcairo-script-interpreter2 arm64 1.16.0-4ubuntu1 [50.7 kB] Get:136 http://ftpmaster.internal/ubuntu focal/main arm64 libexpat1-dev arm64 2.2.9-1build1 [103 kB] Get:137 http://ftpmaster.internal/ubuntu focal/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2ubuntu1 [154 kB] Get:138 http://ftpmaster.internal/ubuntu focal/main arm64 libpng-dev arm64 1.6.37-2 [172 kB] Get:139 http://ftpmaster.internal/ubuntu focal/main arm64 libfreetype-dev arm64 2.10.1-2 [473 kB] Get:140 http://ftpmaster.internal/ubuntu focal/main arm64 libfreetype6-dev arm64 2.10.1-2 [9792 B] Get:141 http://ftpmaster.internal/ubuntu focal/main arm64 uuid-dev arm64 2.34-0.1ubuntu9 [33.9 kB] Get:142 http://ftpmaster.internal/ubuntu focal/main arm64 libfontconfig1-dev arm64 2.13.1-2ubuntu3 [728 kB] Get:143 http://ftpmaster.internal/ubuntu focal/main arm64 xorg-sgml-doctools all 1:1.11-1 [12.9 kB] Get:144 http://ftpmaster.internal/ubuntu focal/main arm64 x11proto-dev all 2019.2-1ubuntu1 [594 kB] Get:145 http://ftpmaster.internal/ubuntu focal/main arm64 x11proto-core-dev all 2019.2-1ubuntu1 [2620 B] Get:146 http://ftpmaster.internal/ubuntu focal/main arm64 libxau-dev arm64 1:1.0.9-0ubuntu1 [9728 B] Get:147 http://ftpmaster.internal/ubuntu focal/main arm64 libxdmcp-dev arm64 1:1.1.3-0ubuntu1 [25.1 kB] Get:148 http://ftpmaster.internal/ubuntu focal/main arm64 xtrans-dev all 1.4.0-1 [68.9 kB] Get:149 http://ftpmaster.internal/ubuntu focal/main arm64 libpthread-stubs0-dev arm64 0.4-1 [5376 B] Get:150 http://ftpmaster.internal/ubuntu focal/main arm64 libxcb1-dev arm64 1.14-2 [80.9 kB] Get:151 http://ftpmaster.internal/ubuntu focal/main arm64 libx11-dev arm64 2:1.6.9-2ubuntu1 [635 kB] Get:152 http://ftpmaster.internal/ubuntu focal/main arm64 libxrender-dev arm64 1:0.9.10-1 [22.9 kB] Get:153 http://ftpmaster.internal/ubuntu focal/main arm64 x11proto-xext-dev all 2019.2-1ubuntu1 [2616 B] Get:154 http://ftpmaster.internal/ubuntu focal/main arm64 libxext-dev arm64 2:1.3.4-0ubuntu1 [82.1 kB] Get:155 http://ftpmaster.internal/ubuntu focal/main arm64 x11-common all 1:7.7+19ubuntu14 [22.3 kB] Get:156 http://ftpmaster.internal/ubuntu focal/main arm64 libice6 arm64 2:1.0.10-0ubuntu1 [37.7 kB] Get:157 http://ftpmaster.internal/ubuntu focal/main arm64 libsm6 arm64 2:1.2.3-1 [15.1 kB] Get:158 http://ftpmaster.internal/ubuntu focal/main arm64 libice-dev arm64 2:1.0.10-0ubuntu1 [46.2 kB] Get:159 http://ftpmaster.internal/ubuntu focal/main arm64 libsm-dev arm64 2:1.2.3-1 [16.4 kB] Get:160 http://ftpmaster.internal/ubuntu focal/main arm64 libpixman-1-dev arm64 0.38.4-0ubuntu1 [147 kB] Get:161 http://ftpmaster.internal/ubuntu focal/main arm64 libxcb-render0-dev arm64 1.14-2 [18.8 kB] Get:162 http://ftpmaster.internal/ubuntu focal/main arm64 libxcb-shm0-dev arm64 1.14-2 [6892 B] Get:163 http://ftpmaster.internal/ubuntu focal/main arm64 libffi-dev arm64 3.3-4 [53.5 kB] Get:164 http://ftpmaster.internal/ubuntu focal/main arm64 libglib2.0-bin arm64 2.64.1-1 [69.2 kB] Get:165 http://ftpmaster.internal/ubuntu focal/main arm64 python3-lib2to3 all 3.8.2-1ubuntu1 [74.1 kB] Get:166 http://ftpmaster.internal/ubuntu focal/main arm64 python3-distutils all 3.8.2-1ubuntu1 [140 kB] Get:167 http://ftpmaster.internal/ubuntu focal/main arm64 libglib2.0-dev-bin arm64 2.64.1-1 [108 kB] Get:168 http://ftpmaster.internal/ubuntu focal/main arm64 libblkid-dev arm64 2.34-0.1ubuntu9 [169 kB] Get:169 http://ftpmaster.internal/ubuntu focal/main arm64 libmount-dev arm64 2.34-0.1ubuntu9 [181 kB] Get:170 http://ftpmaster.internal/ubuntu focal/main arm64 libpcre16-3 arm64 2:8.39-12build1 [126 kB] Get:171 http://ftpmaster.internal/ubuntu focal/main arm64 libpcre32-3 arm64 2:8.39-12build1 [118 kB] Get:172 http://ftpmaster.internal/ubuntu focal/main arm64 libpcrecpp0v5 arm64 2:8.39-12build1 [14.7 kB] Get:173 http://ftpmaster.internal/ubuntu focal/main arm64 libpcre3-dev arm64 2:8.39-12build1 [467 kB] Get:174 http://ftpmaster.internal/ubuntu focal/main arm64 libsepol1-dev arm64 3.0-1 [317 kB] Get:175 http://ftpmaster.internal/ubuntu focal/main arm64 libpcre2-16-0 arm64 10.34-7 [156 kB] Get:176 http://ftpmaster.internal/ubuntu focal/main arm64 libpcre2-32-0 arm64 10.34-7 [147 kB] Get:177 http://ftpmaster.internal/ubuntu focal/main arm64 libpcre2-posix2 arm64 10.34-7 [5820 B] Get:178 http://ftpmaster.internal/ubuntu focal/main arm64 libpcre2-dev arm64 10.34-7 [595 kB] Get:179 http://ftpmaster.internal/ubuntu focal/main arm64 libselinux1-dev arm64 3.0-1build2 [152 kB] Get:180 http://ftpmaster.internal/ubuntu focal/main arm64 libglib2.0-dev arm64 2.64.1-1 [1517 kB] Get:181 http://ftpmaster.internal/ubuntu focal/main arm64 libcairo2-dev arm64 1.16.0-4ubuntu1 [598 kB] Get:182 http://ftpmaster.internal/ubuntu focal/main arm64 libcurl3-gnutls arm64 7.68.0-1ubuntu1 [211 kB] Get:183 http://ftpmaster.internal/ubuntu focal/main arm64 libcurl4-gnutls-dev arm64 7.68.0-1ubuntu1 [307 kB] Get:184 http://ftpmaster.internal/ubuntu focal/main arm64 libdatrie1 arm64 0.2.12-3 [17.9 kB] Get:185 http://ftpmaster.internal/ubuntu focal/universe arm64 libdeflate0 arm64 1.5-3 [51.2 kB] Get:186 http://ftpmaster.internal/ubuntu focal/universe arm64 libdeflate-dev arm64 1.5-3 [42.5 kB] Get:187 http://ftpmaster.internal/ubuntu focal/universe arm64 libdisorder-dev arm64 0.0.2+git20130809.8062ee1-1 [3680 B] Get:188 http://ftpmaster.internal/ubuntu focal/universe arm64 libdivsufsort3 arm64 2.0.1-4 [36.8 kB] Get:189 http://ftpmaster.internal/ubuntu focal/universe arm64 libdivsufsort-dev arm64 2.0.1-4 [19.4 kB] Get:190 http://ftpmaster.internal/ubuntu focal/main arm64 libelf-dev arm64 0.176-1.1build1 [58.9 kB] Get:191 http://ftpmaster.internal/ubuntu focal/main arm64 liblzma-dev arm64 5.2.4-1 [144 kB] Get:192 http://ftpmaster.internal/ubuntu focal/main arm64 libdw-dev arm64 0.176-1.1build1 [201 kB] Get:193 http://ftpmaster.internal/ubuntu focal/universe arm64 libfastahack-dev arm64 1.0.0+dfsg-5build1 [23.6 kB] Get:194 http://ftpmaster.internal/ubuntu focal/universe arm64 libfml0 arm64 0.1-9ubuntu1 [65.0 kB] Get:195 http://ftpmaster.internal/ubuntu focal/universe arm64 libfml-dev arm64 0.1-9ubuntu1 [78.0 kB] Get:196 http://ftpmaster.internal/ubuntu focal/universe arm64 libgflags2.2 arm64 2.2.2-1build1 [67.9 kB] Get:197 http://ftpmaster.internal/ubuntu focal/main arm64 libgfortran5 arm64 10-20200405-0ubuntu1 [342 kB] Get:198 http://ftpmaster.internal/ubuntu focal/main arm64 libgmpxx4ldbl arm64 2:6.2.0+dfsg-4 [8804 B] Get:199 http://ftpmaster.internal/ubuntu focal/main arm64 libgmp-dev arm64 2:6.2.0+dfsg-4 [301 kB] Get:200 http://ftpmaster.internal/ubuntu focal/main arm64 libgraphite2-3 arm64 1.3.13-11build1 [67.7 kB] Get:201 http://ftpmaster.internal/ubuntu focal/main arm64 libharfbuzz0b arm64 2.6.4-1ubuntu4 [353 kB] Get:202 http://ftpmaster.internal/ubuntu focal/universe arm64 libhts3 arm64 1.10.2-3 [316 kB] Get:203 http://ftpmaster.internal/ubuntu focal/universe arm64 libhts-dev arm64 1.10.2-3 [92.1 kB] Get:204 http://ftpmaster.internal/ubuntu focal/main arm64 libicu-dev arm64 66.1-2ubuntu2 [9320 kB] Get:205 http://ftpmaster.internal/ubuntu focal/main arm64 libjansson4 arm64 2.12-1build1 [28.5 kB] Get:206 http://ftpmaster.internal/ubuntu focal/main arm64 libjansson-dev arm64 2.12-1build1 [30.5 kB] Get:207 http://ftpmaster.internal/ubuntu focal/universe arm64 libjemalloc2 arm64 5.2.1-1ubuntu1 [172 kB] Get:208 http://ftpmaster.internal/ubuntu focal/main arm64 libjpeg-turbo8 arm64 2.0.3-0ubuntu1 [101 kB] Get:209 http://ftpmaster.internal/ubuntu focal/main arm64 libjpeg8 arm64 8c-2ubuntu8 [2198 B] Get:210 http://ftpmaster.internal/ubuntu focal/main arm64 liblapack3 arm64 3.9.0-1build1 [1529 kB] Get:211 http://ftpmaster.internal/ubuntu focal/main arm64 libltdl7 arm64 2.4.6-14 [37.5 kB] Get:212 http://ftpmaster.internal/ubuntu focal/main arm64 libmhash2 arm64 0.9.9.9-8 [94.5 kB] Get:213 http://ftpmaster.internal/ubuntu focal/main arm64 libncurses-dev arm64 6.2-0ubuntu2 [327 kB] Get:214 http://ftpmaster.internal/ubuntu focal/main arm64 libncurses5-dev arm64 6.2-0ubuntu2 [976 B] Get:215 http://ftpmaster.internal/ubuntu focal/main arm64 libthai-data all 0.1.28-3 [134 kB] Get:216 http://ftpmaster.internal/ubuntu focal/main arm64 libthai0 arm64 0.1.28-3 [16.8 kB] Get:217 http://ftpmaster.internal/ubuntu focal/main arm64 libpango-1.0-0 arm64 1.44.7-2ubuntu2 [153 kB] Get:218 http://ftpmaster.internal/ubuntu focal/main arm64 libpangoft2-1.0-0 arm64 1.44.7-2ubuntu2 [32.0 kB] Get:219 http://ftpmaster.internal/ubuntu focal/main arm64 libpangocairo-1.0-0 arm64 1.44.7-2ubuntu2 [22.5 kB] Get:220 http://ftpmaster.internal/ubuntu focal/main arm64 libpaper1 arm64 1.1.28 [12.7 kB] Get:221 http://ftpmaster.internal/ubuntu focal/main arm64 libpaper-utils arm64 1.1.28 [8328 B] Get:222 http://ftpmaster.internal/ubuntu focal/main arm64 libprotobuf-lite17 arm64 3.6.1.3-2ubuntu5 [114 kB] Get:223 http://ftpmaster.internal/ubuntu focal/main arm64 libprotobuf17 arm64 3.6.1.3-2ubuntu5 [690 kB] Get:224 http://ftpmaster.internal/ubuntu focal/main arm64 libprotoc17 arm64 3.6.1.3-2ubuntu5 [560 kB] Get:225 http://ftpmaster.internal/ubuntu focal/main arm64 libyajl2 arm64 2.1.0-3 [19.3 kB] Get:226 http://ftpmaster.internal/ubuntu focal/main arm64 libraptor2-0 arm64 2.0.15-0ubuntu1 [146 kB] Get:227 http://ftpmaster.internal/ubuntu focal/main arm64 libxml2-dev arm64 2.9.10+dfsg-4build1 [693 kB] Get:228 http://ftpmaster.internal/ubuntu focal/main arm64 libxslt1-dev arm64 1.1.34-4 [219 kB] Get:229 http://ftpmaster.internal/ubuntu focal/main arm64 libyajl-dev arm64 2.1.0-3 [25.0 kB] Get:230 http://ftpmaster.internal/ubuntu focal/main arm64 libraptor2-dev arm64 2.0.15-0ubuntu1 [194 kB] Get:231 http://ftpmaster.internal/ubuntu focal/main arm64 librasqal3 arm64 0.9.33-0.1 [160 kB] Get:232 http://ftpmaster.internal/ubuntu focal/main arm64 librasqal3-dev arm64 0.9.33-0.1 [207 kB] Get:233 http://ftpmaster.internal/ubuntu focal/main arm64 librdf0 arm64 1.0.17-1.1ubuntu1 [89.6 kB] Get:234 http://ftpmaster.internal/ubuntu focal/main arm64 librdf0-dev arm64 1.0.17-1.1ubuntu1 [230 kB] Get:235 http://ftpmaster.internal/ubuntu focal/main arm64 libsnappy1v5 arm64 1.1.8-1build1 [16.0 kB] Get:236 http://ftpmaster.internal/ubuntu focal/universe arm64 librocksdb5.17 arm64 5.17.2-3 [1508 kB] Get:237 http://ftpmaster.internal/ubuntu focal/universe arm64 librocksdb-dev arm64 5.17.2-3 [2582 kB] Get:238 http://ftpmaster.internal/ubuntu focal/universe arm64 libsmithwaterman0 arm64 0.0+git20160702.2610e25-7build1 [33.3 kB] Get:239 http://ftpmaster.internal/ubuntu focal/universe arm64 libsmithwaterman-dev arm64 0.0+git20160702.2610e25-7build1 [37.1 kB] Get:240 http://ftpmaster.internal/ubuntu focal/universe arm64 libsparsehash-dev all 2.0.3-1 [71.9 kB] Get:241 http://ftpmaster.internal/ubuntu focal/universe arm64 libssw0 arm64 1.1-9 [17.9 kB] Get:242 http://ftpmaster.internal/ubuntu focal/universe arm64 libssw-dev arm64 1.1-9 [20.2 kB] Get:243 http://ftpmaster.internal/ubuntu focal/universe arm64 libtabixpp0 arm64 1.1.0-3 [8456 B] Get:244 http://ftpmaster.internal/ubuntu focal/universe arm64 libtabixpp-dev arm64 1.1.0-3 [6920 B] Get:245 http://ftpmaster.internal/ubuntu focal/main arm64 libtcl8.6 arm64 8.6.10+dfsg-1 [849 kB] Get:246 http://ftpmaster.internal/ubuntu focal/main arm64 libjbig0 arm64 2.1-3.1build1 [24.0 kB] Get:247 http://ftpmaster.internal/ubuntu focal/main arm64 libwebp6 arm64 0.6.1-2 [155 kB] Get:248 http://ftpmaster.internal/ubuntu focal/main arm64 libtiff5 arm64 4.1.0+git191117-2build1 [151 kB] Get:249 http://ftpmaster.internal/ubuntu focal/main arm64 libxft2 arm64 2.3.3-0ubuntu1 [35.9 kB] Get:250 http://ftpmaster.internal/ubuntu focal/main arm64 libxss1 arm64 1:1.2.3-1 [8080 B] Get:251 http://ftpmaster.internal/ubuntu focal/main arm64 libtk8.6 arm64 8.6.10-1 [674 kB] Get:252 http://ftpmaster.internal/ubuntu focal/universe arm64 libtsl-hopscotch-map-dev all 2.2.1-3 [35.2 kB] Get:253 http://ftpmaster.internal/ubuntu focal/universe arm64 libvcflib1 arm64 1.0.1+dfsg-3 [133 kB] Get:254 http://ftpmaster.internal/ubuntu focal/universe arm64 libvcflib-dev arm64 1.0.1+dfsg-3 [27.0 kB] Get:255 http://ftpmaster.internal/ubuntu focal/main arm64 zip arm64 3.0-11build1 [146 kB] Get:256 http://ftpmaster.internal/ubuntu focal/main arm64 unzip arm64 6.0-25ubuntu1 [163 kB] Get:257 http://ftpmaster.internal/ubuntu focal/main arm64 xdg-utils all 1.1.3-2ubuntu1 [61.6 kB] Get:258 http://ftpmaster.internal/ubuntu focal/main arm64 libxt6 arm64 1:1.1.5-1 [128 kB] Get:259 http://ftpmaster.internal/ubuntu focal/universe arm64 r-base-core arm64 3.6.3-2 [24.3 MB] Get:260 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-littler arm64 0.3.9-1 [298 kB] Get:261 http://ftpmaster.internal/ubuntu focal/universe arm64 littler all 0.3.9-1 [2420 B] Get:262 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-pkgkitten all 0.1.5-1 [22.6 kB] Get:263 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-rcpp arm64 1.0.3-1build1 [1846 kB] Get:264 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-plyr arm64 1.8.5-1 [822 kB] Get:265 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-digest arm64 0.6.25-1 [165 kB] Get:266 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-gtable all 0.3.0+dfsg-1 [138 kB] Get:267 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-lazyeval arm64 0.2.2-1 [143 kB] Get:268 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-mass arm64 7.3-51.5-2 [1112 kB] Get:269 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-lattice arm64 0.20-40-1 [1124 kB] Get:270 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-nlme arm64 3.1.144-1 [2219 kB] Get:271 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-matrix arm64 1.2-18-1 [3404 kB] Get:272 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-mgcv arm64 1.8-31-1 [2704 kB] Get:273 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-glue arm64 1.3.1-1 [152 kB] Get:274 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-magrittr all 1.5-5 [152 kB] Get:275 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-stringi arm64 1.4.6-1build1 [688 kB] Get:276 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-stringr all 1.4.0-1 [192 kB] Get:277 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-reshape2 arm64 1.4.3-2build1 [107 kB] Get:278 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-rlang arm64 0.4.4-1 [1110 kB] Get:279 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-farver arm64 2.0.3-1build1 [1323 kB] Get:280 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-labeling all 0.3-3 [61.5 kB] Get:281 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-colorspace arm64 1.4-1+dfsg-1 [1436 kB] Get:282 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-munsell all 0.5.0-1 [206 kB] Get:283 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-r6 all 2.4.1-1 [79.4 kB] Get:284 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-rcolorbrewer all 1.1-2-2 [54.4 kB] Get:285 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-viridislite all 0.3.0-3 [58.9 kB] Get:286 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-lifecycle all 0.1.0-2 [76.7 kB] Get:287 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-scales all 1.1.0-1 [482 kB] Get:288 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-assertthat all 0.2.1-1 [56.7 kB] Get:289 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-crayon all 1.3.4-4ubuntu1 [499 kB] Get:290 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-fansi arm64 0.4.1-1 [341 kB] Get:291 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-cli all 2.0.1-1 [386 kB] Get:292 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-utf8 arm64 1.1.4-1build1 [127 kB] Get:293 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-ellipsis arm64 0.3.0-1 [30.5 kB] Get:294 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-vctrs arm64 0.2.3-1 [816 kB] Get:295 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-pillar all 1.4.3-1 [227 kB] Get:296 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-pkgconfig all 2.0.3-1 [19.7 kB] Get:297 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-tibble arm64 2.1.3-2 [324 kB] Get:298 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-withr all 2.1.2-3 [153 kB] Get:299 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-ggplot2 all 3.2.1+dfsg-2 [2825 kB] Get:300 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-gridbase all 0.4-7-4 [170 kB] Get:301 http://ftpmaster.internal/ubuntu focal/universe arm64 libvcflib-tools arm64 1.0.1+dfsg-3 [559 kB] Get:302 http://ftpmaster.internal/ubuntu focal/main arm64 pv arm64 1.6.6-1 [50.5 kB] Get:303 http://ftpmaster.internal/ubuntu focal/universe arm64 rapidjson-dev all 1.1.0+dfsg2-5ubuntu1 [95.0 kB] Get:304 http://ftpmaster.internal/ubuntu focal/main arm64 raptor2-utils arm64 2.0.15-0ubuntu1 [13.5 kB] Get:305 http://ftpmaster.internal/ubuntu focal/main arm64 rasqal-utils arm64 0.9.33-0.1 [17.8 kB] Get:306 http://ftpmaster.internal/ubuntu focal/universe arm64 rs arm64 20200313-1 [15.6 kB] Get:307 http://ftpmaster.internal/ubuntu focal/universe arm64 samtools arm64 1.10-3 [474 kB] Get:308 http://ftpmaster.internal/ubuntu focal/universe arm64 libjemalloc-dev arm64 5.2.1-1ubuntu1 [298 kB] Get:309 http://ftpmaster.internal/ubuntu focal/main arm64 liblz4-dev arm64 1.9.2-2 [72.1 kB] Get:310 http://ftpmaster.internal/ubuntu focal/main arm64 libprotobuf-dev arm64 3.6.1.3-2ubuntu5 [1079 kB] Get:311 http://ftpmaster.internal/ubuntu focal/main arm64 libprotoc-dev arm64 3.6.1.3-2ubuntu5 [732 kB] Get:312 http://ftpmaster.internal/ubuntu focal/universe arm64 protobuf-compiler arm64 3.6.1.3-2ubuntu5 [27.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 137 MB in 5s (29.2 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 12808 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-4_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-4) ... Selecting previously unselected package libpython3.8-minimal:arm64. Preparing to unpack .../libpython3.8-minimal_3.8.2-1ubuntu1_arm64.deb ... Unpacking libpython3.8-minimal:arm64 (3.8.2-1ubuntu1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.2.9-1build1_arm64.deb ... Unpacking libexpat1:arm64 (2.2.9-1build1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../python3.8-minimal_3.8.2-1ubuntu1_arm64.deb ... Unpacking python3.8-minimal (3.8.2-1ubuntu1) ... Setting up libpython3.8-minimal:arm64 (3.8.2-1ubuntu1) ... Setting up libexpat1:arm64 (2.2.9-1build1) ... Setting up python3.8-minimal (3.8.2-1ubuntu1) ... Selecting previously unselected package python3-minimal. 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Setting up librdf0:arm64 (1.0.17-1.1ubuntu1) ... Setting up r-cran-plyr (1.8.5-1) ... Setting up r-cran-rcolorbrewer (1.1-2-2) ... Setting up r-cran-matrix (1.2-18-1) ... Setting up librdf0-dev (1.0.17-1.1ubuntu1) ... Setting up libvcflib1:arm64 (1.0.1+dfsg-3) ... Setting up r-cran-mgcv (1.8-31-1) ... Setting up libtabixpp-dev:arm64 (1.1.0-3) ... Setting up libvcflib-dev:arm64 (1.0.1+dfsg-3) ... Setting up r-cran-ellipsis (0.3.0-1) ... Setting up rasqal-utils (0.9.33-0.1) ... Setting up r-cran-stringr (1.4.0-1) ... Setting up r-cran-munsell (0.5.0-1) ... Setting up r-cran-reshape2 (1.4.3-2build1) ... Setting up r-cran-scales (1.1.0-1) ... Setting up r-cran-vctrs (0.2.3-1) ... Setting up r-cran-pillar (1.4.3-1) ... Setting up r-cran-tibble (2.1.3-2) ... Setting up r-cran-ggplot2 (3.2.1+dfsg-2) ... Setting up libvcflib-tools (1.0.1+dfsg-3) ... Setting up debhelper (12.10ubuntu1) ... Setting up dh-autoreconf (19) ... Processing triggers for libc-bin (2.31-0ubuntu7) ... Processing triggers for systemd (245.4-2ubuntu1) ... Processing triggers for sgml-base (1.29.1) ... Setting up docbook-xsl (1.79.1+dfsg-2) ... Setting up sgml-data (2.0.11) ... Processing triggers for sgml-base (1.29.1) ... Setting up docbook-xml (4.5-9) ... Setting up docbook (4.5-6) ... Processing triggers for sgml-base (1.29.1) ... Setting up docbook-to-man (1:2.0.0-42) ... Setting up gtk-doc-tools (1.32-4) ... 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rasqal-utils_0.9.33-0.1 readline-common_8.0-4 rs_20200313-1 samtools_1.10-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-vg-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sgml-base_1.29.1 sgml-data_2.0.11 systemd_245.4-2ubuntu1 systemd-sysv_245.4-2ubuntu1 systemd-timesyncd_245.4-2ubuntu1 sysvinit-utils_2.96-2.1ubuntu1 tar_1.30+dfsg-7 tzdata_2019c-3ubuntu1 ubuntu-keyring_2020.02.11.1 ucf_3.0038+nmu1 unzip_6.0-25ubuntu1 util-linux_2.34-0.1ubuntu9 uuid-dev_2.34-0.1ubuntu9 x11-common_1:7.7+19ubuntu14 x11proto-core-dev_2019.2-1ubuntu1 x11proto-dev_2019.2-1ubuntu1 x11proto-xext-dev_2019.2-1ubuntu1 xdg-utils_1.1.3-2ubuntu1 xml-core_0.18+nmu1 xorg-sgml-doctools_1:1.11-1 xsltproc_1.1.34-4 xtrans-dev_1.4.0-1 xz-utils_5.2.4-1 zip_3.0-11build1 zlib1g_1:1.2.11.dfsg-2ubuntu1 zlib1g-dev_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Wed Feb 26 14:09:16 2020 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./vg_1.22.0+ds-1.dsc dpkg-source: info: extracting vg in vg-1.22.0+ds dpkg-source: info: unpacking vg_1.22.0+ds.orig.tar.xz dpkg-source: info: unpacking vg_1.22.0+ds-1.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 disc 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-18984357 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-18984357 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-18984357 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 1.22.0+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/vg-1.22.0+ds' mv include/vg_git_version.hpp debian/ rm -Rf include/* mv debian/vg_git_version.hpp include/ dh_auto_clean || true make -j4 clean make[2]: Entering directory '/<>/vg-1.22.0+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-1.22.0+ds/deps/sonLib' cd C && make clean cd externalTools && make clean make[4]: Entering directory '/<>/vg-1.22.0+ds/deps/sonLib/externalTools' make[4]: Entering directory '/<>/vg-1.22.0+ds/deps/sonLib/C' rm -rf ../bin ../lib cd cutest && make clean make[4]: Leaving directory '/<>/vg-1.22.0+ds/deps/sonLib/C' cd quicktree_1.1 && make clean make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/sonLib/externalTools/cutest' make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/sonLib/externalTools/cutest' make[4]: Leaving directory '/<>/vg-1.22.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/<>/vg-1.22.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/<>/vg-1.22.0+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-1.22.0+ds/deps/gcsa2' make[2]: *** [Makefile:608: clean] Error 2 make[2]: Leaving directory '/<>/vg-1.22.0+ds' dh_auto_clean: error: make -j4 clean returned exit code 2 make[1]: Leaving directory '/<>/vg-1.22.0+ds' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a debian/rules override_dh_autoreconf make[1]: Entering directory '/<>/vg-1.22.0+ds' dh_autoreconf --sourcedirectory=/<>/vg-1.22.0+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-1.22.0+ds' dh_auto_configure -a debian/rules override_dh_auto_build-arch make[1]: Entering directory '/<>/vg-1.22.0+ds' mkdir -p /<>/vg-1.22.0+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-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp" ./install.sh /<>/vg-1.22.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /<>/vg-1.22.0+ds/lib && cp -r src/include/handlegraph /<>/vg-1.22.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /<>/vg-1.22.0+ds/lib/ && cp obj/* /<>/vg-1.22.0+ds/obj && cp src/*.h /<>/vg-1.22.0+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /<>/vg-1.22.0+ds/lib/libsonlib.a && mkdir -p /<>/vg-1.22.0+ds/include/sonLib && cp lib/*.h /<>/vg-1.22.0+ds/include/sonLib make[3]: Entering directory '/<>/vg-1.22.0+ds/deps/gssw' gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -g -c -o obj/gssw.o src/gssw.c Library will be installed in '/<>/vg-1.22.0+ds' make[3]: Entering directory '/<>/vg-1.22.0+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-1.22.0+ds/deps/sonLib/externalTools' cd cutest && make all make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/sonLib/externalTools/cutest' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c -- The C compiler identification is GNU 9.3.0 -- The CXX compiler identification is GNU 9.3.0 -- The CXX compiler identification is GNU 9.3.0 -- Check for working C compiler: /usr/bin/gcc -- The C compiler identification is GNU 9.3.0 -- Check for working CXX compiler: /usr/bin/g++ -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Check for working CXX compiler: /usr/bin/g++ -- works -- Detecting CXX compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/g++ ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ -- Detecting CXX compiler ABI info - done cp CuTest.h ../../lib/ make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make all CC="gcc -std=c99" make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /usr/bin/gcc -- Check for working CXX compiler: /usr/bin/g++ -- works -- Detecting CXX compiler ABI info -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info gcc -std=c99 -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info - done -- Configuring done -- Generating done -- Build files have been written to: /<>/vg-1.22.0+ds/deps/libhandlegraph make[3]: Entering directory '/<>/vg-1.22.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/<>/vg-1.22.0+ds/deps/libhandlegraph -B/<>/vg-1.22.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/vg-1.22.0+ds/deps/libhandlegraph/CMakeFiles /<>/vg-1.22.0+ds/deps/libhandlegraph/CMakeFiles/progress.marks -- 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 make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/vg-1.22.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/libhandlegraph' cd /<>/vg-1.22.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.22.0+ds/deps/libhandlegraph /<>/vg-1.22.0+ds/deps/libhandlegraph /<>/vg-1.22.0+ds/deps/libhandlegraph /<>/vg-1.22.0+ds/deps/libhandlegraph /<>/vg-1.22.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= Scanning dependencies of target handlegraph_objs make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/libhandlegraph' [ 33%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o /usr/bin/g++ -I/<>/vg-1.22.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o -c /<>/vg-1.22.0+ds/deps/libhandlegraph/src/handle.cpp -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success gcc -std=c99 -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS ./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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success gcc -std=c99 -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c -- Performing Test HAVE_CXA_DEMANGLE gcc -std=c99 -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c gcc -std=c99 -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c gcc -std=c99 -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE gcc -std=c99 -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -- 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 -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done gcc -std=c99 -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -- Generating done -- Build files have been written to: /<>/vg-1.22.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/<>/vg-1.22.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/vg-1.22.0+ds/deps/sdsl-lite -B/<>/vg-1.22.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/<>/vg-1.22.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/vg-1.22.0+ds/deps/sdsl-lite -B/<>/vg-1.22.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/vg-1.22.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/<>/vg-1.22.0+ds/deps/sdsl-lite/build' cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.22.0+ds/deps/sdsl-lite /<>/vg-1.22.0+ds/deps/sdsl-lite/lib /<>/vg-1.22.0+ds/deps/sdsl-lite/build /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target sdsl make[6]: Leaving directory '/<>/vg-1.22.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/<>/vg-1.22.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/bits.cpp make[5]: Leaving directory '/<>/vg-1.22.0+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-1.22.0+ds/deps/libhandlegraph' cd /<>/vg-1.22.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.22.0+ds/deps/libhandlegraph /<>/vg-1.22.0+ds/deps/libhandlegraph /<>/vg-1.22.0+ds/deps/libhandlegraph /<>/vg-1.22.0+ds/deps/libhandlegraph /<>/vg-1.22.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= Scanning dependencies of target handlegraph_static make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/libhandlegraph' [ 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[5]: Leaving directory '/<>/vg-1.22.0+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-1.22.0+ds/deps/libhandlegraph' cd /<>/vg-1.22.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.22.0+ds/deps/libhandlegraph /<>/vg-1.22.0+ds/deps/libhandlegraph /<>/vg-1.22.0+ds/deps/libhandlegraph /<>/vg-1.22.0+ds/deps/libhandlegraph /<>/vg-1.22.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= Scanning dependencies of target handlegraph_shared make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libhandlegraph.so -o libhandlegraph.so CMakeFiles/handlegraph_objs.dir/src/handle.cpp.o make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/libhandlegraph' [100%] Built target handlegraph_shared make[4]: Leaving directory '/<>/vg-1.22.0+ds/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /<>/vg-1.22.0+ds/deps/libhandlegraph/CMakeFiles 0 make[3]: Leaving directory '/<>/vg-1.22.0+ds/deps/libhandlegraph' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp In file included from /usr/include/string.h:495, from /<>/vg-1.22.0+ds/include/../debian/include/simde/x86/../simde-common.h:31, from /<>/vg-1.22.0+ds/include/../debian/include/simde/x86/mmx.h:28, from /<>/vg-1.22.0+ds/include/../debian/include/simde/x86/sse2.h:30, from src/gssw.c:32: In function ‘strncpy’, inlined from ‘gssw_node_create’ at src/gssw.c:4957:5: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4953:19: note: length computed here 4953 | int32_t len = strlen(seq); | ^~~~~~~~~~~ In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /<>/vg-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.22.0+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-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.22.0+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-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.22.0+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-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.22.0+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-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.22.0+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-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.22.0+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) { | ^ [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp gcc -std=c99 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/<>/vg-1.22.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/<>/vg-1.22.0+ds/deps/sonLib/C' cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.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/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.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-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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 | ^~~~ # Make dest directory gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.22.0+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-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.22.0+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-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:537:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 537 | if (0!=(w=*(++word))) | ~~^~~~~~~~~~~ In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.22.0+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-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:506:18: warning: array subscript 1 is outside array bounds of ‘uint64_t [1]’ {aka ‘long unsigned int [1]’} [-Warray-bounds] 506 | ((*(word+1) & bits::lo_set[(offset+len)&0x3F]) // set higher bits zero | ^~~~~~~~~ In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.22.0+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 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)) { | ^ gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -g src/example_adj.c -o bin/gssw_example_adj obj/gssw.o -lm -lz [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/config.cpp cc1: warning: command line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /<>/vg-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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 rvs lib/libgssw.a obj/gssw.o ar: creating lib/libgssw.a a - obj/gssw.o make[3]: Leaving directory '/<>/vg-1.22.0+ds/deps/gssw' . ./source_me.sh && cd deps/sublinear-Li-Stephens && make clean && INCLUDE_FLAGS="-I/<>/vg-1.22.0+ds/include" make libs && cp lib/libsublinearLS.a /<>/vg-1.22.0+ds/lib/ && mkdir -p /<>/vg-1.22.0+ds/include/sublinearLS && cp src/*.hpp /<>/vg-1.22.0+ds/include/sublinearLS/ make[3]: Entering directory '/<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens' rm -f /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/bin/* /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/*.o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/test/*.o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/lib/* make[3]: Leaving directory '/<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens' make[3]: Entering directory '/<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens' if [ ! -d /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj ]; then mkdir -p /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj; fi cc1: warning: command line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C if [ ! -d /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/test ]; then mkdir -p /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/test; fi if [ ! -d /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/bin ]; then mkdir -p /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/bin; fi if [ ! -d /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/lib ]; then mkdir -p /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/lib; fi if [ ! -d /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/deps ]; then mkdir -p /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/deps; fi g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -g -I/<>/vg-1.22.0+ds/include -L. -L/<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/src/math.cpp -o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/math.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-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -g -I/<>/vg-1.22.0+ds/include -L. -L/<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/src/reference.cpp -o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/reference.o [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/construct_config.cpp cc1: warning: command line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/construct_isa.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 [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/construct_lcp.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 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:686:75: note: declared here 686 | 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:694:68: note: declared here 694 | 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:695:68: note: declared here 695 | 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 cc1: warning: command line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /<>/vg-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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 cc1: warning: command line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /<>/vg-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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 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 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 [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.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 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-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /<>/vg-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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 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-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -g -I/<>/vg-1.22.0+ds/include -L. -L/<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/src/probability.cpp -o /<>/vg-1.22.0+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 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++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 rm *.o mv sonLib.a ../lib/ gcc -std=c99 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/construct_sa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -g -I/<>/vg-1.22.0+ds/include -L. -L/<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp -o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /<>/vg-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -g -I/<>/vg-1.22.0+ds/include -L. -L/<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp -o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -g -I/<>/vg-1.22.0+ds/include -L. -L/<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp -o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -g -I/<>/vg-1.22.0+ds/include -L. -L/<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp -o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -g -Wno-error=return-type -I/<>/vg-1.22.0+ds/include -L. -L/<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp -o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp: In function ‘char allele::to_char(alleleValue)’: /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/src/allele.cpp:20:1: warning: control reaches end of non-void function [-Wreturn-type] 20 | } | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -g -I/<>/vg-1.22.0+ds/include -L. -L/<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/src/row_set.cpp -o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -g -Wno-error=return-type -I/<>/vg-1.22.0+ds/include -L. -L/<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp -o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /<>/vg-1.22.0+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-1.22.0+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-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -g -I/<>/vg-1.22.0+ds/include -L. -L/<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp -o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o mv ../bin/sonLibTests.tmp ../bin/sonLibTests gcc -std=c99 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -g -I/<>/vg-1.22.0+ds/include -L. -L/<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp -o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o mv ../bin/sonLib_kvDatabaseTest.tmp ../bin/sonLib_kvDatabaseTest gcc -std=c99 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -I inc -I ../lib -o ../bin/sonLib_cigarTest.tmp tests/cigarsTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_cigarTest.tmp ../bin/sonLib_cigarTest gcc -std=c99 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -I inc -I ../lib -o ../bin/sonLib_fastaCTest.tmp tests/fastaCTest.c ../lib/sonLib.a -lm mv ../bin/sonLib_fastaCTest.tmp ../bin/sonLib_fastaCTest make[4]: Leaving directory '/<>/vg-1.22.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/<>/vg-1.22.0+ds/deps/sonLib' . ./source_me.sh && cd deps/structures && make clean && make lib/libstructures.a && cp lib/libstructures.a /<>/vg-1.22.0+ds/lib/ && cp -r src/include/structures /<>/vg-1.22.0+ds/include/ make[3]: Entering directory '/<>/vg-1.22.0+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 make[3]: Leaving directory '/<>/vg-1.22.0+ds/deps/structures' make[3]: Entering directory '/<>/vg-1.22.0+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-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c src/union_find.cpp -o obj/union_find.o [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -g -O3 -Isrc/include -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c src/suffix_tree.cpp -o obj/suffix_tree.o In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /<>/vg-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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 -std=c++11 -g -O3 -Isrc/include -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c src/stable_double.cpp -o obj/stable_double.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-1.22.0+ds/deps/structures' [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -g -I/<>/vg-1.22.0+ds/include -L. -L/<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp -o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/io.cpp In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /<>/vg-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -g -I/<>/vg-1.22.0+ds/include -L. -L/<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/deps/htslib/ -lhts -llzma -lbz2 -lz -lm -lpthread -c /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp -o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o ar rc /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/math.o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/reference.o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/probability.o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/input_haplotype.o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/delay_multiplier.o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/DP_map.o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/penalty_set.o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/allele.o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/row_set.o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_node.o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_state_tree.o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/haplotype_manager.o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/set_of_extensions.o /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/obj/reference_sequence.o ranlib /<>/vg-1.22.0+ds/deps/sublinear-Li-Stephens/lib/libsublinearLS.a make[3]: Leaving directory '/<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security" ./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' [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/louds_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/memory_management.cpp In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /<>/vg-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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' In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /<>/vg-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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/nn_dict_dynamic.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp 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... yes checking for sys/types.h... yes [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o checking for sys/stat.h... cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /<>/vg-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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 | ^~~~ yes /<>/vg-1.22.0+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 | ^~~~ checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_fs.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/ram_fs.cpp yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/rrr_vector_15.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... 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 [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/sd_vector.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... yes checking whether the Boost::Program_Options library is available... In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /<>/vg-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/sfstream.cpp In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /<>/vg-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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 | ^~~~ [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/structure_tree.cpp 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security" ./configure --with-boost-program-options=boost_program_options [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/uint128_t.cpp 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... [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/uint256_t.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... [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/util.cpp 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... [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.22.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/wt_helper.cpp 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... 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... 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... 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-1.22.0+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-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp" && cmake -DCMAKE_VERBOSE_MAKEFILE=ON .. && make yes checking if gcc supports -c -o file.o... -- Setting build type to 'Debug' as none was specified. 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... -- The C compiler identification is GNU 9.3.0 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 -- The CXX compiler identification is GNU 9.3.0 In file included from /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /<>/vg-1.22.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /<>/vg-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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 | ^~~~ checking how to run the C++ preprocessor... g++ -E /<>/vg-1.22.0+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 | ^~~~ -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info 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 -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ 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... -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info . ./source_me.sh && cp deps/mmmultimap/src/mmmultimap.hpp deps/mmmultimap/src/mmmultiset.hpp /<>/vg-1.22.0+ds/include/ . ./source_me.sh && cp -r deps/ips4o/ips4o* /<>/vg-1.22.0+ds/include/ cp ./deps/gfakluge/src/*.hpp /<>/vg-1.22.0+ds/include/ && cp ./deps/gfakluge/src/tinyFA/*.hpp /<>/vg-1.22.0+ds/include/ cd ./deps/lru_cache && cp *.h* /<>/vg-1.22.0+ds/include/ cp deps/sha1/*.h* /<>/vg-1.22.0+ds/include/ cp deps/progress_bar/progress_bar.hpp /<>/vg-1.22.0+ds/include mkdir -p /<>/vg-1.22.0+ds/include/dozeu && cp deps/dozeu/*.h /<>/vg-1.22.0+ds/include/dozeu/ diff: include/vg_environment_version.hpp: No such file or directory . ./source_me.sh && cd deps/progress_bar && make && cp progress_bar.o /<>/vg-1.22.0+ds/obj make[3]: Entering directory '/<>/vg-1.22.0+ds/deps/progress_bar' g++ -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c main.cpp yes checking if g++ supports -c -o file.o... -- Detecting CXX compiler ABI info - done 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) -- Detecting CXX compile features -- Detecting CXX compile features - done GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether g++ supports C++11 features by default... Building in Debug mode -- Configuring done -- Generating done -- Build files have been written to: /<>/vg-1.22.0+ds/deps/DYNAMIC/build yes checking for ANSI C header files... (cached) yes make[3]: Entering directory '/<>/vg-1.22.0+ds/deps/DYNAMIC/build' /usr/bin/cmake -S/<>/vg-1.22.0+ds/deps/DYNAMIC -B/<>/vg-1.22.0+ds/deps/DYNAMIC/build --check-build-system CMakeFiles/Makefile.cmake 0 checking for boostlib >= 1.0... /usr/bin/cmake -E cmake_progress_start /<>/vg-1.22.0+ds/deps/DYNAMIC/build/CMakeFiles /<>/vg-1.22.0+ds/deps/DYNAMIC/build/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/vg-1.22.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/cw-bwt.dir/build.make CMakeFiles/cw-bwt.dir/depend make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/DYNAMIC/build' cd /<>/vg-1.22.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.22.0+ds/deps/DYNAMIC /<>/vg-1.22.0+ds/deps/DYNAMIC /<>/vg-1.22.0+ds/deps/DYNAMIC/build /<>/vg-1.22.0+ds/deps/DYNAMIC/build /<>/vg-1.22.0+ds/deps/DYNAMIC/build/CMakeFiles/cw-bwt.dir/DependInfo.cmake --color= yes checking whether the Boost::Program_Options library is available... Scanning dependencies of target cw-bwt make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/cw-bwt.dir/build.make CMakeFiles/cw-bwt.dir/build make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/DYNAMIC/build' [ 7%] Building CXX object CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o /usr/bin/c++ -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include/internal -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include/algorithms -I/<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -c /<>/vg-1.22.0+ds/deps/DYNAMIC/cw-bwt.cpp [100%] Linking CXX static library libsdsl.a cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /<>/vg-1.22.0+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 g++ -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -c progress_bar.cpp make[6]: Leaving directory '/<>/vg-1.22.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/vg-1.22.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/<>/vg-1.22.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/<>/vg-1.22.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/<>/vg-1.22.0+ds/include/sdsl/*' rm -f '/<>/vg-1.22.0+ds/lib/libsdsl*' make[3]: Entering directory '/<>/vg-1.22.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/vg-1.22.0+ds/deps/sdsl-lite -B/<>/vg-1.22.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/vg-1.22.0+ds/deps/sdsl-lite/build/CMakeFiles /<>/vg-1.22.0+ds/deps/sdsl-lite/build/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/vg-1.22.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/sdsl-lite/build' cd /<>/vg-1.22.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.22.0+ds/deps/sdsl-lite /<>/vg-1.22.0+ds/deps/sdsl-lite/lib /<>/vg-1.22.0+ds/deps/sdsl-lite/build /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib /<>/vg-1.22.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/<>/vg-1.22.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/vg-1.22.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/<>/vg-1.22.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/<>/vg-1.22.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /<>/vg-1.22.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /<>/vg-1.22.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/bits.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/bp_support.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/coder.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/coder_comma.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/config.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/construct.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/construct_config.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/construct_isa.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/construct_sa.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/csa_sada.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/csa_wt.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/cst_fully.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/cst_sada.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/dac_vector.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/enc_vector.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/fast_cache.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/io.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/iterators.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/k2_treap.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/k2_tree.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/lcp.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/louds_tree.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/memory_management.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/qsufsort.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/ram_fs.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/rank_support.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/raster_img.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/rmq_support.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/sd_vector.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/select_support.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/sfstream.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/structure_tree.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/uint128_t.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/uint256_t.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/uintx_t.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/util.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/vectors.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/wm_int.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/wt_ap.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/wt_helper.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/wt_huff.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/wt_int.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/wt_pc.hpp -- Installing: /<>/vg-1.22.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /<>/vg-1.22.0+ds/lib/libsdsl.a make[3]: Leaving directory '/<>/vg-1.22.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/<>/vg-1.22.0+ds/include'. The library files are located in '/<>/vg-1.22.0+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! g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o obj/sha1.o deps/sha1/sha1.cpp g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 main.o progress_bar.o -o progress_bar make[3]: Leaving directory '/<>/vg-1.22.0+ds/deps/progress_bar' ln -s `which shuf` bin/shuf . ./source_me.sh && cp -r deps/gcsa2/include/gcsa /<>/vg-1.22.0+ds/include/ && cd deps/gcsa2 && make libgcsa2.a && mv libgcsa2.a /<>/vg-1.22.0+ds/lib make[3]: Entering directory '/<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c algorithms.cpp . ./source_me.sh && cp -r deps/gbwt/include/gbwt /<>/vg-1.22.0+ds/include/ && cd deps/gbwt && make clean && make && mv libgbwt.a /<>/vg-1.22.0+ds/lib make[3]: Entering directory '/<>/vg-1.22.0+ds/deps/gbwt' rm -f build_gbwt merge_gbwt benchmark metadata_tool remove_seq build_gbwt.o variants.o algorithms.o utils.o cached_gbwt.o metadata.o support.o merge_gbwt.o files.o metadata_tool.o dynamic_gbwt.o benchmark.o gbwt.o bwtmerge.o remove_seq.o internal.o libgbwt.a prepare_text prepare_text.o metadata make[3]: Leaving directory '/<>/vg-1.22.0+ds/deps/gbwt' make[3]: Entering directory '/<>/vg-1.22.0+ds/deps/gbwt' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c algorithms.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=... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... 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-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/sdsl/wt_pc.hpp:25, from /<>/vg-1.22.0+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-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+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-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from /<>/vg-1.22.0+ds/include/gbwt/support.h:29, from /<>/vg-1.22.0+ds/include/gbwt/algorithms.h:31, from algorithms.cpp:25: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ 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 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c bwtmerge.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security" make make[3]: Entering directory '/<>/vg-1.22.0+ds/deps/vowpal_wabbit' Making all in vowpalwabbit make[4]: Entering directory '/<>/vg-1.22.0+ds/deps/vowpal_wabbit/vowpalwabbit' (CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash /<>/vg-1.22.0+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-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from /<>/vg-1.22.0+ds/include/gbwt/support.h:29, from /<>/vg-1.22.0+ds/include/gbwt/internal.h:31, from /<>/vg-1.22.0+ds/include/gbwt/bwtmerge.h:33, from bwtmerge.cpp:26: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+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_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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT hash.lo -MD -MP -MF $depbase.Tpo -c -o hash.lo hash.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -fPIC -DPIC -o .libs/hash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT hash.lo -MD -MP -MF .deps/hash.Tpo -c hash.cc -o hash.o >/dev/null 2>&1 depbase=`echo parser_helper.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -fPIC -DPIC -o .libs/parser_helper.o [ 14%] Linking CXX executable cw-bwt /usr/bin/cmake -E cmake_link_script CMakeFiles/cw-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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/cw-bwt.dir/cw-bwt.cpp.o -o cw-bwt make[5]: Leaving directory '/<>/vg-1.22.0+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-1.22.0+ds/deps/DYNAMIC/build' cd /<>/vg-1.22.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.22.0+ds/deps/DYNAMIC /<>/vg-1.22.0+ds/deps/DYNAMIC /<>/vg-1.22.0+ds/deps/DYNAMIC/build /<>/vg-1.22.0+ds/deps/DYNAMIC/build /<>/vg-1.22.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_bwt.dir/DependInfo.cmake --color= Scanning dependencies of target rle_bwt make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_bwt.dir/build.make CMakeFiles/rle_bwt.dir/build make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/DYNAMIC/build' [ 21%] Building CXX object CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o /usr/bin/c++ -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include/internal -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include/algorithms -I/<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -c /<>/vg-1.22.0+ds/deps/DYNAMIC/rle_bwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c dbg.cpp In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/sdsl/wt_pc.hpp:25, from /<>/vg-1.22.0+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-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT parser_helper.lo -MD -MP -MF .deps/parser_helper.Tpo -c parser_helper.cc -o parser_helper.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c cached_gbwt.cpp In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from /<>/vg-1.22.0+ds/include/gbwt/support.h:29, from /<>/vg-1.22.0+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.22.0+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.22.0+ds/include/gbwt/cached_gbwt.h:29, from cached_gbwt.cpp:25: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+ds/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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -fPIC -DPIC -o .libs/global_data.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c files.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c dynamic_gbwt.cpp In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/sdsl/wt_pc.hpp:25, from /<>/vg-1.22.0+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-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+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 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ [ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/rle_bwt.dir/rle_bwt.cpp.o -o rle_bwt In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from /<>/vg-1.22.0+ds/include/gbwt/support.h:29, from /<>/vg-1.22.0+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.22.0+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.22.0+ds/include/gbwt/dynamic_gbwt.h:31, from dynamic_gbwt.cpp:26: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+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-1.22.0+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-1.22.0+ds/deps/DYNAMIC/build' cd /<>/vg-1.22.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.22.0+ds/deps/DYNAMIC /<>/vg-1.22.0+ds/deps/DYNAMIC /<>/vg-1.22.0+ds/deps/DYNAMIC/build /<>/vg-1.22.0+ds/deps/DYNAMIC/build /<>/vg-1.22.0+ds/deps/DYNAMIC/build/CMakeFiles/h0_lz77.dir/DependInfo.cmake --color= Scanning dependencies of target h0_lz77 make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/h0_lz77.dir/build.make CMakeFiles/h0_lz77.dir/build make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/DYNAMIC/build' [ 35%] Building CXX object CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o /usr/bin/c++ -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include/internal -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include/algorithms -I/<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -c /<>/vg-1.22.0+ds/deps/DYNAMIC/h0_lz77.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT global_data.lo -MD -MP -MF .deps/global_data.Tpo -c global_data.cc -o global_data.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c gcsa.cpp 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT io_buf.lo -MD -MP -MF .deps/io_buf.Tpo -c io_buf.cc -fPIC -DPIC -o .libs/io_buf.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/sdsl/wt_pc.hpp:25, from /<>/vg-1.22.0+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-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT parse_regressor.lo -MD -MP -MF $depbase.Tpo -c -o parse_regressor.lo parse_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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT parse_regressor.lo -MD -MP -MF .deps/parse_regressor.Tpo -c parse_regressor.cc -fPIC -DPIC -o .libs/parse_regressor.o 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:103:3: 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:103:3: warning: catching polymorphic type ‘class VW::vw_exception’ by value [-Wcatch-value=] [ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/h0_lz77.dir/h0_lz77.cpp.o -o h0_lz77 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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-1.22.0+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-1.22.0+ds/deps/DYNAMIC/build' cd /<>/vg-1.22.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.22.0+ds/deps/DYNAMIC /<>/vg-1.22.0+ds/deps/DYNAMIC /<>/vg-1.22.0+ds/deps/DYNAMIC/build /<>/vg-1.22.0+ds/deps/DYNAMIC/build /<>/vg-1.22.0+ds/deps/DYNAMIC/build/CMakeFiles/benchmark.dir/DependInfo.cmake --color= Scanning dependencies of target benchmark make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/benchmark.dir/build.make CMakeFiles/benchmark.dir/build make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/DYNAMIC/build' [ 50%] Building CXX object CMakeFiles/benchmark.dir/benchmark.cpp.o /usr/bin/c++ -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include/internal -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include/algorithms -I/<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/benchmark.dir/benchmark.cpp.o -c /<>/vg-1.22.0+ds/deps/DYNAMIC/benchmark.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from /<>/vg-1.22.0+ds/include/gbwt/files.h:29, from files.cpp:26: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+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-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c gbwt.cpp In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from /<>/vg-1.22.0+ds/include/gbwt/support.h:29, from /<>/vg-1.22.0+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.22.0+ds/include/gbwt/gbwt.h:29, from gbwt.cpp:26: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/benchmark.dir/benchmark.cpp.o -o benchmark make[5]: Leaving directory '/<>/vg-1.22.0+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-1.22.0+ds/deps/DYNAMIC/build' cd /<>/vg-1.22.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.22.0+ds/deps/DYNAMIC /<>/vg-1.22.0+ds/deps/DYNAMIC /<>/vg-1.22.0+ds/deps/DYNAMIC/build /<>/vg-1.22.0+ds/deps/DYNAMIC/build /<>/vg-1.22.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_lz77_v2.dir/DependInfo.cmake --color= Scanning dependencies of target rle_lz77_v2 make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_lz77_v2.dir/build.make CMakeFiles/rle_lz77_v2.dir/build make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/DYNAMIC/build' [ 64%] Building CXX object CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o /usr/bin/c++ -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include/internal -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include/algorithms -I/<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -c /<>/vg-1.22.0+ds/deps/DYNAMIC/rle_lz77_v2.cpp 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT parse_primitives.lo -MD -MP -MF $depbase.Tpo -c -o parse_primitives.lo parse_primitives.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -fPIC -DPIC -o .libs/parse_primitives.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT parse_primitives.lo -MD -MP -MF .deps/parse_primitives.Tpo -c parse_primitives.cc -o parse_primitives.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c internal.cpp depbase=`echo unique_sort.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -fPIC -DPIC -o .libs/unique_sort.o In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from /<>/vg-1.22.0+ds/include/gbwt/support.h:29, from /<>/vg-1.22.0+ds/include/gbwt/internal.h:31, from internal.cpp:26: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+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 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++/9/memory:81, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, from memory.h:5, from v_array.h:21, from example.h:10, from unique_sort.cc:6: /usr/include/c++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT unique_sort.lo -MD -MP -MF .deps/unique_sort.Tpo -c unique_sort.cc -o unique_sort.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c metadata.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c internal.cpp In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from /<>/vg-1.22.0+ds/include/gbwt/support.h:29, from /<>/vg-1.22.0+ds/include/gbwt/internal.h:31, from metadata.cpp:25: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+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-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/sdsl/wt_pc.hpp:25, from /<>/vg-1.22.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/internal.h:37, from internal.cpp:26: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -fPIC -DPIC -o .libs/cache.o [ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/rle_lz77_v2.dir/rle_lz77_v2.cpp.o -o rle_lz77_v2 make[5]: Leaving directory '/<>/vg-1.22.0+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-1.22.0+ds/deps/DYNAMIC/build' cd /<>/vg-1.22.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.22.0+ds/deps/DYNAMIC /<>/vg-1.22.0+ds/deps/DYNAMIC /<>/vg-1.22.0+ds/deps/DYNAMIC/build /<>/vg-1.22.0+ds/deps/DYNAMIC/build /<>/vg-1.22.0+ds/deps/DYNAMIC/build/CMakeFiles/rle_lz77_v1.dir/DependInfo.cmake --color= Scanning dependencies of target rle_lz77_v1 make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/rle_lz77_v1.dir/build.make CMakeFiles/rle_lz77_v1.dir/build make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/DYNAMIC/build' [ 78%] Building CXX object CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o /usr/bin/c++ -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include/internal -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include/algorithms -I/<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -c /<>/vg-1.22.0+ds/deps/DYNAMIC/rle_lz77_v1.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c lcp.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c support.cpp 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++/9/memory:81, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, from memory.h:5, from v_array.h:21, from cache.h:7, from cache.cc:6: /usr/include/c++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/sdsl/wt_pc.hpp:25, from /<>/vg-1.22.0+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-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT cache.lo -MD -MP -MF .deps/cache.Tpo -c cache.cc -o cache.o >/dev/null 2>&1 In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from /<>/vg-1.22.0+ds/include/gbwt/support.h:29, from /<>/vg-1.22.0+ds/include/gbwt/internal.h:31, from support.cpp:26: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT rand48.lo -MD -MP -MF $depbase.Tpo -c -o rand48.lo rand48.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -fPIC -DPIC -o .libs/rand48.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o >/dev/null 2>&1 depbase=`echo simple_label.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c path_graph.cpp 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++/9/memory:81, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, from memory.h:5, from v_array.h:21, from cache.h:7, from simple_label.cc:6: /usr/include/c++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/sdsl/wt_pc.hpp:25, from /<>/vg-1.22.0+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-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT simple_label.lo -MD -MP -MF .deps/simple_label.Tpo -c simple_label.cc -o simple_label.o >/dev/null 2>&1 In file included from /<>/vg-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+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-1.22.0+ds/include/sdsl/wt_pc.hpp:28, from /<>/vg-1.22.0+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-1.22.0+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); | ^~~~~~~~ [ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/rle_lz77_v1.dir/rle_lz77_v1.cpp.o -o rle_lz77_v1 make[5]: Leaving directory '/<>/vg-1.22.0+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-1.22.0+ds/deps/DYNAMIC/build' cd /<>/vg-1.22.0+ds/deps/DYNAMIC/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.22.0+ds/deps/DYNAMIC /<>/vg-1.22.0+ds/deps/DYNAMIC /<>/vg-1.22.0+ds/deps/DYNAMIC/build /<>/vg-1.22.0+ds/deps/DYNAMIC/build /<>/vg-1.22.0+ds/deps/DYNAMIC/build/CMakeFiles/debug.dir/DependInfo.cmake --color= Scanning dependencies of target debug make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/DYNAMIC/build' make -f CMakeFiles/debug.dir/build.make CMakeFiles/debug.dir/build make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/DYNAMIC/build' [ 92%] Building CXX object CMakeFiles/debug.dir/debug.cpp.o /usr/bin/c++ -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include/internal -I/<>/vg-1.22.0+ds/deps/DYNAMIC/include/algorithms -I/<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp --std=c++11 -g -g3 -ggdb -o CMakeFiles/debug.dir/debug.cpp.o -c /<>/vg-1.22.0+ds/deps/DYNAMIC/debug.cpp 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -fPIC -DPIC -o .libs/multiclass.o [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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp --std=c++11 -g -g3 -ggdb -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/debug.dir/debug.cpp.o -o debug make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/DYNAMIC/build' [100%] Built target debug make[4]: Leaving directory '/<>/vg-1.22.0+ds/deps/DYNAMIC/build' /usr/bin/cmake -E cmake_progress_start /<>/vg-1.22.0+ds/deps/DYNAMIC/build/CMakeFiles 0 make[3]: Leaving directory '/<>/vg-1.22.0+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-1.22.0+ds/deps/DYNAMIC/include/* include/dynamic . ./source_me.sh && cd ./deps/pinchesAndCacti && make && cd /<>/vg-1.22.0+ds/./deps/sonLib && cp lib/stPinchesAndCacti.a /<>/vg-1.22.0+ds/lib/libpinchesandcacti.a && cp lib/3EdgeConnected.a /<>/vg-1.22.0+ds/lib/lib3edgeconnected.a && mkdir -p /<>/vg-1.22.0+ds/include/sonLib && cp lib/*.h /<>/vg-1.22.0+ds/include/sonLib make[3]: Entering directory '/<>/vg-1.22.0+ds/deps/pinchesAndCacti' cd externalTools && make all make[4]: Entering directory '/<>/vg-1.22.0+ds/deps/pinchesAndCacti/externalTools' cd threeEdgeConnected && make all 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); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I ../..//../sonLib/lib/ -c impl/*.c In file included from /usr/include/c++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected' make[4]: Leaving directory '/<>/vg-1.22.0+ds/deps/pinchesAndCacti/externalTools' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I /<>/vg-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -I inc -I .//../sonLib/lib/ -c impl/*.c /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c utils.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT multiclass.lo -MD -MP -MF .deps/multiclass.Tpo -c multiclass.cc -o multiclass.o >/dev/null 2>&1 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-1.22.0+ds/include -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from utils.cpp:26: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+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-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c variants.cpp 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -fPIC -DPIC -o .libs/oaa.o make[3]: Leaving directory '/<>/vg-1.22.0+ds/deps/pinchesAndCacti' rm -f /<>/vg-1.22.0+ds/include/vg.pb.h /<>/vg-1.22.0+ds/include/vg/vg.pb.h rm -Rf /<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp" && cd deps/libvgio && rm -Rf CMakeCache.txt CMakeFiles *.cmake install_manifest.txt *.pb.cc *.pb.h *.a && PKG_CONFIG_PATH=/<>/vg-1.22.0+ds/lib/pkgconfig: cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_PREFIX_PATH=/<>/vg-1.22.0+ds -DCMAKE_LIBRARY_PATH=/<>/vg-1.22.0+ds/lib -DCMAKE_INSTALL_PREFIX=/<>/vg-1.22.0+ds -DCMAKE_INSTALL_LIBDIR=lib . && make clean && VERBOSE=1 make && make install -- The CXX compiler identification is GNU 9.3.0 -- Check for working CXX compiler: /usr/bin/g++ -- Check for working CXX compiler: /usr/bin/g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") -- Found Protobuf: /usr/lib/aarch64-linux-gnu/libprotobuf.so (found version "3.6.1") -- Checking for module 'protobuf' -- Found protobuf, version 3.6.1 -- Found Threads: TRUE -- Checking for module 'htslib' -- Found htslib, version 1.10.2-3 CMake Warning at CMakeLists.txt:160 (export): Cannot create package registry file: /sbuild-nonexistent/.cmake/packages/VGio/1b8066596f7fef94aba0eff22f5a4908 No such file or directory -- Configuring done -- Generating done -- Build files have been written to: /<>/vg-1.22.0+ds/deps/libvgio make[3]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' make -f CMakeFiles/Makefile2 clean make[4]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/clean make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio_static.dir/cmake_clean.cmake make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/clean make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/vgio.dir/cmake_clean.cmake make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/clean make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' /usr/bin/cmake -P CMakeFiles/link_target.dir/cmake_clean.cmake make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' make[4]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' make[3]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' make[3]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' /usr/bin/cmake -S/<>/vg-1.22.0+ds/deps/libvgio -B/<>/vg-1.22.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from /<>/vg-1.22.0+ds/include/gbwt/variants.h:29, from variants.cpp:25: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ /usr/bin/cmake -E cmake_progress_start /<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles /<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' cd /<>/vg-1.22.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= Dependee "/<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake" is newer than depender "/<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". Dependee "/<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles/link_target.dir/depend.internal". Scanning dependencies of target link_target make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' [ 0%] Built target link_target make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' [ 3%] Running cpp protocol buffer compiler on deps/vg.proto /usr/bin/protoc --cpp_out /<>/vg-1.22.0+ds/deps/libvgio -I /<>/vg-1.22.0+ds/deps/libvgio/deps /<>/vg-1.22.0+ds/deps/libvgio/deps/vg.proto cd /<>/vg-1.22.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= Dependee "/<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake" is newer than depender "/<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Dependee "/<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/depend.internal". Scanning dependencies of target vgio_static make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' [ 7%] Building CXX object CMakeFiles/vgio_static.dir/vg.pb.cc.o /usr/bin/g++ -I/<>/vg-1.22.0+ds/deps/libvgio/include -I/<>/vg-1.22.0+ds/deps/libvgio -I/<>/vg-1.22.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/vg.pb.cc.o -c /<>/vg-1.22.0+ds/deps/libvgio/vg.pb.cc 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT oaa.lo -MD -MP -MF .deps/oaa.Tpo -c oaa.cc -o oaa.o >/dev/null 2>&1 /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c build_gbwt.cpp In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from /<>/vg-1.22.0+ds/include/gbwt/support.h:29, from /<>/vg-1.22.0+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.22.0+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.22.0+ds/include/gbwt/dynamic_gbwt.h:31, from build_gbwt.cpp:32: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c support.cpp In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/sdsl/wt_pc.hpp:25, from /<>/vg-1.22.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from include/gcsa/support.h:29, from support.cpp:26: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ [ 11%] Building CXX object CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o /usr/bin/g++ -I/<>/vg-1.22.0+ds/deps/libvgio/include -I/<>/vg-1.22.0+ds/deps/libvgio -I/<>/vg-1.22.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/basic_stream.cpp.o -c /<>/vg-1.22.0+ds/deps/libvgio/src/basic_stream.cpp 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -fPIC -DPIC -o .libs/multilabel_oaa.o [ 15%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -I/<>/vg-1.22.0+ds/deps/libvgio/include -I/<>/vg-1.22.0+ds/deps/libvgio -I/<>/vg-1.22.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_input_stream.cpp.o -c /<>/vg-1.22.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 19%] Building CXX object CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -I/<>/vg-1.22.0+ds/deps/libvgio/include -I/<>/vg-1.22.0+ds/deps/libvgio -I/<>/vg-1.22.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/blocked_gzip_output_stream.cpp.o -c /<>/vg-1.22.0+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp [ 23%] Building CXX object CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o /usr/bin/g++ -I/<>/vg-1.22.0+ds/deps/libvgio/include -I/<>/vg-1.22.0+ds/deps/libvgio -I/<>/vg-1.22.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/hfile_cppstream.cpp.o -c /<>/vg-1.22.0+ds/deps/libvgio/src/hfile_cppstream.cpp 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ [ 26%] Building CXX object CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o /usr/bin/g++ -I/<>/vg-1.22.0+ds/deps/libvgio/include -I/<>/vg-1.22.0+ds/deps/libvgio -I/<>/vg-1.22.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_emitter.cpp.o -c /<>/vg-1.22.0+ds/deps/libvgio/src/message_emitter.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c merge_gbwt.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c utils.cpp [ 30%] Building CXX object CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o /usr/bin/g++ -I/<>/vg-1.22.0+ds/deps/libvgio/include -I/<>/vg-1.22.0+ds/deps/libvgio -I/<>/vg-1.22.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/message_iterator.cpp.o -c /<>/vg-1.22.0+ds/deps/libvgio/src/message_iterator.cpp In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from /<>/vg-1.22.0+ds/include/gbwt/support.h:29, from /<>/vg-1.22.0+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.22.0+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.22.0+ds/include/gbwt/dynamic_gbwt.h:31, from merge_gbwt.cpp:28: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+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-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/sdsl/wt_pc.hpp:25, from /<>/vg-1.22.0+ds/include/sdsl/wavelet_trees.hpp:32, from include/gcsa/utils.h:36, from utils.cpp:26: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT multilabel_oaa.lo -MD -MP -MF .deps/multilabel_oaa.Tpo -c multilabel_oaa.cc -o multilabel_oaa.o >/dev/null 2>&1 [ 34%] Building CXX object CMakeFiles/vgio_static.dir/src/registry.cpp.o /usr/bin/g++ -I/<>/vg-1.22.0+ds/deps/libvgio/include -I/<>/vg-1.22.0+ds/deps/libvgio -I/<>/vg-1.22.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/registry.cpp.o -c /<>/vg-1.22.0+ds/deps/libvgio/src/registry.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c benchmark.cpp 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-1.22.0+ds/deps/gcsa2' /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c metadata_tool.cpp In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from /<>/vg-1.22.0+ds/include/gbwt/support.h:29, from /<>/vg-1.22.0+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.22.0+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.22.0+ds/include/gbwt/cached_gbwt.h:29, from benchmark.cpp:31: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+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-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from /<>/vg-1.22.0+ds/include/gbwt/support.h:29, from /<>/vg-1.22.0+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.22.0+ds/include/gbwt/gbwt.h:29, from metadata_tool.cpp:25: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+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/stream.cpp.o /usr/bin/g++ -I/<>/vg-1.22.0+ds/deps/libvgio/include -I/<>/vg-1.22.0+ds/deps/libvgio -I/<>/vg-1.22.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream.cpp.o -c /<>/vg-1.22.0+ds/deps/libvgio/src/stream.cpp /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c remove_seq.cpp [ 42%] Building CXX object CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o /usr/bin/g++ -I/<>/vg-1.22.0+ds/deps/libvgio/include -I/<>/vg-1.22.0+ds/deps/libvgio -I/<>/vg-1.22.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/stream_multiplexer.cpp.o -c /<>/vg-1.22.0+ds/deps/libvgio/src/stream_multiplexer.cpp In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from /<>/vg-1.22.0+ds/include/gbwt/support.h:29, from /<>/vg-1.22.0+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.22.0+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.22.0+ds/include/gbwt/dynamic_gbwt.h:31, from remove_seq.cpp:28: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT boosting.lo -MD -MP -MF $depbase.Tpo -c -o boosting.lo boosting.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -fPIC -DPIC -o .libs/boosting.o ar rcs libgbwt.a algorithms.o bwtmerge.o cached_gbwt.o dynamic_gbwt.o files.o gbwt.o internal.o metadata.o support.o utils.o variants.o depbase=`echo ect.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -fPIC -DPIC -o .libs/ect.o [ 46%] Building CXX object CMakeFiles/vgio_static.dir/src/vpkg.cpp.o /usr/bin/g++ -I/<>/vg-1.22.0+ds/deps/libvgio/include -I/<>/vg-1.22.0+ds/deps/libvgio -I/<>/vg-1.22.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=gnu++14 -o CMakeFiles/vgio_static.dir/src/vpkg.cpp.o -c /<>/vg-1.22.0+ds/deps/libvgio/src/vpkg.cpp /usr/bin/g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -o build_gbwt build_gbwt.o libgbwt.a -L/<>/vg-1.22.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -o merge_gbwt merge_gbwt.o libgbwt.a -L/<>/vg-1.22.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -o benchmark benchmark.o libgbwt.a -L/<>/vg-1.22.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -o metadata_tool metadata_tool.o libgbwt.a -L/<>/vg-1.22.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 /usr/bin/g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.22.0+ds/include -I/<>/vg-1.22.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -o remove_seq remove_seq.o libgbwt.a -L/<>/vg-1.22.0+ds/lib -lsdsl -ldivsufsort -ldivsufsort64 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ [ 50%] 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/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/hfile_cppstream.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-1.22.0+ds/deps/libvgio' [ 50%] Built target vgio_static make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' cd /<>/vg-1.22.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= Dependee "/<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake" is newer than depender "/<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Dependee "/<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles/vgio.dir/depend.internal". Scanning dependencies of target vgio make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' [ 53%] Building CXX object CMakeFiles/vgio.dir/vg.pb.cc.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.22.0+ds/deps/libvgio/include -I/<>/vg-1.22.0+ds/deps/libvgio -I/<>/vg-1.22.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/vg.pb.cc.o -c /<>/vg-1.22.0+ds/deps/libvgio/vg.pb.cc make[3]: Leaving directory '/<>/vg-1.22.0+ds/deps/gbwt' [ 57%] Building CXX object CMakeFiles/vgio.dir/src/basic_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.22.0+ds/deps/libvgio/include -I/<>/vg-1.22.0+ds/deps/libvgio -I/<>/vg-1.22.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/basic_stream.cpp.o -c /<>/vg-1.22.0+ds/deps/libvgio/src/basic_stream.cpp 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ [ 61%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.22.0+ds/deps/libvgio/include -I/<>/vg-1.22.0+ds/deps/libvgio -I/<>/vg-1.22.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/blocked_gzip_input_stream.cpp.o -c /<>/vg-1.22.0+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp [ 65%] Building CXX object CMakeFiles/vgio.dir/src/blocked_gzip_output_stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.22.0+ds/deps/libvgio/include 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-D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT ect.lo -MD -MP -MF .deps/ect.Tpo -c ect.cc -o ect.o >/dev/null 2>&1 [ 73%] Building CXX object CMakeFiles/vgio.dir/src/message_emitter.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.22.0+ds/deps/libvgio/include -I/<>/vg-1.22.0+ds/deps/libvgio -I/<>/vg-1.22.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_emitter.cpp.o -c /<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT boosting.lo -MD -MP -MF .deps/boosting.Tpo -c boosting.cc -o boosting.o >/dev/null 2>&1 [ 76%] Building CXX object CMakeFiles/vgio.dir/src/message_iterator.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.22.0+ds/deps/libvgio/include -I/<>/vg-1.22.0+ds/deps/libvgio -I/<>/vg-1.22.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/message_iterator.cpp.o -c /<>/vg-1.22.0+ds/deps/libvgio/src/message_iterator.cpp [ 80%] Building CXX object CMakeFiles/vgio.dir/src/registry.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.22.0+ds/deps/libvgio/include -I/<>/vg-1.22.0+ds/deps/libvgio -I/<>/vg-1.22.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/registry.cpp.o -c /<>/vg-1.22.0+ds/deps/libvgio/src/registry.cpp [ 84%] Building CXX object CMakeFiles/vgio.dir/src/stream.cpp.o /usr/bin/g++ -Dvgio_EXPORTS -I/<>/vg-1.22.0+ds/deps/libvgio/include -I/<>/vg-1.22.0+ds/deps/libvgio -I/<>/vg-1.22.0+ds/deps/libvgio/src -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -fPIC -std=gnu++14 -o CMakeFiles/vgio.dir/src/stream.cpp.o -c /<>/vg-1.22.0+ds/deps/libvgio/src/stream.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT marginal.lo -MD -MP -MF $depbase.Tpo -c -o marginal.lo marginal.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -fPIC -DPIC -o .libs/marginal.o [ 88%] Building CXX object 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/<>/vg-1.22.0+ds/deps/libvgio/src/vpkg.cpp depbase=`echo autolink.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT autolink.lo -MD -MP -MF $depbase.Tpo -c -o autolink.lo autolink.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -fPIC -DPIC -o .libs/autolink.o depbase=`echo binary.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -fPIC -DPIC -o .libs/binary.o [ 96%] 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvgio.so -o libvgio.so CMakeFiles/vgio.dir/vg.pb.cc.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/hfile_cppstream.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 -lprotobuf -lhts 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' [100%] Built target vgio make[4]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles 0 make[3]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' make[3]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' /usr/bin/cmake -S/<>/vg-1.22.0+ds/deps/libvgio -B/<>/vg-1.22.0+ds/deps/libvgio --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles /<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/depend make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' cd /<>/vg-1.22.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles/link_target.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' make -f CMakeFiles/link_target.dir/build.make CMakeFiles/link_target.dir/build make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' /usr/bin/cmake -E create_symlink . vg make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' [ 0%] Built target link_target make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/depend make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' cd /<>/vg-1.22.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles/vgio_static.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' make -f CMakeFiles/vgio_static.dir/build.make CMakeFiles/vgio_static.dir/build make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio_static.dir/build'. make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' [ 50%] Built target vgio_static make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/depend make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' cd /<>/vg-1.22.0+ds/deps/libvgio && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio /<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles/vgio.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' make -f CMakeFiles/vgio.dir/build.make CMakeFiles/vgio.dir/build make[5]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' make[5]: Nothing to be done for 'CMakeFiles/vgio.dir/build'. make[5]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' [100%] Built target vgio make[4]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' /usr/bin/cmake -E cmake_progress_start /<>/vg-1.22.0+ds/deps/libvgio/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/<>/vg-1.22.0+ds/deps/libvgio' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "" -- Installing: /<>/vg-1.22.0+ds/lib/libvgio.so -- Installing: /<>/vg-1.22.0+ds/lib/libvgio.a -- Up-to-date: /<>/vg-1.22.0+ds/include -- Installing: /<>/vg-1.22.0+ds/include/vg -- Installing: /<>/vg-1.22.0+ds/include/vg/io -- Installing: /<>/vg-1.22.0+ds/include/vg/io/blocked_gzip_output_stream.hpp -- Installing: /<>/vg-1.22.0+ds/include/vg/io/vpkg.hpp -- Installing: /<>/vg-1.22.0+ds/include/vg/io/message_emitter.hpp -- Installing: /<>/vg-1.22.0+ds/include/vg/io/registry.hpp -- Installing: /<>/vg-1.22.0+ds/include/vg/io/message_iterator.hpp -- Installing: /<>/vg-1.22.0+ds/include/vg/io/stream_multiplexer.hpp -- Installing: /<>/vg-1.22.0+ds/include/vg/io/hfile_internal.hpp -- Installing: /<>/vg-1.22.0+ds/include/vg/io/protobuf_iterator.hpp -- Installing: /<>/vg-1.22.0+ds/include/vg/io/stream.hpp -- Installing: /<>/vg-1.22.0+ds/include/vg/io/loader.hpp -- Installing: /<>/vg-1.22.0+ds/include/vg/io/protobuf_emitter.hpp -- Installing: /<>/vg-1.22.0+ds/include/vg/io/fdstream.hpp -- Installing: /<>/vg-1.22.0+ds/include/vg/io/hfile_cppstream.hpp -- Installing: /<>/vg-1.22.0+ds/include/vg/io/basic_stream.hpp -- Installing: /<>/vg-1.22.0+ds/include/vg/io/blocked_gzip_input_stream.hpp -- Installing: /<>/vg-1.22.0+ds/include/vg/vg.pb.h -- Installing: /<>/vg-1.22.0+ds/lib/cmake/VGio/VGioTargets.cmake -- Installing: /<>/vg-1.22.0+ds/lib/cmake/VGio/VGioTargets-noconfig.cmake -- Installing: /<>/vg-1.22.0+ds/lib/cmake/VGio/VGioConfig.cmake -- Installing: /<>/vg-1.22.0+ds/lib/cmake/VGio/VGioConfigVersion.cmake make[3]: Leaving directory '/<>/vg-1.22.0+ds/deps/libvgio' . ./source_me.sh && rm -Rf /<>/vg-1.22.0+ds/include/bdsg && cd deps/libbdsg && make clean && CPLUS_INCLUDE_PATH=/<>/vg-1.22.0+ds/include:/<>/vg-1.22.0+ds/include/dynamic: CXXFLAGS="-I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp" make && cp lib/libbdsg.a /<>/vg-1.22.0+ds/lib && pwd && cp -r include/bdsg /<>/vg-1.22.0+ds/include make[3]: Entering directory '/<>/vg-1.22.0+ds/deps/libbdsg' rm -r obj rm -r lib rm -r bin make[3]: Leaving directory '/<>/vg-1.22.0+ds/deps/libbdsg' make[3]: Entering directory '/<>/vg-1.22.0+ds/deps/libbdsg' g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -fopenmp -c src/eades_algorithm.cpp -o obj/eades_algorithm.o 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -fopenmp -c src/hash_graph.cpp -o obj/hash_graph.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT binary.lo -MD -MP -MF .deps/binary.Tpo -c binary.cc -o binary.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT autolink.lo -MD -MP -MF .deps/autolink.Tpo -c autolink.cc -o autolink.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT marginal.lo -MD -MP -MF .deps/marginal.Tpo -c marginal.cc -o marginal.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -fopenmp -c src/is_single_stranded.cpp -o obj/is_single_stranded.o 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -fPIC -DPIC -o .libs/cost_sensitive.o g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -fopenmp -c src/node.cpp -o obj/node.o 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT lrq.lo -MD -MP -MF .deps/lrq.Tpo -c lrq.cc -o lrq.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT cost_sensitive.lo -MD -MP -MF .deps/cost_sensitive.Tpo -c cost_sensitive.cc -o cost_sensitive.o >/dev/null 2>&1 g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -fopenmp -c src/odgi.cpp -o obj/odgi.o g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -fopenmp -c src/packed_graph.cpp -o obj/packed_graph.o 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -fPIC -DPIC -o .libs/multilabel.o 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -fPIC -DPIC -o .libs/label_dictionary.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT multilabel.lo -MD -MP -MF .deps/multilabel.Tpo -c multilabel.cc -o multilabel.o >/dev/null 2>&1 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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:149:5: 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 | ^~~~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT label_dictionary.lo -MD -MP -MF .deps/label_dictionary.Tpo -c label_dictionary.cc -o label_dictionary.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -fPIC -DPIC -o .libs/csoaa.o g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -fopenmp -c src/packed_structs.cpp -o obj/packed_structs.o 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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:57:5: 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 | ^~~~~~~~~ g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -fopenmp -c src/path_position_overlays.cpp -o obj/path_position_overlays.o 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -fPIC -DPIC -o .libs/cb.o g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -fopenmp -c src/packed_path_position_overlays.cpp -o obj/packed_path_position_overlays.o 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++/9/memory:81, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, from memory.h:5, from v_array.h:21, from example.h:10, from cb.cc:8: /usr/include/c++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -fopenmp -c src/vectorizable_overlays.cpp -o obj/vectorizable_overlays.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT cb.lo -MD -MP -MF .deps/cb.Tpo -c cb.cc -o cb.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT csoaa.lo -MD -MP -MF .deps/csoaa.Tpo -c csoaa.cc -o csoaa.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT cb_adf.lo -MD -MP -MF .deps/cb_adf.Tpo -c cb_adf.cc -fPIC -DPIC -o .libs/cb_adf.o g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -fopenmp -c src/split_strand_graph.cpp -o obj/split_strand_graph.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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -Iinclude -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -fopenmp -c src/utility.cpp -o obj/utility.o 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT cb_algs.lo -MD -MP -MF $depbase.Tpo -c -o cb_algs.lo cb_algs.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT cb_algs.lo -MD -MP -MF .deps/cb_algs.Tpo -c cb_algs.cc -fPIC -DPIC -o .libs/cb_algs.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT search.lo -MD -MP -MF $depbase.Tpo -c -o search.lo search.cc &&\ mv -f $depbase.Tpo $depbase.Plo 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_overlays.o obj/vectorizable_overlays.o obj/split_strand_graph.o obj/utility.o ar: creating lib/libbdsg.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -fPIC -DPIC -o .libs/search.o make[3]: Leaving directory '/<>/vg-1.22.0+ds/deps/libbdsg' /<>/vg-1.22.0+ds/deps/libbdsg rm -f lib/libxg.a cp -r deps/xg/src/*.hpp /<>/vg-1.22.0+ds/include . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -c -o deps/xg/xg.o deps/xg/src/xg.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::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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/bits/stl_algobase.h:64, from /usr/include/c++/9/bits/char_traits.h:39, from /usr/include/c++/9/ios:40, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair’ declared here 208 | 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++/9/bits/stl_algobase.h:64, from /usr/include/c++/9/bits/char_traits.h:39, from /usr/include/c++/9/ios:40, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair’ declared here 208 | 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++/9/bits/stl_algobase.h:64, from /usr/include/c++/9/bits/char_traits.h:39, from /usr/include/c++/9/ios:40, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair’ declared here 208 | 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++/9/bits/stl_algobase.h:64, from /usr/include/c++/9/bits/char_traits.h:39, from /usr/include/c++/9/ios:40, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iostream:39, from global_data.h:8, from vw.h:15, from search.cc:9: /usr/include/c++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair’ declared here 208 | 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:932:5: 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 | ^~~~~~~~~~~~~ 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:71:5: 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:83:17: 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 | ^~~~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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_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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -fPIC -DPIC -o .libs/search_meta.o 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++/9/bits/stl_algobase.h:64, from /usr/include/c++/9/bits/char_traits.h:39, from /usr/include/c++/9/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++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair’ declared here 208 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/bits/stl_algobase.h:64, from /usr/include/c++/9/bits/char_traits.h:39, from /usr/include/c++/9/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++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair > >’ declared here 208 | 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++/9/bits/stl_algobase.h:64, from /usr/include/c++/9/bits/char_traits.h:39, from /usr/include/c++/9/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++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair > >’ declared here 208 | 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++/9/bits/stl_algobase.h:64, from /usr/include/c++/9/bits/char_traits.h:39, from /usr/include/c++/9/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++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 208 | 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++/9/bits/stl_algobase.h:64, from /usr/include/c++/9/bits/char_traits.h:39, from /usr/include/c++/9/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++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair > >, std::__cxx11::basic_string*>’ declared here 208 | 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++/9/bits/stl_algobase.h:64, from /usr/include/c++/9/bits/char_traits.h:39, from /usr/include/c++/9/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++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair’ declared here 208 | 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++/9/bits/stl_algobase.h:64, from /usr/include/c++/9/bits/char_traits.h:39, from /usr/include/c++/9/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++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair’ declared here 208 | struct pair | ^~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -fPIC -DPIC -o .libs/search_sequencetask.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT search_meta.lo -MD -MP -MF .deps/search_meta.Tpo -c search_meta.cc -o search_meta.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT search.lo -MD -MP -MF .deps/search.Tpo -c search.cc -o search.o >/dev/null 2>&1 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT search_sequencetask.lo -MD -MP -MF .deps/search_sequencetask.Tpo -c search_sequencetask.cc -o search_sequencetask.o >/dev/null 2>&1 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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++/9/bits/stl_algobase.h:64, from /usr/include/c++/9/bits/char_traits.h:39, from /usr/include/c++/9/ios:40, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/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++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair’ declared here 208 | 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++/9/bits/stl_algobase.h:64, from /usr/include/c++/9/bits/char_traits.h:39, from /usr/include/c++/9/ios:40, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/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++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair’ declared here 208 | struct pair | ^~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT search_hooktask.lo -MD -MP -MF $depbase.Tpo -c -o search_hooktask.lo search_hooktask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -fPIC -DPIC -o .libs/search_hooktask.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT search_dep_parser.lo -MD -MP -MF .deps/search_dep_parser.Tpo -c search_dep_parser.cc -o search_dep_parser.o >/dev/null 2>&1 depbase=`echo search_multiclasstask.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT search_multiclasstask.lo -MD -MP -MF .deps/search_multiclasstask.Tpo -c search_multiclasstask.cc -fPIC -DPIC -o .libs/search_multiclasstask.o 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT search_hooktask.lo -MD -MP -MF .deps/search_hooktask.Tpo -c search_hooktask.cc -o search_hooktask.o >/dev/null 2>&1 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT search_entityrelationtask.lo -MD -MP -MF $depbase.Tpo -c -o search_entityrelationtask.lo search_entityrelationtask.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -fPIC -DPIC -o .libs/search_entityrelationtask.o depbase=`echo search_graph.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ ar rs lib/libxg.a deps/xg/xg.o ar: creating lib/libxg.a . ./source_me.sh && cp -r deps/gbwtgraph/include/gbwtgraph /<>/vg-1.22.0+ds/include/ && cd deps/gbwtgraph && make clean && make && mv libgbwtgraph.a /<>/vg-1.22.0+ds/lib make[3]: Entering directory '/<>/vg-1.22.0+ds/deps/gbwtgraph' rm -f utils.o gfa2gbwt.o gfa.o path_cover.o gbwtgraph.o minimizer.o libgbwtgraph.a gfa2gbwt make[3]: Leaving directory '/<>/vg-1.22.0+ds/deps/gbwtgraph' make[3]: Entering directory '/<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c gbwtgraph.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT search_entityrelationtask.lo -MD -MP -MF .deps/search_entityrelationtask.Tpo -c search_entityrelationtask.cc -o search_entityrelationtask.o >/dev/null 2>&1 In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from /<>/vg-1.22.0+ds/include/gbwt/support.h:29, from /<>/vg-1.22.0+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.22.0+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.22.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gbwtgraph.cpp:1: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT parse_example.lo -MD -MP -MF .deps/parse_example.Tpo -c parse_example.cc -o parse_example.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c gfa.cpp In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from /<>/vg-1.22.0+ds/include/gbwt/support.h:29, from /<>/vg-1.22.0+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.22.0+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.22.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/gfa.h:6, from gfa.cpp:1: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT scorer.lo -MD -MP -MF $depbase.Tpo -c -o scorer.lo scorer.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -fPIC -DPIC -o .libs/scorer.o depbase=`echo network.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT network.lo -MD -MP -MF $depbase.Tpo -c -o network.lo network.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -fPIC -DPIC -o .libs/network.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c minimizer.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT network.lo -MD -MP -MF .deps/network.Tpo -c network.cc -o network.o >/dev/null 2>&1 depbase=`echo parse_args.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -fPIC -DPIC -o .libs/parse_args.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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from include/gbwtgraph/minimizer.h:11, from minimizer.cpp:1: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1442:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1442 | inline auto | ^~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -fPIC -DPIC -o .libs/accumulate.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c path_cover.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT scorer.lo -MD -MP -MF .deps/scorer.Tpo -c scorer.cc -o scorer.o >/dev/null 2>&1 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from /<>/vg-1.22.0+ds/include/gbwt/support.h:29, from /<>/vg-1.22.0+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.22.0+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.22.0+ds/include/gbwt/dynamic_gbwt.h:31, from include/gbwtgraph/path_cover.h:4, from path_cover.cpp:1: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+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 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT accumulate.lo -MD -MP -MF .deps/accumulate.Tpo -c accumulate.cc -o accumulate.o >/dev/null 2>&1 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -fPIC -DPIC -o .libs/learner.o /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -c utils.cpp 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ /usr/bin/g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT learner.lo -MD -MP -MF .deps/learner.Tpo -c learner.cc -o learner.o >/dev/null 2>&1 In file included from /<>/vg-1.22.0+ds/include/sdsl/bit_vectors.hpp:8, from /<>/vg-1.22.0+ds/include/gbwt/utils.h:35, from /<>/vg-1.22.0+ds/include/gbwt/support.h:29, from /<>/vg-1.22.0+ds/include/gbwt/algorithms.h:31, from /<>/vg-1.22.0+ds/include/gbwt/gbwt.h:29, from /<>/vg-1.22.0+ds/include/gbwt/cached_gbwt.h:29, from include/gbwtgraph/gbwtgraph.h:6, from gfa2gbwt.cpp:6: /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1402:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1402 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1410:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1410 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1418:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1418 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1426:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1426 | inline auto | ^~~~ /<>/vg-1.22.0+ds/include/sdsl/int_vector.hpp:1434:8: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 1434 | inline auto | ^~~~ /<>/vg-1.22.0+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 gbwtgraph.o gfa.o minimizer.o path_cover.o utils.o /usr/bin/g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -fopenmp -pthread -O3 -ffast-math -funroll-loops -DHAVE_CXA_DEMANGLE -Iinclude -I/<>/vg-1.22.0+ds/include -o gfa2gbwt gfa2gbwt.o libgbwtgraph.a -L/<>/vg-1.22.0+ds/lib -lgbwt -lhandlegraph -lsdsl -ldivsufsort -ldivsufsort64 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT mwt.lo -MD -MP -MF $depbase.Tpo -c -o mwt.lo mwt.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -fPIC -DPIC -o .libs/mwt.o make[3]: Leaving directory '/<>/vg-1.22.0+ds/deps/gbwtgraph' depbase=`echo lda_core.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -fPIC -DPIC -o .libs/lda_core.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT parse_args.lo -MD -MP -MF .deps/parse_args.Tpo -c parse_args.cc -o parse_args.o >/dev/null 2>&1 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT mwt.lo -MD -MP -MF .deps/mwt.Tpo -c mwt.cc -o mwt.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT lda_core.lo -MD -MP -MF .deps/lda_core.Tpo -c lda_core.cc -o lda_core.o >/dev/null 2>&1 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT gd_mf.lo -MD -MP -MF $depbase.Tpo -c -o gd_mf.lo gd_mf.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -fPIC -DPIC -o .libs/gd_mf.o depbase=`echo mf.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -fPIC -DPIC -o .libs/mf.o 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT mf.lo -MD -MP -MF .deps/mf.Tpo -c mf.cc -o mf.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT gd_mf.lo -MD -MP -MF .deps/gd_mf.Tpo -c gd_mf.cc -o gd_mf.o >/dev/null 2>&1 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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: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: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: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: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: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) | ^~~~~ 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -fPIC -DPIC -o .libs/noop.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT gd.lo -MD -MP -MF .deps/gd.Tpo -c gd.cc -o gd.o >/dev/null 2>&1 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -fPIC -DPIC -o .libs/print.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT noop.lo -MD -MP -MF .deps/noop.Tpo -c noop.cc -o noop.o >/dev/null 2>&1 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT bfgs.lo -MD -MP -MF .deps/bfgs.Tpo -c bfgs.cc -o bfgs.o >/dev/null 2>&1 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -fPIC -DPIC -o .libs/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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT print.lo -MD -MP -MF .deps/print.Tpo -c print.cc -o print.o >/dev/null 2>&1 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT example.lo -MD -MP -MF .deps/example.Tpo -c example.cc -o example.o >/dev/null 2>&1 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -fPIC -DPIC -o .libs/parser.o 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT loss_functions.lo -MD -MP -MF $depbase.Tpo -c -o loss_functions.lo loss_functions.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo sender.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -fPIC -DPIC -o .libs/loss_functions.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -fPIC -DPIC -o .libs/sender.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++/9/memory:81, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, from memory.h:5, from v_array.h:21, from io_buf.h:14, from sender.cc:18: /usr/include/c++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT loss_functions.lo -MD -MP -MF .deps/loss_functions.Tpo -c loss_functions.cc -o loss_functions.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT sender.lo -MD -MP -MF .deps/sender.Tpo -c sender.cc -o sender.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT parser.lo -MD -MP -MF .deps/parser.Tpo -c parser.cc -o parser.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT nn.lo -MD -MP -MF $depbase.Tpo -c -o nn.lo nn.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -fPIC -DPIC -o .libs/nn.o depbase=`echo confidence.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT confidence.lo -MD -MP -MF .deps/confidence.Tpo -c confidence.cc -o confidence.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT nn.lo -MD -MP -MF .deps/nn.Tpo -c nn.cc -o nn.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT bs.lo -MD -MP -MF $depbase.Tpo -c -o bs.lo bs.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -fPIC -DPIC -o .libs/bs.o depbase=`echo cbify.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -fPIC -DPIC -o .libs/cbify.o 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT bs.lo -MD -MP -MF .deps/bs.Tpo -c bs.cc -o bs.o >/dev/null 2>&1 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT explore_eval.lo -MD -MP -MF .deps/explore_eval.Tpo -c explore_eval.cc -fPIC -DPIC -o .libs/explore_eval.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT cbify.lo -MD -MP -MF .deps/cbify.Tpo -c cbify.cc -o cbify.o >/dev/null 2>&1 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -fPIC -DPIC -o .libs/topk.o 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT topk.lo -MD -MP -MF .deps/topk.Tpo -c topk.cc -o topk.o >/dev/null 2>&1 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -fPIC -DPIC -o .libs/log_multi.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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT recall_tree.lo -MD -MP -MF .deps/recall_tree.Tpo -c recall_tree.cc -fPIC -DPIC -o .libs/recall_tree.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT log_multi.lo -MD -MP -MF .deps/log_multi.Tpo -c log_multi.cc -o log_multi.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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT active_cover.lo -MD -MP -MF $depbase.Tpo -c -o active_cover.lo active_cover.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -fPIC -DPIC -o .libs/active_cover.o depbase=`echo cs_active.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT cs_active.lo -MD -MP -MF $depbase.Tpo -c -o cs_active.lo cs_active.cc &&\ mv -f $depbase.Tpo $depbase.Plo 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT kernel_svm.lo -MD -MP -MF $depbase.Tpo -c -o kernel_svm.lo kernel_svm.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -fPIC -DPIC -o .libs/kernel_svm.o depbase=`echo best_constant.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT best_constant.lo -MD -MP -MF .deps/best_constant.Tpo -c best_constant.cc -fPIC -DPIC -o .libs/best_constant.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT active_cover.lo -MD -MP -MF .deps/active_cover.Tpo -c active_cover.cc -o active_cover.o >/dev/null 2>&1 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT ftrl.lo -MD -MP -MF $depbase.Tpo -c -o ftrl.lo ftrl.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -fPIC -DPIC -o .libs/ftrl.o depbase=`echo svrg.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT kernel_svm.lo -MD -MP -MF .deps/kernel_svm.Tpo -c kernel_svm.cc -o kernel_svm.o >/dev/null 2>&1 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -fPIC -DPIC -o .libs/lrqfa.o 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT ftrl.lo -MD -MP -MF .deps/ftrl.Tpo -c ftrl.cc -o ftrl.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT lrqfa.lo -MD -MP -MF .deps/lrqfa.Tpo -c lrqfa.cc -o lrqfa.o >/dev/null 2>&1 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -fPIC -DPIC -o .libs/interact.o 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT comp_io.lo -MD -MP -MF $depbase.Tpo -c -o comp_io.lo comp_io.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -fPIC -DPIC -o .libs/comp_io.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT interact.lo -MD -MP -MF .deps/interact.Tpo -c interact.cc -o interact.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT comp_io.lo -MD -MP -MF .deps/comp_io.Tpo -c comp_io.cc -o comp_io.o >/dev/null 2>&1 depbase=`echo interactions.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT interactions.lo -MD -MP -MF $depbase.Tpo -c -o interactions.lo interactions.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -fPIC -DPIC -o .libs/interactions.o depbase=`echo vw_exception.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT vw_exception.lo -MD -MP -MF $depbase.Tpo -c -o vw_exception.lo vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -fPIC -DPIC -o .libs/vw_exception.o depbase=`echo vw_validate.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT vw_validate.lo -MD -MP -MF $depbase.Tpo -c -o vw_validate.lo vw_validate.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT vw_validate.lo -MD -MP -MF .deps/vw_validate.Tpo -c vw_validate.cc -fPIC -DPIC -o .libs/vw_validate.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT vw_exception.lo -MD -MP -MF .deps/vw_exception.Tpo -c vw_exception.cc -o vw_exception.o >/dev/null 2>&1 depbase=`echo audit_regressor.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -fPIC -DPIC -o .libs/audit_regressor.o 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT interactions.lo -MD -MP -MF .deps/interactions.Tpo -c interactions.cc -o interactions.o >/dev/null 2>&1 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT cb_explore.lo -MD -MP -MF $depbase.Tpo -c -o cb_explore.lo cb_explore.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT gen_cs_example.lo -MD -MP -MF .deps/gen_cs_example.Tpo -c gen_cs_example.cc -o gen_cs_example.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -fPIC -DPIC -o .libs/cb_explore.o depbase=`echo action_score.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT action_score.lo -MD -MP -MF $depbase.Tpo -c -o action_score.lo action_score.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -fPIC -DPIC -o .libs/action_score.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT action_score.lo -MD -MP -MF .deps/action_score.Tpo -c action_score.cc -o action_score.o >/dev/null 2>&1 depbase=`echo cb_explore_adf.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 | ^~~~~~~ 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT audit_regressor.lo -MD -MP -MF .deps/audit_regressor.Tpo -c audit_regressor.cc -o audit_regressor.o >/dev/null 2>&1 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -fPIC -DPIC -o .libs/OjaNewton.o 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT cb_explore.lo -MD -MP -MF .deps/cb_explore.Tpo -c cb_explore.cc -o cb_explore.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT parse_example_json.lo -MD -MP -MF $depbase.Tpo -c -o parse_example_json.lo parse_example_json.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -fPIC -DPIC -o .libs/parse_example_json.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT parse_example_json.lo -MD -MP -MF .deps/parse_example_json.Tpo -c parse_example_json.cc -o parse_example_json.o >/dev/null 2>&1 depbase=`echo baseline.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT OjaNewton.lo -MD -MP -MF .deps/OjaNewton.Tpo -c OjaNewton.cc -o OjaNewton.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT classweight.lo -MD -MP -MF $depbase.Tpo -c -o classweight.lo classweight.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -fPIC -DPIC -o .libs/classweight.o depbase=`echo allreduce_sockets.lo | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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++/9/memory:81, 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++/9/bits/shared_ptr.h:103:11: note: ‘class std::shared_ptr, std::__cxx11::basic_string > >’ declared here 103 | 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT allreduce_threads.lo -MD -MP -MF $depbase.Tpo -c -o allreduce_threads.lo allreduce_threads.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/include -Wall -Wno-unused-local-typedefs -pedantic -I /usr/include/rapidjson -O3 -fomit-frame-pointer -DNDEBUG -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT allreduce_threads.lo -MD -MP -MF .deps/allreduce_threads.Tpo -c allreduce_threads.cc -fPIC -DPIC -o .libs/allreduce_threads.o depbase=`echo active_interactor.o | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT classweight.lo -MD -MP -MF .deps/classweight.Tpo -c classweight.cc -o classweight.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o active_interactor active_interactor.o -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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/9/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/9/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-1.22.0+ds/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/9 -L/usr/lib/gcc/aarch64-linux-gnu/9/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/9/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/<>/vg-1.22.0+ds/lib -L. -L/usr/lib/gcc/aarch64-linux-gnu/9/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/9/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/9/../../../aarch64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,liballreduce.so.0 -o .libs/liballreduce.so.0.0.0 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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/9/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/9/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-1.22.0+ds/deps/vowpal_wabbit/vowpalwabbit/.libs ./.libs/liballreduce.so -L/usr/lib -lboost_program_options -L/lib -lz -lpthread -L/<>/vg-1.22.0+ds/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/9 -L/usr/lib/gcc/aarch64-linux-gnu/9/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/9/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/<>/vg-1.22.0+ds/lib -L. -L/usr/lib/gcc/aarch64-linux-gnu/9/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/9/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/9/../../../aarch64-linux-gnu/crtn.o -O3 -O3 -ggdb -g -g -O2 -fstack-protector-strong -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libvw.so.0 -o .libs/libvw.so.0.0.0 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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -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-1.22.0+ds/deps/vowpal_wabbit/vowpalwabbit' make[4]: Leaving directory '/<>/vg-1.22.0+ds/deps/vowpal_wabbit/vowpalwabbit' Making all in cluster make[4]: Entering directory '/<>/vg-1.22.0+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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -MT ../vowpalwabbit/vw_exception.o -MD -MP -MF $depbase.Tpo -c -o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/vw_exception.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/bash ../libtool --tag=CXX --mode=link g++ -I/usr/include -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib -lboost_program_options -L/lib -lz -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o ../vowpalwabbit/liballreduce.la libtool: link: g++ -I/usr/include -I/include -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/spanning_tree spanning_tree_main.o ../vowpalwabbit/spanning_tree.o ../vowpalwabbit/vw_exception.o -L/usr/lib -lboost_program_options -L/lib -lz -lpthread ../vowpalwabbit/.libs/liballreduce.so make[4]: Leaving directory '/<>/vg-1.22.0+ds/deps/vowpal_wabbit/cluster' Making all in library make[4]: Entering directory '/<>/vg-1.22.0+ds/deps/vowpal_wabbit/library' depbase=`echo library_example.o | sed 's|[^/]*$|.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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib -lboost_program_options -L/lib -lz -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib -lboost_program_options -L/lib -lz -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib -lboost_program_options -L/lib -lz -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -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-1.22.0+ds/deps/vowpal_wabbit/library' make[4]: Entering directory '/<>/vg-1.22.0+ds/deps/vowpal_wabbit' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/<>/vg-1.22.0+ds/deps/vowpal_wabbit' make[3]: Leaving directory '/<>/vg-1.22.0+ds/deps/vowpal_wabbit' . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/.libs/libvw.a vowpalwabbit/.libs/liballreduce.a /<>/vg-1.22.0+ds/lib/ . ./source_me.sh && cd deps/vowpal_wabbit && mkdir -p /<>/vg-1.22.0+ds/include/vowpalwabbit . ./source_me.sh && cd deps/vowpal_wabbit && cp vowpalwabbit/*.h /<>/vg-1.22.0+ds/include/vowpalwabbit/ . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/main.o src/main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/json2pb.o src/json2pb.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/augment.o src/augment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/multipath_mapper.o src/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/utility.o src/utility.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/chunker.o src/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/stream_sorter.o src/stream_sorter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/path.o src/path.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/haplotype_extracter.o src/haplotype_extracter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/readfilter.o src/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/split_strand_graph.o src/split_strand_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/version.o src/version.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/graph.o src/graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/edit.o src/edit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/packer.o src/packer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/small_snarl_simplifier.o src/small_snarl_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/traversal_support.o src/traversal_support.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/feature_set.o src/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/filter.o src/filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/mem.o src/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/phased_genome.o src/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/translator.o src/translator.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/region.o src/region.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/snarls.o src/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/region_expander.o src/region_expander.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/transcriptome.o src/transcriptome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/graph_synchronizer.o src/graph_synchronizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/graph_caller.o src/graph_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/mapper.o src/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/ssw_aligner.o src/ssw_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/genotypekit.o src/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/extra_node_graph.o src/extra_node_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/watchdog.o src/watchdog.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/prune.o src/prune.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/progressive.o src/progressive.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/subgraph_overlay.o src/subgraph_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/constructor.o src/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/gfa.o src/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/min_distance.o src/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/source_sink_overlay.o src/source_sink_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/viz.o src/viz.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/proto_handle_graph.o src/proto_handle_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/aligner.o src/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/funnel.o src/funnel.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/variant_recall.o src/variant_recall.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/memoizing_graph.o src/memoizing_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/name_mapper.o src/name_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/vg.o src/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/traversal_finder.o src/traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/indexed_vg.o src/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/option.o src/option.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/stream_index.o src/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/vcf_buffer.o src/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/build_index.o src/build_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/identity_overlay.o src/identity_overlay.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/vg_set.o src/vg_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/alignment.o src/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/path_component_index.o src/path_component_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/flow_sort.o src/flow_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/haplotypes.o src/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/multipath_alignment.o src/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/path_index.o src/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/genotyper.o src/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/msa_converter.o src/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/deconstructor.o src/deconstructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/nested_traversal_finder.o src/nested_traversal_finder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/seed_clusterer.o src/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/rare_variant_simplifier.o src/rare_variant_simplifier.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/scanner.o src/scanner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/variant_adder.o src/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/gapless_extender.o src/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/homogenizer.o src/homogenizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/gff_reader.o src/gff_reader.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/preflight.o src/preflight.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/srpe.o src/srpe.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/cluster.o src/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/genome_state.o src/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/kmer.o src/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/snarl_caller.o src/snarl_caller.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/memusage.o src/memusage.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/mcmc_genotyper.o src/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/phase_unfolder.o src/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/dagified_graph.o src/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/multipath_alignment_graph.o src/multipath_alignment_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/cactus.o src/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/reverse_graph.o src/reverse_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/convert_handle.o src/convert_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/sampler.o src/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/entropy.o src/entropy.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/tree_subgraph.o src/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/index.o src/index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/crash.o src/crash.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/subgraph.o src/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/minimizer_mapper.o src/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/vectorizer.o src/vectorizer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/xdrop_aligner.o src/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/alignment_emitter.o src/alignment_emitter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/benchmark.o src/benchmark.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/surjector.o src/surjector.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/position.o src/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/banded_global_aligner.o src/banded_global_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/null_masking_graph.o src/null_masking_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/statistics.o src/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/path_subgraph.o src/path_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/gbwt_helper.o src/gbwt_helper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/split_strands.o src/algorithms/split_strands.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/reverse_complement.o src/algorithms/reverse_complement.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/shortest_cycle.o src/algorithms/shortest_cycle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/normalize.o src/algorithms/normalize.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/dijkstra.o src/algorithms/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/kmer.o src/algorithms/kmer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/dfs.o src/algorithms/dfs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/coverage_depth.o src/algorithms/coverage_depth.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/is_acyclic.o src/algorithms/is_acyclic.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/are_equivalent.o src/algorithms/are_equivalent.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/subgraph.o src/algorithms/subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/merge.o src/algorithms/merge.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/expand_context.o src/algorithms/expand_context.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/to_gfa.o src/algorithms/to_gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/dagify.o src/algorithms/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/count_walks.o src/algorithms/count_walks.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/simplify_siblings.o src/algorithms/simplify_siblings.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/walk.o src/algorithms/walk.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/path_string.o src/algorithms/path_string.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/id_sort.o src/algorithms/id_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/extend.o src/algorithms/extend.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/unchop.o src/algorithms/unchop.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/eades_algorithm.o src/algorithms/eades_algorithm.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/topological_sort.o src/algorithms/topological_sort.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/algorithms/copy_graph.o src/algorithms/copy_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/io/register_loader_saver_gbwtgraph.o src/io/register_loader_saver_gbwtgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/variant_adder.o src/unittest/variant_adder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/statistics.o src/unittest/statistics.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/haplotypes.o src/unittest/haplotypes.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/snarls.o src/unittest/snarls.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/mapper.o src/unittest/mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/tree_subgraph.o src/unittest/tree_subgraph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/dijkstra.o src/unittest/dijkstra.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/cluster.o src/unittest/cluster.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/alignment.o src/unittest/alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/overlays.o src/unittest/overlays.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/vcf_buffer.o src/unittest/vcf_buffer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/constructor.o src/unittest/constructor.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/handle.o src/unittest/handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/chunker.o src/unittest/chunker.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/mcmc_genotyper.o src/unittest/mcmc_genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/phase_unfolder.o src/unittest/phase_unfolder.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/mapping.o src/unittest/mapping.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/cactus.o src/unittest/cactus.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/genotypekit.o src/unittest/genotypekit.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/driver.o src/unittest/driver.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/mem.o src/unittest/mem.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/phased_genome.o src/unittest/phased_genome.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/position.o src/unittest/position.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/pinned_alignment.o src/unittest/pinned_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/minimizer_mapper.o src/unittest/minimizer_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/xdrop_aligner.o src/unittest/xdrop_aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/random_graph.o src/unittest/random_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/gfa.o src/unittest/gfa.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/stream.o src/unittest/stream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/dagify.o src/unittest/dagify.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/vg.o src/unittest/vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/packed_graph.o src/unittest/packed_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/multipath_mapper.o src/unittest/multipath_mapper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/multipath_alignment.o src/unittest/multipath_alignment.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/vpkg.o src/unittest/vpkg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/min_distance.o src/unittest/min_distance.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/seed_clusterer.o src/unittest/seed_clusterer.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/vg_algorithms.o src/unittest/vg_algorithms.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/indexed_vg.o src/unittest/indexed_vg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/distributions.o src/unittest/distributions.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/readfilter.o src/unittest/readfilter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/stream_index.o src/unittest/stream_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/annotation.o src/unittest/annotation.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/sampler.o src/unittest/sampler.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/xg.o src/unittest/xg.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/hfile_cppstream.o src/unittest/hfile_cppstream.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/gapless_extender.o src/unittest/gapless_extender.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/genotyper.o src/unittest/genotyper.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/convert_handle.o src/unittest/convert_handle.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/dagified_graph.o src/unittest/dagified_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/hash_graph.o src/unittest/hash_graph.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/feature_set.o src/unittest/feature_set.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/aligner.o src/unittest/aligner.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/genome_state.o src/unittest/genome_state.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/srpe_filter.o src/unittest/srpe_filter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/path_index.o src/unittest/path_index.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/msa_converter.o src/unittest/msa_converter.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/surject.o src/unittest/surject.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -c -o obj/unittest/packed_structs.o src/unittest/packed_structs.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/mod_main.o src/subcommand/mod_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/mcmc_main.o src/subcommand/mcmc_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/circularize_main.o src/subcommand/circularize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/help_main.o src/subcommand/help_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/explode_main.o src/subcommand/explode_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/depth_main.o src/subcommand/depth_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/version_main.o src/subcommand/version_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/index_main.o src/subcommand/index_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/snarls_main.o src/subcommand/snarls_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/rna_main.o src/subcommand/rna_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/annotate_main.o src/subcommand/annotate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/test_main.o src/subcommand/test_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/pack_main.o src/subcommand/pack_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/dotplot_main.o src/subcommand/dotplot_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/crash_main.o src/subcommand/crash_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/ids_main.o src/subcommand/ids_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/recalibrate_main.o src/subcommand/recalibrate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/surject_main.o src/subcommand/surject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/call_main.o src/subcommand/call_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/genotype_main.o src/subcommand/genotype_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/stats_main.o src/subcommand/stats_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/gamcompare_main.o src/subcommand/gamcompare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/concat_main.o src/subcommand/concat_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/kmers_main.o src/subcommand/kmers_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/paths_main.o src/subcommand/paths_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/prune_main.o src/subcommand/prune_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/srpe_main.o src/subcommand/srpe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/map_main.o src/subcommand/map_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/locify_main.o src/subcommand/locify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/msga_main.o src/subcommand/msga_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/deconstruct_main.o src/subcommand/deconstruct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/simplify_main.o src/subcommand/simplify_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/minimizer_main.o src/subcommand/minimizer_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/validate_main.o src/subcommand/validate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/mpmap_main.o src/subcommand/mpmap_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/sort_main.o src/subcommand/sort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/subcommand.o src/subcommand/subcommand.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/augment_main.o src/subcommand/augment_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/trace_main.o src/subcommand/trace_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/view_main.o src/subcommand/view_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/inject_main.o src/subcommand/inject_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/convert_main.o src/subcommand/convert_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/find_main.o src/subcommand/find_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/sift_main.o src/subcommand/sift_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/vectorize_main.o src/subcommand/vectorize_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/gamsort_main.o src/subcommand/gamsort_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/compare_main.o src/subcommand/compare_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/add_main.o src/subcommand/add_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/benchmark_main.o src/subcommand/benchmark_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/join_main.o src/subcommand/join_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/translate_main.o src/subcommand/translate_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/gaffe_main.o src/subcommand/gaffe_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/construct_main.o src/subcommand/construct_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/gbwt_main.o src/subcommand/gbwt_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/chunk_main.o src/subcommand/chunk_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/align_main.o src/subcommand/align_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/viz_main.o src/subcommand/viz_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/bugs_main.o src/subcommand/bugs_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/cluster_main.o src/subcommand/cluster_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/sim_main.o src/subcommand/sim_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/combine_main.o src/subcommand/combine_main.cpp . ./source_me.sh && g++ -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c -o obj/subcommand/filter_main.o src/subcommand/filter_main.cpp rm -f lib/libvg.a ar rs lib/libvg.a obj/json2pb.o obj/augment.o obj/multipath_mapper.o obj/utility.o obj/chunker.o obj/stream_sorter.o obj/path.o obj/haplotype_extracter.o obj/readfilter.o obj/split_strand_graph.o obj/version.o obj/graph.o obj/edit.o obj/packer.o obj/small_snarl_simplifier.o obj/traversal_support.o obj/feature_set.o obj/filter.o obj/mem.o obj/phased_genome.o obj/translator.o obj/region.o obj/snarls.o obj/region_expander.o obj/transcriptome.o obj/graph_synchronizer.o obj/graph_caller.o obj/mapper.o obj/ssw_aligner.o obj/genotypekit.o obj/extra_node_graph.o obj/watchdog.o obj/prune.o obj/progressive.o obj/subgraph_overlay.o obj/constructor.o obj/gfa.o obj/min_distance.o obj/source_sink_overlay.o obj/viz.o obj/proto_handle_graph.o obj/aligner.o obj/funnel.o obj/variant_recall.o obj/memoizing_graph.o obj/name_mapper.o obj/vg.o obj/traversal_finder.o obj/indexed_vg.o obj/option.o obj/stream_index.o obj/vcf_buffer.o obj/build_index.o obj/identity_overlay.o obj/vg_set.o obj/alignment.o obj/path_component_index.o obj/flow_sort.o obj/haplotypes.o obj/multipath_alignment.o obj/path_index.o obj/genotyper.o obj/msa_converter.o obj/deconstructor.o obj/nested_traversal_finder.o obj/seed_clusterer.o obj/rare_variant_simplifier.o obj/scanner.o obj/variant_adder.o obj/gapless_extender.o obj/homogenizer.o obj/gff_reader.o obj/preflight.o obj/srpe.o obj/cluster.o obj/genome_state.o obj/kmer.o obj/snarl_caller.o obj/memusage.o obj/mcmc_genotyper.o obj/phase_unfolder.o obj/dagified_graph.o obj/multipath_alignment_graph.o obj/cactus.o obj/reverse_graph.o obj/convert_handle.o obj/sampler.o obj/entropy.o obj/tree_subgraph.o obj/index.o obj/crash.o obj/subgraph.o obj/minimizer_mapper.o obj/vectorizer.o obj/xdrop_aligner.o obj/alignment_emitter.o obj/benchmark.o obj/surjector.o obj/position.o obj/banded_global_aligner.o obj/null_masking_graph.o obj/statistics.o obj/path_subgraph.o obj/gbwt_helper.o obj/algorithms/is_single_stranded.o obj/algorithms/split_strands.o obj/algorithms/reverse_complement.o obj/algorithms/shortest_cycle.o obj/algorithms/normalize.o obj/algorithms/dijkstra.o obj/algorithms/jump_along_path.o obj/algorithms/kmer.o obj/algorithms/dfs.o obj/algorithms/alignment_path_offsets.o obj/algorithms/coverage_depth.o obj/algorithms/remove_high_degree.o obj/algorithms/next_pos_chars.o obj/algorithms/strongly_connected_components.o obj/algorithms/sorted_id_ranges.o obj/algorithms/is_acyclic.o obj/algorithms/find_shortest_paths.o obj/algorithms/are_equivalent.o obj/algorithms/subgraph.o obj/algorithms/merge.o obj/algorithms/apply_bulk_modifications.o obj/algorithms/expand_context.o obj/algorithms/extract_extending_graph.o obj/algorithms/to_gfa.o obj/algorithms/dagify.o obj/algorithms/count_walks.o obj/algorithms/weakly_connected_components.o obj/algorithms/simplify_siblings.o obj/algorithms/approx_path_distance.o obj/algorithms/distance_to_head.o obj/algorithms/distance_to_tail.o obj/algorithms/nearest_offsets_in_paths.o obj/algorithms/extract_containing_graph.o obj/algorithms/walk.o obj/algorithms/path_string.o obj/algorithms/id_sort.o obj/algorithms/extend.o obj/algorithms/unchop.o obj/algorithms/extract_connecting_graph.o obj/algorithms/eades_algorithm.o obj/algorithms/topological_sort.o obj/algorithms/copy_graph.o obj/io/register_loader_saver_gbwt.o obj/io/register_loader_saver_snarl_manager.o obj/io/register_loader_saver_distance_index.o obj/io/register_loader_saver_gbwtgraph.o obj/io/register_loader_saver_packed_graph.o obj/io/register_loader_saver_odgi.o obj/io/register_loader_saver_minimizer.o obj/io/register_loader_saver_xg.o obj/io/register_loader_saver_lcp.o obj/io/register_loader_saver_vg.o obj/io/register_loader_saver_hash_graph.o obj/io/register_loader_saver_gcsa.o obj/io/register_libvg_io.o obj/io/load_proto_to_graph.o obj/progress_bar.o obj/sha1.o ar: creating lib/libvg.a . ./source_me.sh && g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/<>/vg-1.22.0+ds/lib /<>/vg-1.22.0+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 -lebl -ldl -llzma -lrocksdb -lbz2 -ljemalloc rm -f lib/vg_is_static . ./source_me.sh && g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/<>/vg-1.22.0+ds/include -I. -I/<>/vg-1.22.0+ds/src -I/<>/vg-1.22.0+ds/src/unittest -I/<>/vg-1.22.0+ds/src/subcommand -I/<>/vg-1.22.0+ds/include/dynamic -I/<>/vg-1.22.0+ds/include/sonLib -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -MMD -MP -g -O2 -fdebug-prefix-map=/<>/vg-1.22.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -o bin/vg obj/main.o obj/unittest/variant_adder.o obj/unittest/statistics.o obj/unittest/haplotypes.o obj/unittest/snarls.o obj/unittest/mapper.o obj/unittest/tree_subgraph.o obj/unittest/dijkstra.o obj/unittest/cluster.o obj/unittest/alignment.o obj/unittest/overlays.o obj/unittest/vcf_buffer.o obj/unittest/constructor.o obj/unittest/handle.o obj/unittest/chunker.o obj/unittest/mcmc_genotyper.o obj/unittest/phase_unfolder.o obj/unittest/mapping.o obj/unittest/cactus.o obj/unittest/genotypekit.o obj/unittest/driver.o obj/unittest/mem.o obj/unittest/phased_genome.o obj/unittest/flow_sort_test.o obj/unittest/position.o obj/unittest/pinned_alignment.o obj/unittest/minimizer_mapper.o obj/unittest/xdrop_aligner.o obj/unittest/random_graph.o obj/unittest/gfa.o obj/unittest/stream.o obj/unittest/dagify.o obj/unittest/blocked_gzip_output_stream.o obj/unittest/banded_global_aligner.o obj/unittest/vg.o obj/unittest/packed_graph.o obj/unittest/multipath_mapper.o obj/unittest/multipath_alignment.o obj/unittest/vpkg.o obj/unittest/min_distance.o obj/unittest/seed_clusterer.o obj/unittest/vg_algorithms.o obj/unittest/indexed_vg.o obj/unittest/source_sink_overlay.o obj/unittest/distributions.o obj/unittest/readfilter.o obj/unittest/stream_index.o obj/unittest/annotation.o obj/unittest/sampler.o obj/unittest/xg.o obj/unittest/hfile_cppstream.o obj/unittest/gapless_extender.o obj/unittest/genotyper.o obj/unittest/convert_handle.o obj/unittest/dagified_graph.o obj/unittest/multipath_alignment_graph.o obj/unittest/hash_graph.o obj/unittest/feature_set.o obj/unittest/path_component_index.o obj/unittest/aligner.o obj/unittest/genome_state.o obj/unittest/srpe_filter.o obj/unittest/blocked_gzip_input_stream.o obj/unittest/path_index.o obj/unittest/msa_converter.o obj/unittest/surject.o obj/unittest/packed_structs.o obj/subcommand/mod_main.o obj/subcommand/mcmc_main.o obj/subcommand/circularize_main.o obj/subcommand/help_main.o obj/subcommand/explode_main.o obj/subcommand/depth_main.o obj/subcommand/version_main.o obj/subcommand/index_main.o obj/subcommand/snarls_main.o obj/subcommand/rna_main.o obj/subcommand/annotate_main.o obj/subcommand/test_main.o obj/subcommand/pack_main.o obj/subcommand/dotplot_main.o obj/subcommand/crash_main.o obj/subcommand/ids_main.o obj/subcommand/recalibrate_main.o obj/subcommand/surject_main.o obj/subcommand/call_main.o obj/subcommand/genotype_main.o obj/subcommand/stats_main.o obj/subcommand/gamcompare_main.o obj/subcommand/concat_main.o obj/subcommand/kmers_main.o obj/subcommand/paths_main.o obj/subcommand/prune_main.o obj/subcommand/srpe_main.o obj/subcommand/map_main.o obj/subcommand/locify_main.o obj/subcommand/msga_main.o obj/subcommand/deconstruct_main.o obj/subcommand/simplify_main.o obj/subcommand/minimizer_main.o obj/subcommand/validate_main.o obj/subcommand/mpmap_main.o obj/subcommand/sort_main.o obj/subcommand/subcommand.o obj/subcommand/augment_main.o obj/subcommand/trace_main.o obj/subcommand/view_main.o obj/subcommand/inject_main.o obj/subcommand/convert_main.o obj/subcommand/find_main.o obj/subcommand/sift_main.o obj/subcommand/vectorize_main.o obj/subcommand/gamsort_main.o obj/subcommand/compare_main.o obj/subcommand/add_main.o obj/subcommand/benchmark_main.o obj/subcommand/join_main.o obj/subcommand/translate_main.o obj/subcommand/gaffe_main.o obj/subcommand/construct_main.o obj/subcommand/gbwt_main.o obj/subcommand/chunk_main.o obj/subcommand/align_main.o obj/subcommand/viz_main.o obj/subcommand/bugs_main.o obj/subcommand/cluster_main.o obj/subcommand/sim_main.o obj/subcommand/combine_main.o obj/subcommand/filter_main.o -lvg -L/<>/vg-1.22.0+ds/lib /<>/vg-1.22.0+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 -lebl -ldl -llzma -lrocksdb -lbz2 -ljemalloc make[2]: Leaving directory '/<>/vg-1.22.0+ds' cp bin/vg debian/help/ PATH=$PATH:/<>/vg-1.22.0+ds/debian/help help2man --no-discard-stderr --no-info --help-option=help --version-option=version vg > debian/vg.1 make[1]: Leaving directory '/<>/vg-1.22.0+ds' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/<>/vg-1.22.0+ds' export PATH=$PATH:/<>/vg-1.22.0+ds/debian/help && . ./source_me.sh && cd test && prove -v t index file /tmp/vg-HKZy04/vg-Acamq2.fai not found, generating... index file /tmp/vg-HKZy04/vg-uvAWX5.fai not found, generating... index file /tmp/vg-HKZy04/vg-49klX3.fai not found, generating... warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) x 9 sv1 N 99 PASS AC=1;CIEND=-3,0;CIPOS=0,3;END=29;NA=1;NS=1;SVTYPE=DEL GT ! index file /tmp/vg-HKZy04/vg-hW5bI2.fai not found, generating... index file /tmp/vg-HKZy04/vg-ZPK9q5.fai not found, generating... index file /tmp/vg-HKZy04/vg-pkVaz5.fai not found, generating... index file /tmp/vg-HKZy04/vg-wHwGl2.fai not found, generating... index file /tmp/vg-HKZy04/vg-oGPA82.fai not found, generating... index file /tmp/vg-HKZy04/vg-zB0lY5.fai not found, generating... index file /tmp/vg-HKZy04/vg-m4SUa6.fai not found, generating... index file /tmp/vg-HKZy04/vg-caXNV6.fai not found, generating... index file /tmp/vg-HKZy04/vg-ecYPd4.fai not found, generating... index file /tmp/vg-HKZy04/vg-g1Akl6.fai not found, generating... Warning: deletion END and SVLEN do not agree [canonicalize] x 9 sv1 N 99 PASS AC=1;CIEND=-3,0;CIPOS=0,3;END=29;NA=1;NS=1;SPAN=19;SVLEN=-19;SVTYPE=DEL GT END: 29 SVLEN: -19 index file /tmp/vg-HKZy04/vg-ILk4Z3.fai not found, generating... Warning: deletion END and SVLEN do not agree [canonicalize] x 9 sv1 N 99 PASS AC=1;CIEND=-3,0;CIPOS=0,3;END=29;NA=1;NS=1;SPAN=19;SVLEN=-19;SVTYPE=DEL GT END: 29 SVLEN: -19 index file /tmp/vg-HKZy04/vg-4P9qr6.fai not found, generating... index file /tmp/vg-HKZy04/vg-rVHFd3.fai not found, generating... index file /tmp/vg-HKZy04/vg-obFWa5.fai not found, generating... index file /tmp/vg-HKZy04/vg-M3M7Z5.fai not found, generating... index file /tmp/vg-HKZy04/vg-tZwXw5.fai not found, generating... index file /tmp/vg-HKZy04/vg-nTI1B6.fai not found, generating... index file /tmp/vg-HKZy04/vg-85k9q5.fai not found, generating... index file /tmp/vg-HKZy04/vg-Iv89w3.fai not found, generating... index file /tmp/vg-HKZy04/vg-GhmGA5.fai not found, generating... Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;CIPOS=0,3;END=18;NA=1;NS=1;SEQ=ACTG;SPAN=4;SVLEN=4;SVTYPE=INS GT END: 18 POS: 9 index file /tmp/vg-HKZy04/vg-fRB9Y4.fai not found, generating... Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;CIPOS=0,3;END=18;NA=1;NS=1;SEQ=ACTG;SPAN=4;SVLEN=4;SVTYPE=INS GT END: 18 POS: 9 index file /tmp/vg-HKZy04/vg-BJtVq6.fai not found, generating... Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;CIPOS=0,3;END=13;NA=1;NS=1;SEQ=ACTG;SPAN=4;SVLEN=4;SVTYPE=INS GT END: 13 POS: 9 Warning: VCF writer incorrecty produced END = POS + SVLEN for an insertion. Fixing END to POS. index file /tmp/vg-HKZy04/vg-t6oUG6.fai not found, generating... Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] x 9 sv1 N 99 PASS AC=1;CIPOS=0,3;END=13;NA=1;NS=1;SEQ=ACTG;SPAN=4;SVLEN=4;SVTYPE=INS GT END: 13 POS: 9 Warning: VCF writer incorrecty produced END = POS + SVLEN for an insertion. Fixing END to POS. index file /tmp/vg-HKZy04/vg-tQqmv2.fai not found, generating... index file /tmp/vg-HKZy04/vg-Gpzjc5.fai not found, generating... index file /tmp/vg-HKZy04/vg-jaKdx4.fai not found, generating... warning:[vg::Constructor] Lowercase characters found in x; coercing to uppercase. index file /tmp/vg-HKZy04/vg-BBfK03.fai not found, generating... warning:[vg::Constructor] Lowercase characters found in x; coercing to uppercase. index file /tmp/vg-HKZy04/vg-hu7Oc3.fai not found, generating... index file /tmp/vg-HKZy04/vg-ktasA3.fai not found, generating... index file /tmp/vg-HKZy04/vg-K5UqX6.fai not found, generating... index file /tmp/vg-HKZy04/vg-slfGB2.fai not found, generating... Warning: Cactus does not currently support finding snarls in a single-node connected component warning:[GSSWAligner::maximum_mapping_quality_exact]: Max score of 0 is the padding score; changing to -10 warning:[GSSWAligner::maximum_mapping_quality_approx]: Max score of 0 is the padding score; changing to -10 t/00_unittest.t ....... 1..1 =============================================================================== All tests passed (7534116 assertions in 388 test cases) ok 1 - vg unit tests complete successfully ok t/01_build_graph.t .... 1..1 ok 1 - graph building with the API ok warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AFR_AF=0;AMR_AF=0;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;DP=15541;EAS_AF=0;END=1017354;EUR_AF=0.001;NS=2504;SAS_AF=0;SVLEN=-3562;SVTYPE=DEL ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AFR_AF=0.0303;AMR_AF=0.0043;AN=5008;CS=ALU_umary;DP=18053;EAS_AF=0;EUR_AF=0;MEINFO=AluUndef,2,281,+;NS=2504;SAS_AF=0;SVLEN=279;SVTYPE=ALU;TSD=null ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 490168 DUP_gs_CNV_20_1490168_1549769 G 100 PASS AC=1;AF=0.000199681;AFR_AF=0;AMR_AF=0;AN=5008;CS=DUP_gs;DP=21874;EAS_AF=0;END=1549769;EUR_AF=0;NS=2504;SAS_AF=0.001;SVTYPE=DUP ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AFR_AF=0;AMR_AF=0;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;DP=15541;EAS_AF=0;END=1017354;EUR_AF=0.001;NS=2504;SAS_AF=0;SVLEN=-3562;SVTYPE=DEL ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AFR_AF=0.0303;AMR_AF=0.0043;AN=5008;CS=ALU_umary;DP=18053;EAS_AF=0;EUR_AF=0;MEINFO=AluUndef,2,281,+;NS=2504;SAS_AF=0;SVLEN=279;SVTYPE=ALU;TSD=null ! Restricting to gi|568815592:29791752-29792749 from 1 to end index file sv/x.fa.fai not found, generating... t/02_vg_construct.t ... 1..25 ok 1 - construction produces the right number of nodes ok 2 - construction produces the right number of edges ok 3 - construction obeys rename and region options ok 4 - construction of a 1 megabase graph from the 1000 Genomes succeeds ok 5 - the 1mb graph has the expected number of nodes ok 6 - the 1mb graph has the expected number of edges ok 7 - node size is manageable by default ok 8 - construction of a very complex region succeeds ok 9 - the complex graph has the expected number of nodes ok 10 - the complex graph has the expected number of edges ok 11 - the ordering of variants at the same position has no effect on the resulting graph ok 12 - construction does not fail when the first position in the VCF is repeated and has an indel ok 13 - the size of the regions used in construction has no effect on the graph ok 14 - the number of threads used in construction has no effect on the graph ok 15 - the number of threads and regions used in construction has no effect on the graph ok 16 - construction of a graph with two head nodes succeeds ok 17 - the graph contains all the sequence in the reference and VCF ok 18 - varying the max node size does not affect graph length ok 19 - nodes are correctly capped in size ok 20 - -R --region flag is respected ok 21 - vg construct does not require a vcf ok 22 - vg construct respects node size limit ok 23 - --region can be interpreted to be a reference sequence (and not parsed as a region spec) ok 24 - vg constructs the correct graph for inversions ok 25 - vg construct skips variants with . ALTs ok terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_xahAyV/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_u9taZF/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_TC1AQr/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph t/03_vg_view.t ........ 1..20 ok 1 - view produces the expected number of lines of dot output ok 2 - view produces the expected number of lines of GFA output ok 3 - view converts back and forth between GFA and vg format ok 4 - view can convert BAM to GAM not ok 5 - view can round-trip JSON and GAM # got: '5b9458e2d6d1f262977b932998bb8d3a -' # expected: '7d450e53c0870ff504f33af188613e5d -' Binary files x.vg and - differ not ok 6 - view can reconstruct a VG graph from JSON # got: '1' # expected: '0' ok 7 - view can pass through VG when loading as vg::VG ok 8 - view can pass through semantically identical VG normally ok 9 - view parses sample names ok 10 - view can handle fastq input not ok 11 - unnamed test # got: '4' # expected: 'view can translate graphs with 2-node cycles' ok 12 - view outputs properly oriented GFA ok 13 - view produces the expected number of lines of dot output from a cyclic graph ok 14 - streaming JSON output produces the expected number of chunks ok 15 - duplicate warnings can be suppressed when loading as vg::VG ok 16 - gfa graphs are bluntified on import ok 17 - a more complex GFA can be imported ok 18 - GFA import rejects a GFA file with an overlap that goes beyond its sequences ok 19 - GFA import produces a concise error message in that case ok 20 - GFA import accepts that file when the offending overlap length is fixed Failed 3/20 subtests [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes t/04_vg_align.t ....... 1..20 ok 1 - alignment traverses the correct path ok 2 - alignment score is as expected ok 3 - full length bonus works and is included by default ok 4 - bonuses are included on only one end for pinned alignments ok 5 - scoring parameters are respected ok 6 - score-matrix file should give same results as --match 2 --mismatch 2: scoring parameters are respected ok 7 - alignment does not contain excessive soft clips under lenient scoring ok 8 - score-matrix file should give same results as --match 2 --mismatch 2: alignment does not contain excessive soft clips under lenient scoring ok 9 - alignment score does not overflow at 255 when using 8x16bit vectors ok 10 - score-matrix file should give same results as --match 2 --mismatch 2: alignment score does not overflow at 255 when using 8x16bit vectors ok 11 - Ns do not cause excessive soft clipping ok 12 - nodes are only referenced if they have mappings ok 13 - align can use query names and outputs GAM ok 14 - alignment to cyclic graphs works ok 15 - graphs where duplicated nodes need flipping can be used for alignment ok 16 - node flipping doesn't destroy the alignment ok 17 - alignment correctly handles an inversion ok 18 - the exploding graph doesn't blow up ok 19 - pinning doesn't cause problems for gssw ok 20 - left pinning is correctly handled ok graph path 'x' invalid: edge from 202 end to 205 start does not exist [vg view] warning: graph is invalid! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_mzFYKs/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Could not open test.xg while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_IfrKoa/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Could not open w.xg while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Unreadable stream while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph t/05_vg_find.t ........ 1..28 ok 1 - construction ok 2 - a path can be queried from the xg index ok 3 - a node near another can be obtained using context from the xg index ok 4 - each perfect read contains one maximal exact match ok 5 - vg find -D finds approximate distance between 2 adjacent node starts ok 6 - vg find -D finds approximate distance between node start and adjacent snp ok 7 - vg find -D jumps deletion ok 8 - vg find -D jumps deletion from other allele in snp ok 9 - vg find -L finds same number of nodes (with -c 1) ok 10 - vg find -L works with -r. it scans from start position of first node in range ok 11 - vg find -L tracks length from start position of input node ok 12 - vg find -L works with more than one input node ok 13 - we find the 4 canonical SMEMs from @lh3's bwa mem poster ok 14 - we can find the right MEMs for a sequence with Ns ok 15 - we find the same MEMs sequences with different lengths of Ns ok 16 - the index can return the set of alignments mapping to a particular node ok 17 - a subgraph query may be used to obtain a particular subset of alignments ok 18 - the GAM index can return the set of alignments mapping to a node ok 19 - a subgraph query may be used to obtain a particular subset of alignments from a sorted GAM ok 20 - the index can be queried using GAM alignments ok 21 - find gets connected edges between queried nodes by default ok 22 - find gets nodes provided in a node file list not ok 23 - extracting by path adds no extra edges # got: '' # expected: '1' not ok 24 - pattern based path extraction works # got: '0' # expected: '38' ok 25 - path DAG range query works ok 26 - we can extract a set of targets to separate files ok 27 - the same extraction can be made using BED input ok 28 - we see the expected number of kmers in the given targets Failed 2/28 subtests t/06_vg_index.t: line 8: warning: setlocale: LC_ALL: cannot change locale (en_US.utf8): No such file or directory error: could not parse i from argument "x.vg" t/06_vg_index.t ....... 1..62 ok 1 - building an XG index of a graph ok 2 - building a GCSA index of a graph ok 3 - building both indexes at once ok 4 - the indexes are identical when built one at a time and together ok 5 - building GCSA from XG ok 6 - the GCSA indexes are identical when built from vg and from xg ok 7 - building a GBWT index of a graph with haplotypes ok 8 - building an XG index of a graph with haplotypes ok 9 - xg index does not contain alt paths by default ok 10 - building an XG index of a graph with haplotypes and alt paths included ok 11 - xg index does contains alt paths with index -L ok 12 - building a GCSA index of a graph with haplotypes ok 13 - building all indexes at once ok 14 - the indexes are identical ok 15 - building all indexes at once, while leaving alt paths in xg ok 16 - the indexes are identical with -L ok 17 - xg index does contains alt paths with index -L all at once ok 18 - storing a VCF parse for a graph with haplotypes ok 19 - building a GBWT index from the VCF parse ok 20 - the indexes are identical ok 21 - samples can be excluded from haplotype indexing ok 22 - excluded samples were not included in the GBWT index ok 23 - building GBWT index for a regional graph ok 24 - no warnings about missing variants produced ok 25 - building an XG index of multiple graphs ok 26 - building a GCSA index of multiple graphs ok 27 - building both indexes at once ok 28 - the indexes are identical ok 29 - building a GBWT index of multiple graphs with haplotypes ok 30 - building an XG index of multiple graphs with haplotypes ok 31 - building a GCSA index of multiple graphs with haplotypes ok 32 - building all three indexes at once ok 33 - the indexes are identical ok 34 - storing a VCF parse for multiple graphs with haplotypes ok 35 - building a GBWT index from the VCF parses ok 36 - the indexes are identical ok 37 - GBWT can be built for paths ok 38 - GBWT can be built for both paths and haplotypes ok 39 - fail with nonexistent file ok 40 - a prebuilt deBruijn graph in GCSA2 format may be used ok 41 - index can store alignments ok 42 - index can dump alignments ok 43 - alignment index stores unmapped reads ok 44 - alignment index can be loaded using sequential invocations; next_nonce persistence ok 45 - index stores all mappings ok 46 - vg index and vg gamsort produce identical sorted GAM indexes ok 47 - threads may be exported to binary for use in GBWT construction ok 48 - storage of multiple graphs in an index succeeds ok 49 - can index backward nodes ok 50 - can index kmers for backward nodes ok 51 - index can store alignments to backward nodes ok 52 - index can store alignments to cyclic graphs ok 53 - GCSA2 index works on cyclic graphs with heads and tails ok 54 - GCSA2 index works on cyclic graphs with no heads or tails ok 55 - GCSA2 index works on cyclic graphs with self loops ok 56 - GCSA2 index works on general cyclic graphs ok 57 - GCSA2 indexing of a tiny graph works ok 58 - GCSA2 indexing succeeds on a single-node graph ok 59 - GCSA2 indexing succeeds on graph with heads but no tails ok 60 - a useful error message is produced when nodes are too large ok 61 - building a distance index of a graph ok 62 - building a distance index of a graph without maximum index ok [vg::alignment.cpp] couldn't open reads/NONEXISTENT [vg::alignment.cpp] couldn't open reads/NONEXISTENT [vg::alignment.cpp] couldn't open reads/NONEXISTENT [vg::alignment.cpp] couldn't open reads/NONEXISTENT terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_3hP5vG/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_wfLlO2/stacktrace.txt Please include the stack trace file in your bug report! index file t.fa.fai not found, generating... t/07_vg_map.t ......... 1..55 ok 1 - offset counts unused bases from the start of the node on the forward strand ok 2 - xdrop alignment obtains the expected result ok 3 - xdrop alignment obtains the expected result for the reverse complement ok 4 - score-matrix defaults match 1 mismatch -4 should produce same results: with matrixoffset counts unused bases from the start of the node on the forward strand ok 5 - negative of score-matrix defaults should not produce same results: with matrixoffset counts unused bases from the start of the node on the forward strand ok 6 - offset counts unused bases from the start of the node on the reverse strand ok 7 - global alignment traverses the correct path ok 8 - alignment score is as expected ok 9 - scoring parameters are respected ok 10 - score-matrix file should give same results as --match 2 --mismatch 2: scoring parameters are respected ok 11 - full length bonus always be included ok 12 - full length bonus can be set to 0 ok 13 - vg map takes -d as input without a variant graph ok 14 - vg map can align across a SNP ok 15 - alignment works on a small graph ok 16 - binary alignment format is equivalent to json version ok 17 - alignment from BAM correctly handles qualities ok 18 - chunky-banded alignment works ok 19 - multiple alignments are returned in descending score order ok 20 - only a single primary alignment is returned ok 21 - mapping of BAM file produces expected number of alignments ok 22 - mapping from a fastq produces the expected number of alignments ok 23 - allowing secondary alignments with MEM mapping does not change number of primary alignments ok 24 - vg connects paired-end reads in gam output ok 25 - mapping to graphs that can't be oriented without swapping edges works correctly ok 26 - reads multi-map to multiple possible locations ok 27 - vg map works based on gcsa and xg indexes ok 28 - the mapping quality may be capped ok 29 - paired read alignments forced to be consistent have lower score than unrestricted alignments ok 30 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments ok 31 - only primary alignments have mapping quality scores ok 32 - unpaired reads produce mapping quality scores ok 33 - map returns same output on xg and vg (single threaded) ok 34 - base quality adjusted alignment produces higher scores if mismatches have low quality ok 35 - error on vg map -f (unpaired) ok 36 - error on vg map -f (interleaved) ok 37 - error on vg map -f (paired, LHS) ok 38 - error on vg map -f (paired, RHS) ok 39 - mapping a read that touches unused nodes gets the base score ok 40 - mapping a read that matches a haplotype gets a small penalty ok 41 - mapping a read that matches a haplotype with exponent 0 gets the base score ok 42 - mapping a read that matches no haplotypes gets a larger penalty not ok 43 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 44 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 45 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 46 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 47 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '163 # 83' not ok 48 - surjection of unpaired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 49 - surjection of unpaired reads to SAM yields correct pair partner positions # got: '' # expected: '0 # 0' not ok 50 - surjection of unpaired reads to SAM yields distinct QNAMEs # got: '0' # expected: '2' not ok 51 - surjection of unpaired reads to SAM produces absent partner contigs # got: '' # expected: '* # *' not ok 52 - surjection of unpaired reads to SAM produces correct flags # got: '' # expected: '0 # 16' ok 53 - mapper can read FASTA input ok 54 - mapper can read multiline FASTA input ok 55 - xdrop works on a reversed read Failed 10/55 subtests t/08_vg_ids.t ......... 1..10 ok 1 - minimum node as expected (id compaction correct) ok 2 - maximum node is as expected (id compaction correct) ok 3 - correctly generated joint id space for several graphs ok 4 - can sort and re-number a graph with self loops ok 5 - can sort and renumber a complex cyclic graph ok 6 - sorting removes back-edges in a DAG ok 7 - sorting assigns node IDs in topological order ok 8 - sorting does not affect id range ok 9 - sorting does not affect id range of vg ok 10 - sorting does not affect id range of hg ok t/09_vg_concat.t ...... 1..1 ok 1 - concat doubles the number of nodes ok t/100_code_quality.t .. 1..1 ok 1 - code quality is acceptable ok warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 13790 BI_GS_DEL1_B1_P2734_15 T 100 PASS AC=1;AF=0.000199681;AFR_AF=0;AMR_AF=0;AN=5008;CIEND=-75,76;CIPOS=-75,76;CS=DEL_union;DP=15541;EAS_AF=0;END=1017354;EUR_AF=0.001;NS=2504;SAS_AF=0;SVLEN=-3562;SVTYPE=DEL ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 14169 ALU_umary_ALU_12010 G 100 PASS AC=43;AF=0.00858626;AFR_AF=0.0303;AMR_AF=0.0043;AN=5008;CS=ALU_umary;DP=18053;EAS_AF=0;EUR_AF=0;MEINFO=AluUndef,2,281,+;NS=2504;SAS_AF=0;SVLEN=279;SVTYPE=ALU;TSD=null ! warning:[vg::Constructor] Unsupported variant allele ""; Skipping variant(s) z 490168 DUP_gs_CNV_20_1490168_1549769 G 100 PASS AC=1;AF=0.000199681;AFR_AF=0;AMR_AF=0;AN=5008;CS=DUP_gs;DP=21874;EAS_AF=0;END=1549769;EUR_AF=0;NS=2504;SAS_AF=0.001;SVTYPE=DUP ! t/10_vg_stats.t ....... 1..11 ok 1 - vg stats reports the expected number of nodes ok 2 - vg stats reports the expected number of edges ok 3 - vg stats reports the expected graph length ok 4 - vg stats reports the correct number of subgraphs ok 5 - vg stats reports the correct subgraph length ok 6 - distance to head is correct ok 7 - distance to tail is correct ok 8 - aligned read stats are computed correctly ok 9 - basic stats agree between graph formats ok 10 - stats can be computed for GAM files without graphs ok 11 - a path overlap description of a test graph has the expected length ok t/11_vg_paths.t ....... 1..13 ok 1 - path listing works from vg ok 2 - path listing works from XG ok 3 - thread listing works from GBWT ok 4 - thread selection by name prefix works correctly ok 5 - thread selection by sample name works correctly ok 6 - no threads are reported for invalid samples ok 7 - vg paths may be used to extract threads ok 8 - Fasta extracted from xg is the same as the input fasta ok 9 - Fasta extracted from vg is the same as the input fasta ok 10 - Fasta extracted from threads has correct number of lines ok 11 - a single path may be retained ok 12 - path filtering does not modify the graph ok 13 - alt allele paths can be dropped ok warning[vg mod]: -o is deprecated. Dangling edges are now automatically removed. t/12_vg_kmers.t ....... 1..10 ok 1 - correct numbers of kmers in the graph ok 2 - to_end edges are handled correctly ok 3 - from_start edges are handled correctly ok 4 - GCSA2 output produces the expected number of lines ok 5 - GCSA2 binary output produces the expected number bytes ok 6 - GCSA2 output works when next position is multiple ok 7 - GCSA2 output works when previous characters are multiple ok 8 - edge-max correctly bounds the number of kmers in a complex graph ok 9 - start/stop node IDs can be specified in GCSA2 output ok 10 - attempting to generate kmers longer than the longest path in a graph correctly yields no kmers ok index file n.fa.fai not found, generating... t/13_vg_sim.t ......... 1..14 ok 1 - vg sim creates the correct number of reads ok 2 - end bonuses are included ok 3 - alignments may be generated rather than read sequences ok 4 - alignments are produced on both strands ok 5 - high simulated error rates do not change the number of bases generated ok 6 - vg sim creates forward-strand reads when asked ok 7 - vg sim can simulate from just a path ok 8 - vg sim can simulate from just a path in FASTQ mode ok 9 - pairs simulated even when fragments overlap ok 10 - sim does not emit reads with Ns ok 11 - sim can emit reads with Ns when asked to ok 12 - sim doesn't emit Ns even with pair and errors ok 13 - ngs trained simulator works ok 14 - ngs trained simulator generates gam ok warning[load_proto_to_graph]: dangling edges on missing node 199474497 and 2 other missing nodes removed [algorithms::normalize] iteration 1 current length 160 [algorithms::normalize] iteration 2 current length 154 [algorithms::normalize] iteration 3 current length 154 [algorithms::normalize] normalized in 2 steps [algorithms::normalize] iteration 1 current length 160 [algorithms::normalize] iteration 2 current length 154 [algorithms::normalize] iteration 3 current length 154 [algorithms::normalize] normalized in 2 steps [algorithms::normalize] iteration 1 current length 160 [algorithms::normalize] iteration 2 current length 154 [algorithms::normalize] iteration 3 current length 154 [algorithms::normalize] normalized in 2 steps [algorithms::normalize] iteration 1 current length 95 [algorithms::normalize] iteration 2 current length 95 [algorithms::normalize] normalized in 1 steps terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_BQqfBq/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_rdstFw/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_dmZ4YQ/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_ZdiNJk/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph [algorithms::normalize] iteration 1 current length 5 [algorithms::normalize] normalized in 0 steps [algorithms::normalize] iteration 1 current length 5 [algorithms::normalize] normalized in 0 steps [algorithms::normalize] iteration 1 current length 106 [algorithms::normalize] iteration 2 current length 105 [algorithms::normalize] iteration 3 current length 105 [algorithms::normalize] normalized in 2 steps [algorithms::normalize] iteration 1 current length 103 [algorithms::normalize] iteration 2 current length 100 [algorithms::normalize] iteration 3 current length 100 [algorithms::normalize] normalized in 2 steps t/14_vg_mod.t ......... 1..32 ok 1 - vg mod yields a graph with only a particular path ok 2 - orphan edge removal is automatic ok 3 - graph complexity reduction works as expected ok 4 - short subgraph pruning works ok 5 - normalization produces the correct number of nodes ok 6 - normalization removes redundant SNP alleles ok 7 - normalization produces a valid graph ok 8 - looped normalization produces a valid graph ok 9 - unchop produces a valid graph ok 10 - normalization removes redundant sequence in the graph ok 11 - normalization doesn't introduce cycles and does remove redundancy in bubbles ok 12 - vg mod removes non-path nodes and edge not ok 13 - chopping a graph works correctly with reverse mappings # got: '1' # expected: '0' ok 14 - unchop correctly handles paths ok 15 - unchop correctly handles a graph with an inversion not ok 16 - unchop handles doubly-reversing edges # got: '' # expected: '1' ok 17 - normalization works on a graph with an inversion ok 18 - mod successfully unchops a difficult graph ok 19 - chopping self-cycling nodes retains the cycle ok 20 - unrolling works and produces a valid graph ok 21 - unfolding works and produces a valid graph ok 22 - dagify-unroll produces a graph with the same kmers as the original graph ok 23 - unfold produces a graph with the same kmers as the original graph ok 24 - dagify handles a graph with two strongly connected components ok 25 - unfold followed by dagify produces a graph with no cycles ok 26 - unfold followed by dagify produces a graph with the same kmers as the original graph ok 27 - dagify unrolls the un-unrollable graph ok 28 - sibling simplification does not disrupt paths ok 29 - dagify correctly calculates the minimum distance through the unrolled component ok 30 - dagify produces a graph of the correct size ok 31 - subsetting a flat-alleles graph to a sample graph works ok 32 - removal of high-degree nodes results in the expected number of subgraphs Failed 2/32 subtests terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_vcrLw8/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_DcGNxV/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_0ler0L/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_a8QQh0/stacktrace.txt Please include the stack trace file in your bug report! t/15_vg_surject.t ..... 1..27 ok 1 - reads are generated ok 2 - vg surject works perfectly for perfect reads without misaligned homopolymer indels derived from the reference ok 3 - vg surject actually places reads on the correct path ok 4 - vg surject doesn't need to be told which path to use ok 5 - vg surject works for every read simulated from a dense graph ok 6 - vg surject spliced algorithm works for every read simulated from a dense graph ok 7 - vg surject produces valid SAM output ok 8 - vg map may surject reads to produce valid SAM output ok 9 - vg map may surject reads to produce valid BAM output not ok 10 - vg surject retains read names # got: '0' # expected: '100' ok 11 - vg surject can set sample and read group ok 12 - we respect the original mapping's softclips ok 13 - forward and reverse orientations of a read produce the same surjected SAM, ignoring flags ok 14 - vg surject produces valid BAM output not ok 15 - mapping quality is preserved through surjection # got: '' # expected: '99' not ok 16 - read pairing is preserved through GAM->GAM surjection # got: '' # expected: 'read/1' not ok 17 - surjection of paired reads to SAM yields correct positions # got: '' # expected: '321 # 762' not ok 18 - surjection of paired reads to SAM yields correct pair partner positions # got: '' # expected: '762 # 321' not ok 19 - surjection of paired reads to SAM yields properly matched QNAMEs # got: '0' # expected: '1' not ok 20 - surjection of paired reads to SAM produces correct pair partner contigs # got: '' # expected: '= # =' not ok 21 - surjection of paired reads to SAM produces correct flags # got: '' # expected: '83 # 163' not ok 22 - surjection of paired reads to SAM tags both reads with a read group # got: '0' # expected: '2' not ok 23 - surjection of paired reads to SAM creates RG header # got: '0' # expected: '1' ok 24 - surjection works for a longer (151bp) read ok 25 - surjection works for another difficult read ok 26 - mapping reproduces qualities from BAM input ok 27 - mapping reproduces qualities from fastq input Failed 10/27 subtests [algorithms::normalize] iteration 1 current length 1014 [algorithms::normalize] normalized in 0 steps [algorithms::normalize] iteration 1 current length 1014 [algorithms::normalize] normalized in 0 steps [algorithms::normalize] iteration 1 current length 100 [algorithms::normalize] normalized in 0 steps could not open msgas/t.fa error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph could not open msgas/t.fa error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph [algorithms::normalize] iteration 1 current length 100 [algorithms::normalize] iteration 2 current length 100 [algorithms::normalize] normalized in 1 steps index file msgas/s-rev.fa.fai not found, generating... [algorithms::normalize] iteration 1 current length 100 [algorithms::normalize] normalized in 0 steps index file GRCh38_alts/FASTA/HLA/K-3138.fa.fai not found, generating... index file msgas/inv.fa.fai not found, generating... [algorithms::normalize] iteration 1 current length 210 [algorithms::normalize] iteration 2 current length 210 [algorithms::normalize] normalized in 1 steps index file GRCh38_alts/FASTA/HLA/B-3106.fa.fai not found, generating... t/16_vg_msga.t ........ 1..14 ok 1 - MSGA produces the expected graph for GRCh38 HLA-V ok 2 - X-drop DP MSGA produces the expected graph for GRCh38 HLA-V {"edge": [{"from": "5", "from_start": true, "to": "6", "to_end": true}, {"from": "5", "from_start": true, "to": "7", "to_end": true}, {"from": "6", "to": "7"}], "node": [{"id": "5", "sequence": "GGACTAAGGACAAAGGTGCGGGGAG"}, {"id": "7", "sequence": "AACTACTCCACATCAAAGCTACCCAGGCCATTTTAAGTTTCCTGT"}, {"id": "6", "sequence": "TCAGATTCTCATCCCTCCTCAAGGGCTTCT"}], "path": [{"mapping": [{"edit": [{"from_length": 30, "to_length": 30}], "position": {"node_id": "6"}, "rank": "1"}, {"edit": [{"from_length": 45, "to_length": 45}], "position": {"node_id": "7"}, "rank": "2"}, {"edit": [{"from_length": 25, "to_length": 25}], "position": {"node_id": "5"}, "rank": "3"}], "name": "s1"}, {"mapping": [{"edit": [{"from_length": 30, "to_length": 30}], "position": {"node_id": "6"}, "rank": "1"}, {"edit": [{"from_length": 25, "to_length": 25}], "position": {"node_id": "5"}, "rank": "2"}], "name": "s2"}]} ok 3 - soft clips at node boundaries (start) are included correctly ok 4 - soft clips at node boundaries (end) are included correctly ok 5 - region hints (-p) produce same graph ok 6 - adding in existing sequences in reverse doesn't change graph ok 7 - the paths of the graph encode the original sequences used to build it ok 8 - even when banding the paths of the graph encode the original sequences used to build it ok 9 - HLA K-3138 correctly includes all input paths ok 10 - a difficult cyclic path can be included to produce a valid graph ok 11 - a reference sequence set representing an inversion in it may be msga'd and detected ok 12 - edges in cycles with two nodes are correctly included ok 13 - HLA B-3106 is assembled into a valid graph ok 14 - odd-sized overlaps may be used for chunked alignment ok terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_U61biy/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_dB3asC/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: -a / --augmentation-mode option is deprecated error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathMutableHandleGraph error:[get_input_file] could not open file "edits-embedded.gam" error[VPKG::load_one]: Correct input type not found in augmented.vg while loading handlegraph::PathHandleGraph [vg augment] warning: -a / --augmentation-mode option is deprecated error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathMutableHandleGraph error[VPKG::load_one]: Correct input type not found in augmented.m1.vg while loading handlegraph::PathHandleGraph terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_MlMnDr/stacktrace.txt Please include the stack trace file in your bug report! [vg augment] warning: -a / --augmentation-mode option is deprecated error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathMutableHandleGraph error:[get_input_file] could not open file "edit-embedded.gam" error[VPKG::load_one]: Correct input type not found in augmented.vg while loading handlegraph::PathHandleGraph [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes warning: when streaming in a GAM with -A, the output GAM will lose all non-Path related fields from the input t/17_vg_augment.t: line 50: jq.: command not found [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes [vg augment] warning: reading the entire GAM from stdin into memory. it is recommended to pass in a filename rather than - so it can be streamed over two passes t/17_vg_augment.t ..... 1..37 not ok 1 - direct augmentation embeds reads fully for well-supported SNPs # got: '0' # expected: '36' not ok 2 - adding a well-supported SNP by direct augmentation adds 3 more nodes # got: '' # expected: '18' not ok 3 - adding a well-supported SNP by direct augmentation adds 3 more nodes with -m 1 # got: '' # expected: '18' not ok 4 - direct augmentation embeds reads fully for probable errors # got: '0' # expected: '3' not ok 5 - adding a probable error by direct augmentation adds 3 more nodes # got: '' # expected: '18' ok 6 - path inclusion does not modify the graph when alignment is a perfect match ok 7 - path inclusion does not modify the graph when alignment has a SNP but doesnt meet the coverage threshold ok 8 - path inclusion does not modify the included path when alignment has a SNP but doesnt meet the coverage threshold ok 9 - 0 ok 10 - path inclusion with a complex variant introduces the right number of nodes ok 11 - path inclusion works for deletions ok 12 - SNPs can be included in the graph ok 13 - a soft clip at read start becomes a new head of the graph ok 14 - a soft clip at read end becomes a new tail of the graph ok 15 - augment -s works as desired ok 16 - the expected graph translation is exported when the graph is edited ok 17 - editing the graph with many SNP-containing alignments does not introduce duplicate identical nodes ok 18 - augmenting 2 snps with -m 1 produces the same nodes as default ok 19 - augmenting 2 snps and 2 errors with -m 11 produces the same nodes as with just the snps ok 20 - augmenting with 2snps makes correct number of nodes ok 21 - low-quality snp is filtered ok 22 - augmenting a packed graph produces same results as a vg graph ok 23 - augmenting a hash graph produces same results as a vg graph ok 24 - augmenting between nodes without filters works as expected ok 25 - augmenting between nodes with inactive filters works as expected ok 26 - augmenting between nodes N filter works as expected ok 27 - augmenting between nodes without filters works as expected on reverse strand ok 28 - augmenting between nodes with inactive filters works as expected on reverse strand ok 29 - augmenting between nodes N filter works as expected on reverse strand ok 30 - augmenting within node without filters works as expected ok 31 - augmenting within node with inactive filters works as expected ok 32 - augmenting within node with N filter works as expected ok 33 - augmenting within node without filters works as expected on reverse strand ok 34 - augmenting within node with inactive filters works as expected on reverse strand ok 35 - augmenting within node with N filter works as expected on reverse strand ok 36 - sequence in filtered alignment has removed insertion ok 37 - sequence in filtered alignment has removed insertion on reverse strand Failed 5/37 subtests terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_zYDKOh/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathMutableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error[VPKG::load_one]: Could not open tiny_aug.xg while loading handlegraph::HandleGraph error:[get_input_file] could not open file "tiny_aug.xg" index file inverting/miniFasta.fa.fai not found, generating... index file m.fa.fai not found, generating... t/18_vg_call.t ........ 1..6 ok 1 - calling empty gam gives empty VCF ok 2 - Called microinversion ok 3 - Fewer than 6 differences between called and true SV genotypes ok 4 - call output same on vg as xg ok 5 - call output same on vg as xg ok 6 - vg call finds true homozygous variants in a cyclic graph ok t/19_vg_compare.t ..... skipped: (no reason given) rapper: Parsing file with parser turtle and base URI http://example.org/vg rapper: Parsing returned 85 triples rapper: Parsing file with parser turtle and base URI http://example.org/vg rapper: Parsing returned 75 triples t/20_vgtordf.t ........ 1..6 ok 1 - vg view produces the expected number of lines of turtle ok 2 - vg view produces the expected number of lines of turtle ok 3 - rapper passed ok 4 - rapper passed ok 5 - vg view produces the expected number of lines of turtle ok 6 - vg view produces the expected number of lines of turtle ok terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_NQOQsl/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_P45tt6/stacktrace.txt Please include the stack trace file in your bug report! t/21_vg_filter.t ...... 1..10 ok 1 - vg filter with no options preserves input. ok 2 - vg filter downsamples correctly ok 3 - samtools 1.0+ and vg filter agree on how to select downsampled paired reads ok 4 - samtools 1.0+ and vg filter agree on how to select downsampled unpaired reads ok 5 - reads with refpos annotations not matching an exclusion regex are let through ok 6 - reads with refpos annotations matching an exclusion regex are removed ok 7 - negating a non-filter results in no reads ok 8 - a filter and its complement should form the entire file ok 9 - read pairs can be tropped by feature not ok 10 - read pairs can be kept if only one read fails # got: '0' # expected: '2' Failed 1/10 subtests t/22_ggsv.t ........... skipped: (no reason given) t/23_vectorize.t ...... skipped: (no reason given) t/25_circularize.t .... 1..2 ok 1 - a path may be circularized ok 2 - a circular path survives a round trip to/from xg ok [algorithms::normalize] iteration 1 current length 1014 [algorithms::normalize] normalized in 0 steps t/26_deconstruct.t .... 1..19 ok 1 - deconstruct retrieved original VCF (modulo adjacent snp allele) ok 2 - deconstructed hla vcf has correct number of sites ok 3 - deconstructed hla vcf has correct insertion ok 4 - deconstructed hla vcf with other path has correct number of sites ok 5 - deconstructed hla vcf has correct deletion ok 6 - path-based and exhaustive decontruction give equivalent sites when expected ok 7 - path that differs from reference in every alt has correct genotype ok 8 - path that is same as reference in every alt has correct genotype ok 9 - reference contig correctly written ok 10 - deconstruct correctly handles a simple inversion ok 11 - deconstruct correctly handles a simple inversion when the reference contains the reversing edge ok 12 - deconstruct correctly handles a cycle in the reference path when contained inside snarl ok 13 - deconstruct correctly handles a cycle in the alt path ok 14 - cyclic reference deconstruction has correct number of variants ok 15 - deconstruct correctly handles cycle in the reference path that spans snarl ok 16 - -P -A options return correct number of variants ok 17 - -P -A options use correct reference name ok 18 - -P -A identifies conflict in alt1 in second variant ok 19 - deconstructing vg graph gives same output as xg graph ok Statistics: Number of Non-Degenerate Snarls: 4 Snarls traversed by reads: 4 Snarls on reference: 0 Snarl length distribution: Statistics: Number of Non-Degenerate Snarls: 4 Snarls traversed by reads: 4 Snarls on reference: 4 Snarl length distribution: 2 1 1 3 index file flat1.fa.fai not found, generating... index file flat2.fa.fai not found, generating... Statistics: Number of Non-Degenerate Snarls: 8 Snarls traversed by reads: 8 Snarls on reference: 0 Snarl length distribution: index file flats.fa.fai not found, generating... terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_cqGOgY/stacktrace.txt Please include the stack trace file in your bug report! Warning: realigned read AGGGCTCATTGT doesn't touch either end of its snarl! Warning: realigned read CTCATTGTAACG doesn't touch either end of its snarl! Warning: realigned read TATGTCTGTAGG doesn't touch either end of its snarl! Warning: realigned read GCTCATTGTAAC doesn't touch either end of its snarl! Warning: realigned read TACAGACATATC doesn't touch either end of its snarl! Warning: realigned read CTGTAGGGCTCA doesn't touch either end of its snarl! Warning: realigned read TAGGGCTCATTG doesn't touch either end of its snarl! Warning: realigned read GTTACAATGAGC doesn't touch either end of its snarl! Warning: realigned read GAGCCCTACAGA doesn't touch either end of its snarl! Warning: realigned read GCCCTACAGACA doesn't touch either end of its snarl! Warning: realigned read TGTCTGTAGGGC doesn't touch either end of its snarl! Warning: realigned read ACGTTACAATGA doesn't touch either end of its snarl! Warning: realigned read TACAATGAGCCC doesn't touch either end of its snarl! Warning: realigned read CCTACAGACATA doesn't touch either end of its snarl! Warning: realigned read TGTCTGTAGGGC doesn't touch either end of its snarl! Warning: realigned read TGAGCCCTACAG doesn't touch either end of its snarl! Warning: realigned read GTAGGGCTCATT doesn't touch either end of its snarl! Warning: realigned read GCTCATTGTAAC doesn't touch either end of its snarl! Warning: realigned read ACGTTACAATGA doesn't touch either end of its snarl! Warning: realigned read GTCTGTAGGGCT doesn't touch either end of its snarl! Warning: realigned read TACAATGAGCCC doesn't touch either end of its snarl! Warning: realigned read GGGCTCATTGTA doesn't touch either end of its snarl! Warning: realigned read CTGTAGGGCTCA doesn't touch either end of its snarl! Warning: realigned read TTACAATGAGCC doesn't touch either end of its snarl! Warning: realigned read CCCTACAGACAT doesn't touch either end of its snarl! Statistics: Number of Non-Degenerate Snarls: 1 Snarls traversed by reads: 1 Snarls on reference: 1 Snarl length distribution: 0 1 t/27_vg_genotype.t .... 1..5 ok 1 - vg genotype runs successfully ok 2 - vg genotype runs successfully when emitting vcf ok 3 - called genotypes are correct in a small simulated example ok 4 - genotype format can be converted to and from JSON ok 5 - genotype finds big insert ok terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_rGxOY4/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_JhQlqp/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_wtIVjK/stacktrace.txt Please include the stack trace file in your bug report! [algorithms::normalize] iteration 1 current length 55 [algorithms::normalize] normalized in 0 steps [algorithms::normalize] iteration 1 current length 55 [algorithms::normalize] normalized in 0 steps terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_xh84cA/stacktrace.txt Please include the stack trace file in your bug report! t/28_translate.t ...... 1..2 ok 1 - alignments used to modify a graph may be projected back to the original graph and used to regenerate the same graph not ok 2 - translation overlay works and produces a sane result # got: '7477871ee13fab8541090e128d02a7f4' # expected: '3ce4390abe667b24eb5148e216a2f5ec' Failed 1/2 subtests Statistics: Number of Non-Degenerate Snarls: 4 Snarls traversed by reads: 4 Snarls on reference: 0 Snarl length distribution: Statistics: Number of Non-Degenerate Snarls: 4 Snarls traversed by reads: 4 Snarls on reference: 0 Snarl length distribution: t/29_vg_locify.t ...... 1..9 ok 1 - locify produces output for each input alignment ok 2 - the sorted list of loci has one locus per snarl ok 3 - the first locus is as expected ok 4 - a middle locus is as expected ok 5 - the last locus is as expected ok 6 - limitation to 2-best works ok 7 - limitation to 3-best works ok 8 - limitation to 4-best works ok 9 - we always get one allele when all the reads match the graph ok [vg] warning: node ID 44 appears multiple times. Skipping. [vg] warning: node ID 45 appears multiple times. Skipping. [vg] warning: node ID 43 appears multiple times. Skipping. [vg] warning: edge 43 end <-> 44 start appears multiple times. Skipping. [vg] warning: edge 43 end <-> 45 start appears multiple times. Skipping. [vg] warning: node ID 87 appears multiple times. Skipping. [vg] warning: node ID 88 appears multiple times. Skipping. [vg] warning: node ID 85 appears multiple times. Skipping. [vg] warning: node ID 86 appears multiple times. Skipping. [vg] warning: edge 87 end <-> 88 start appears multiple times. Skipping. [vg] warning: edge 85 end <-> 87 start appears multiple times. Skipping. [vg] warning: edge 85 end <-> 86 start appears multiple times. Skipping. [vg] warning: edge 86 end <-> 88 start appears multiple times. Skipping. [vg] warning: node ID 130 appears multiple times. Skipping. [vg] warning: node ID 131 appears multiple times. Skipping. [vg] warning: node ID 129 appears multiple times. Skipping. [vg] warning: edge 130 end <-> 131 start appears multiple times. Skipping. [vg] warning: edge 129 end <-> 130 start appears multiple times. Skipping. [vg] warning: edge 129 end <-> 131 start appears multiple times. Skipping. [vg] warning: node ID 173 appears multiple times. Skipping. [vg] warning: node ID 174 appears multiple times. Skipping. [vg] warning: node ID 172 appears multiple times. Skipping. [vg] warning: edge 173 end <-> 174 start appears multiple times. Skipping. [vg] warning: edge 172 end <-> 173 start appears multiple times. Skipping. [vg] warning: edge 172 end <-> 174 start appears multiple times. Skipping. Restricting to x from 1 to end Restricting to y from 1 to end t/30_vg_chunk.t ....... 1..24 ok 1 - vg chunk with no options preserves nodes ok 2 - vg chunk with no options preserves edges ok 3 - chunk has path going through node 9 ok 4 - chunk has path going through node 9 ok 5 - -s produces correct number of chunks ok 6 - gam chunker produces correct number of graphs ok 7 - gam chunker produces correct number of gams ok 8 - gam chunker produces bed with correct number of chunks ok 9 - gam chunker emits each matching read at most once ok 10 - chunk contains the expected number of alignments ok 11 - id chunker produces correct chunk size ok 12 - id chunker produces correct single chunk ok 13 - id chunker traces correct chunk size ok 14 - chunker extracts no threads from an empty gPBWT ok 15 - chunker extracts 2 local threads from a gBWT with 2 locally distinct threads in it ok 16 - chunker can extract a partial haplotype from a GBWT ok 17 - n-chunking works and chunks over the full graph ok 18 - path-based components finds subgraphs ok 19 - x gam chunk has correct number of reads ok 20 - y gam chunk has correct number of reads ok 21 - x gam chunk has correct number of reads with -p path ok 22 - y gam chunk has correct number of reads with -p path ok 23 - path-based component contains correct path length ok 24 - components finds subgraphs ok index file add/ref.fa.fai not found, generating... Variant 1: 3 haplotypes at ref:18: 32 bp vs. 33 bp haplotypes vs. graphs average Variant 2: 3 haplotypes at ref:21: 32 bp vs. 34 bp haplotypes vs. graphs average Variant 3: 3 haplotypes at ref:23: 33 bp vs. 34 bp haplotypes vs. graphs average Variant 1: 3 haplotypes at chrR:18: 32 bp vs. 33 bp haplotypes vs. graphs average Variant 2: 3 haplotypes at chrR:21: 32 bp vs. 34 bp haplotypes vs. graphs average Variant 3: 3 haplotypes at chrR:23: 33 bp vs. 34 bp haplotypes vs. graphs average Variant 1: 4 haplotypes at ref:2: 33 bp vs. 34 bp haplotypes vs. graphs average Variant 2: 4 haplotypes at ref:21: 33 bp vs. 36 bp haplotypes vs. graphs average Variant 3: 4 haplotypes at ref:32: 33 bp vs. 36 bp haplotypes vs. graphs average index file add/refN.fa.fai not found, generating... Variant 1: 4 haplotypes at ref:2: 33 bp vs. 34 bp haplotypes vs. graphs average Variant 2: 4 haplotypes at ref:21: 33 bp vs. 36 bp haplotypes vs. graphs average Variant 3: 4 haplotypes at ref:32: 33 bp vs. 36 bp haplotypes vs. graphs average index file add/ngap.fa.fai not found, generating... Variant 1: 2 haplotypes at ngap:10923: 224 bp vs. 224 bp haplotypes vs. graphs average Variant 2: 5 haplotypes at ngap:11014: 256 bp vs. 258 bp haplotypes vs. graphs average Variant 3: 5 haplotypes at ngap:11030: 256 bp vs. 261 bp haplotypes vs. graphs average Variant 4: 5 haplotypes at ngap:11035: 256 bp vs. 261 bp haplotypes vs. graphs average Variant 5: 5 haplotypes at ngap:11043: 256 bp vs. 261 bp haplotypes vs. graphs average Variant 1: 2 haplotypes at x:9: 160 bp vs. 161 bp haplotypes vs. graphs average Variant 2: 2 haplotypes at x:10: 160 bp vs. 167 bp haplotypes vs. graphs average Variant 3: 2 haplotypes at x:14: 160 bp vs. 167 bp haplotypes vs. graphs average Variant 4: 2 haplotypes at x:34: 160 bp vs. 167 bp haplotypes vs. graphs average Variant 5: 2 haplotypes at x:39: 160 bp vs. 167 bp haplotypes vs. graphs average Variant 6: 2 haplotypes at x:52: 224 bp vs. 231 bp haplotypes vs. graphs average Variant 7: 2 haplotypes at x:58: 224 bp vs. 232 bp haplotypes vs. graphs average Variant 8: 2 haplotypes at x:100: 256 bp vs. 265 bp haplotypes vs. graphs average Variant 9: 2 haplotypes at x:103: 256 bp vs. 267 bp haplotypes vs. graphs average Variant 10: 2 haplotypes at x:122: 288 bp vs. 299 bp haplotypes vs. graphs average Variant 11: 2 haplotypes at x:142: 288 bp vs. 301 bp haplotypes vs. graphs average Variant 12: 2 haplotypes at x:160: 306 bp vs. 319 bp haplotypes vs. graphs average Variant 13: 2 haplotypes at x:172: 338 bp vs. 353 bp haplotypes vs. graphs average Variant 14: 2 haplotypes at x:178: 313 bp vs. 327 bp haplotypes vs. graphs average Variant 15: 2 haplotypes at x:187: 313 bp vs. 327 bp haplotypes vs. graphs average Variant 16: 2 haplotypes at x:200: 294 bp vs. 306 bp haplotypes vs. graphs average Variant 17: 2 haplotypes at x:204: 294 bp vs. 306 bp haplotypes vs. graphs average Variant 18: 2 haplotypes at x:218: 288 bp vs. 300 bp haplotypes vs. graphs average Variant 19: 2 haplotypes at x:221: 288 bp vs. 300 bp haplotypes vs. graphs average Variant 20: 2 haplotypes at x:272: 256 bp vs. 266 bp haplotypes vs. graphs average Variant 21: 2 haplotypes at x:277: 256 bp vs. 272 bp haplotypes vs. graphs average Variant 22: 2 haplotypes at x:287: 256 bp vs. 272 bp haplotypes vs. graphs average Variant 23: 2 haplotypes at x:294: 256 bp vs. 272 bp haplotypes vs. graphs average Variant 24: 2 haplotypes at x:297: 291 bp vs. 305 bp haplotypes vs. graphs average Variant 25: 2 haplotypes at x:312: 323 bp vs. 340 bp haplotypes vs. graphs average Variant 26: 2 haplotypes at x:313: 323 bp vs. 341 bp haplotypes vs. graphs average Variant 27: 2 haplotypes at x:345: 291 bp vs. 306 bp haplotypes vs. graphs average Variant 28: 2 haplotypes at x:347: 323 bp vs. 339 bp haplotypes vs. graphs average Variant 29: 2 haplotypes at x:353: 311 bp vs. 326 bp haplotypes vs. graphs average Variant 30: 2 haplotypes at x:373: 291 bp vs. 306 bp haplotypes vs. graphs average Variant 31: 2 haplotypes at x:397: 288 bp vs. 307 bp haplotypes vs. graphs average Variant 32: 2 haplotypes at x:398: 288 bp vs. 307 bp haplotypes vs. graphs average Variant 33: 2 haplotypes at x:405: 241 bp vs. 258 bp haplotypes vs. graphs average Variant 34: 2 haplotypes at x:408: 241 bp vs. 258 bp haplotypes vs. graphs average Variant 35: 2 haplotypes at x:466: 254 bp vs. 260 bp haplotypes vs. graphs average Variant 36: 2 haplotypes at x:474: 286 bp vs. 295 bp haplotypes vs. graphs average Variant 37: 2 haplotypes at x:489: 286 bp vs. 296 bp haplotypes vs. graphs average Variant 38: 2 haplotypes at x:500: 286 bp vs. 297 bp haplotypes vs. graphs average Variant 39: 2 haplotypes at x:523: 300 bp vs. 309 bp haplotypes vs. graphs average Variant 40: 2 haplotypes at x:533: 289 bp vs. 299 bp haplotypes vs. graphs average Variant 41: 1 haplotypes at x:553: 257 bp vs. 263 bp haplotypes vs. graphs average Variant 42: 1 haplotypes at x:566: 257 bp vs. 263 bp haplotypes vs. graphs average Variant 43: 2 haplotypes at x:629: 277 bp vs. 281 bp haplotypes vs. graphs average Variant 44: 2 haplotypes at x:647: 278 bp vs. 285 bp haplotypes vs. graphs average Variant 45: 2 haplotypes at x:654: 278 bp vs. 287 bp haplotypes vs. graphs average Variant 46: 2 haplotypes at x:668: 310 bp vs. 320 bp haplotypes vs. graphs average Variant 47: 2 haplotypes at x:669: 310 bp vs. 321 bp haplotypes vs. graphs average Variant 48: 2 haplotypes at x:681: 289 bp vs. 299 bp haplotypes vs. graphs average Variant 49: 2 haplotypes at x:688: 289 bp vs. 299 bp haplotypes vs. graphs average Variant 50: 2 haplotypes at x:698: 280 bp vs. 289 bp haplotypes vs. graphs average Variant 51: 2 haplotypes at x:714: 299 bp vs. 307 bp haplotypes vs. graphs average Variant 52: 2 haplotypes at x:757: 287 bp vs. 299 bp haplotypes vs. graphs average Variant 53: 2 haplotypes at x:775: 273 bp vs. 285 bp haplotypes vs. graphs average Variant 54: 2 haplotypes at x:777: 273 bp vs. 286 bp haplotypes vs. graphs average Variant 55: 2 haplotypes at x:789: 273 bp vs. 287 bp haplotypes vs. graphs average Variant 56: 2 haplotypes at x:795: 273 bp vs. 287 bp haplotypes vs. graphs average Variant 57: 2 haplotypes at x:813: 287 bp vs. 300 bp haplotypes vs. graphs average Variant 58: 2 haplotypes at x:823: 287 bp vs. 302 bp haplotypes vs. graphs average Variant 59: 2 haplotypes at x:827: 319 bp vs. 334 bp haplotypes vs. graphs average Variant 60: 2 haplotypes at x:858: 297 bp vs. 310 bp haplotypes vs. graphs average Variant 61: 2 haplotypes at x:859: 297 bp vs. 312 bp haplotypes vs. graphs average Variant 62: 2 haplotypes at x:860: 297 bp vs. 312 bp haplotypes vs. graphs average Variant 63: 2 haplotypes at x:877: 287 bp vs. 303 bp haplotypes vs. graphs average Variant 64: 2 haplotypes at x:888: 244 bp vs. 262 bp haplotypes vs. graphs average Variant 65: 2 haplotypes at x:899: 243 bp vs. 263 bp haplotypes vs. graphs average Variant 66: 2 haplotypes at x:901: 243 bp vs. 264 bp haplotypes vs. graphs average Variant 67: 2 haplotypes at x:916: 224 bp vs. 243 bp haplotypes vs. graphs average Variant 68: 2 haplotypes at x:917: 224 bp vs. 243 bp haplotypes vs. graphs average Variant 69: 2 haplotypes at x:923: 223 bp vs. 243 bp haplotypes vs. graphs average Variant 70: 2 haplotypes at x:925: 223 bp vs. 243 bp haplotypes vs. graphs average Variant 71: 2 haplotypes at x:929: 222 bp vs. 242 bp haplotypes vs. graphs average Variant 72: 2 haplotypes at x:939: 204 bp vs. 223 bp haplotypes vs. graphs average Variant 73: 2 haplotypes at x:945: 204 bp vs. 223 bp haplotypes vs. graphs average Variant 74: 2 haplotypes at x:972: 177 bp vs. 194 bp haplotypes vs. graphs average Variant 75: 2 haplotypes at x:1000: 136 bp vs. 149 bp haplotypes vs. graphs average terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_l04pO9/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'std::runtime_error' what(): Contig ref mentioned in VCF but not found in graph ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_mhd3vc/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_fl6gsL/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'std::runtime_error' what(): Contig ref mentioned in VCF but not found in graph ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_C0G1WM/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::PathHandleGraph t/31_vg_add.t ......... 1..9 ok 1 - vg add can create a graph ok 2 - vg add can create a graph with contig renames ok 3 - vg add produces the same graph from VCFs with different contig names ok 4 - having reference Ns does not affect the graph topology ok 5 - adding variants adds only the alt bases near large N gaps ok 6 - vg add can create a slightly larger graph ok 7 - ranks are calculated for emitted paths not ok 8 - graphs with backward nodes can be added to # got: '' # expected: '5' not ok 9 - graphs with backward and forward nodes can be added to # got: '' # expected: '5' Failed 2/9 subtests terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_lY1pRq/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::PathHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error:[get_input_file] could not open file "snarls.xg" Restricting to x from 1 to end Restricting to y from 1 to end t/32_vg_snarls.t ...... 1..9 not ok 1 - vg snarls made right number of protobuf Snarls # got: '0' # expected: '3' not ok 2 - vg snarls made right number of protobuf SnarlTraversals # got: '0' # expected: '6' not ok 3 - vg snarls on xg made right number of protobuf Snarls # got: '0' # expected: '3' not ok 4 - vg snarls on xg made right number of protobuf SnarlTraversals # got: '0' # expected: '6' ok 5 - vcf traversals are the same as exhaustive traversals for tiny graph ok 6 - vcf traversals are the same as exhaustive traversals for inversion ok 7 - vcf traversals are the same as exhaustive traversals for ins_and_del graph ok 8 - correct number of snarls when parallelizing on compoents ok 9 - same number of snarls when parallelizing on components Failed 4/9 subtests warning:[vg mpmap] Could not find 1000 unambiguous read pair mappings to estimate fragment length ditribution. Mapping read pairs as independent single-ended reads. Consider decreasing sample size (-b). warning:[vg mpmap] Could not find 1000 unambiguous read pair mappings to estimate fragment length ditribution. Mapping read pairs as independent single-ended reads. Consider decreasing sample size (-b). t/33_vg_mpmap.t ....... 1..14 ok 1 - MAPQ is 0 without haplotype info ok 2 - haplotype match can disambiguate ok 3 - MAPQ is 0 when paired without haplotype info ok 4 - haplotype match can disambiguate paired ok 5 - use of haplotype-aware mapping is recorded ok 6 - Haplotype-oblivious mapping places read on the wrong contig ok 7 - Haplotype-oblivious mapping places read with MAPQ 0 ok 8 - Haplotype-aware mapping places read on the right contig ok 9 - Haplotype-aware mapping places read with nonzero MAPQ ok 10 - paired read alignments forced to be consistent have lower score than unrestricted alignments ok 11 - paired read alignments forced to be consistent are closer together in node id space than unrestricted alignments ok 12 - paired read alignments forced to be near each other are closer together in node id space than those forced to be far apart ok 13 - small batches are still all paired in the output ok 14 - multipath mapping works in scenarios that trigger branch point trimming ok t/34_vg_pack.t ........ 1..17 ok 1 - allele observation packing detects 2 SNPs ok 2 - pileup packs agree with graph coverage ok 3 - graph coverages are merged from multiple .cx indexes ok 4 - edit records are merged from multiple .cx indexes ok 5 - binned edit accumulation does not affect the result ok 6 - pack records are filtered by node id ok 7 - pack records are filtered by node id ok 8 - pack index merging produces the expected result ok 9 - pack index merging produces the expected result for edges ok 10 - pack computes the same total edge coverage as pileup ok 11 - pack stores the correct edge pileup to disk ok 12 - qual-adjust packing detects 1 base with 0 quality ok 13 - qual-adjust packing gets correct edge support ok 14 - node packs on vg same as xg ok 15 - edge packs on vg same as xg ok 16 - node packs same on vg when using 3 threads as when using 1 ok 17 - edge packs same on vg when using 2 threads as when using 1 ok terminate called after throwing an instance of 'j2pb_error' what(): Load failed: unable to decode byte 0xff ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_VHNsIm/stacktrace.txt Please include the stack trace file in your bug report! error[VPKG::load_one]: Correct input type not found while loading handlegraph::HandleGraph error:[get_input_file] could not open file "circular_path.xg" t/36_vg_annotate.t .... 1..7 ok 1 - we can detect when reads contain non-reference variation ok 2 - vg annotate finds the right number of reads overlapping a feature ok 3 - all reads overlapping a feature fall on its node ok 4 - vg annotate finds no reads touching both of two distant features ok 5 - vg annotate shows reads having to go through one feature to get to another at the end ok 6 - vg annotate shows all reads overlapping a whole-reference-covering feature not ok 7 - annotations derived from BED can span the end/start joins of circular paths # got: '' # expected: '{"node_id":"1","offset":"5"} # {"node_id":"1"}' Failed 1/7 subtests t/37_vg_gbwt.t ........ 1..42 ok 1 - chromosome x: 2 threads ok 2 - chromosome x: 1 contig ok 3 - chromosome x: 2 haplotypes ok 4 - chromosome x: 1 sample ok 5 - chromosome x: 2 thread names ok 6 - chromosome x: 1 contig name ok 7 - chromosome x: 1 sample name ok 8 - chromosome y: 2 threads ok 9 - chromosome y: 1 contig ok 10 - chromosome y: 2 haplotypes ok 11 - chromosome y: 1 sample ok 12 - GBWT indexes can be merged ok 13 - merge: 4 threads ok 14 - merge: 2 contigs ok 15 - merge: 2 haplotypes ok 16 - merge: 1 sample ok 17 - GBWT indexes can be merged with the fast algorithm ok 18 - fast merge: 4 threads ok 19 - fast merge: 2 contigs ok 20 - fast merge: 2 haplotypes ok 21 - fast merge: 1 sample ok 22 - the merged indexes are identical ok 23 - there is 1 thread in the index ok 24 - there are 3 threads in the index ok 25 - samples can be removed from a GBWT index ok 26 - the sample was removed ok 27 - threads can be extracted from GBWT ok 28 - the thread files are identical ok 29 - GBWTGraph construction was successful ok 30 - GBWTGraph was correctly serialized ok 31 - GBWT/GBWTGraph construction from path cover was successful ok 32 - GBWTGraph was correctly serialized ok 33 - path cover: 32 threads ok 34 - path cover: 2 contigs ok 35 - path cover: 16 haplotypes ok 36 - path cover: 16 samples ok 37 - GBWT/GBWTGraph construction from local haplotypes was successful ok 38 - GBWTGraph was correctly serialized ok 39 - local haplotypes: 32 threads ok 40 - local haplotypes: 2 contigs ok 41 - local haplotypes: 16 haplotypes ok 42 - local haplotypes: 16 samples ok t/38_vg_prune.t ....... 1..18 ok 1 - pruning produces the correct number of components ok 2 - pruning leaves the correct number of nodes ok 3 - pruning leaves the correct number of edges ok 4 - pruning without high-degree nodes produces the correct number of components ok 5 - pruning without high-degree nodes leaves the correct number of nodes ok 6 - pruning without high-degree nodes leaves the correct number of edges ok 7 - pruning with path restoring produces the correct number of components ok 8 - pruning with path restoring leaves the correct number of nodes ok 9 - pruning with path restoring leaves the correct number of edges ok 10 - pruning with path/thread unfolding produces the correct number of components ok 11 - pruning with path/thread unfolding produces the correct number of nodes ok 12 - pruning with path/thread unfolding produces the correct number of edges ok 13 - pruning with path unfolding produces the correct number of components ok 14 - pruning with path unfolding produces the correct number of nodes ok 15 - pruning with path unfolding produces the correct number of edges ok 16 - empty mapping starts from the right node id ok 17 - the first unfolded graph adds the correct number of nodes to the mapping ok 18 - the second unfolded graph adds the correct number of nodes to the mapping ok t/39_vg_inject.t ...... 1..10 ok 1 - reads are generated ok 2 - vg inject works for all reads included in the original bam ok 3 - vg inject retains read names ok 4 - vg inject works perfectly for the position of alignment in the simple graph ok 5 - vg inject works perfectly for the position of alignment ok 6 - vg inject works perfectly for the mapping quality of alignment ok 7 - vg inject works perfectly for the cigar of alignment in the simple graph ok 8 - vg inject works perfectly for the cigar of alignment ok 9 - vg inject preserves all reads ok 10 - vg inject works perfectly for the reads flagged as is_reverse ok 1000 reads correct t/40_vg_gamcompare.t .. 1..2 ok 1 - gamcompare completes ok 2 - gamcompare says the truth is correctly mapped ok t/41_vg_viz.t ......... 1..1 ok 1 - vg viz runs ok t/42_vg_gamsort.t ..... 1..3 ok 1 - Sorting a GAM orders the alignments by min node ID ok 2 - sorted GAMs can be indexed during the sort ok 3 - Sorting a GAM with RocksDB orders the alignments by min node ID ok t/43_vg_simplify.t .... 1..5 ok 1 - vg simplify runs through when popping small bubbles ok 2 - simplification pops all the bubbles in a simple graph ok 3 - vg simplify runs through when removing rare variants ok 4 - the graph is valid after removing rare variants ok 5 - simplification keeps only some variants ok t/44_vg_benchmark.t ... 1..1 ok 1 - vg benchmark completes succesfully ok t/45_vg_sort.t ........ 1..6 ok 1 - ids in our test graph are not initially in sorted order ok 2 - a vg graph can be sorted and indexed by ID without crashing ok 3 - sort by ID actually puts nodes in ID order ok 4 - a vg graph can be sorted topologically ok 5 - a vg graph can be sorted with Eades algorithm without crashing ok 6 - a vg graph can be sorted with the max-flow algorithm without crashing ok t/46_vg_minimizer.t ... 1..10 ok 1 - default parameters ok 2 - single-threaded construction ok 3 - construction is deterministic ok 4 - minimizer parameters ok 5 - setting -k -w works correctly ok 6 - construction from GBWTGraph ok 7 - construction is deterministic ok 8 - multiple graphs: first ok 9 - multiple graphs: second ok 10 - construction is deterministic ok t/47_vg_dotplot.t ..... 1..1 ok 1 - vg dotplot runs successfully ok t/48_vg_convert.t ..... 1..3 ok 1 - vg convert maintains same nodes throughout xg conversion ok 2 - vg convert maintains same nodes throughout hash-graph conversion ok 3 - vg convert maintains same nodes throughout packed-graph conversion ok t/49_vg_depth.t ....... 1..3 ok 1 - vg depth gets correct depth from gam ok 2 - vg depth gets correct depth from pack ok 3 - vg depth gets correct number of bins ok Test Summary Report ------------------- t/03_vg_view.t (Wstat: 0 Tests: 20 Failed: 3) Failed tests: 5-6, 11 t/05_vg_find.t (Wstat: 0 Tests: 28 Failed: 2) Failed tests: 23-24 t/07_vg_map.t (Wstat: 0 Tests: 55 Failed: 10) Failed tests: 43-52 t/14_vg_mod.t (Wstat: 0 Tests: 32 Failed: 2) Failed tests: 13, 16 t/15_vg_surject.t (Wstat: 0 Tests: 27 Failed: 10) Failed tests: 10, 15-23 t/17_vg_augment.t (Wstat: 0 Tests: 37 Failed: 5) Failed tests: 1-5 t/21_vg_filter.t (Wstat: 0 Tests: 10 Failed: 1) Failed test: 10 t/28_translate.t (Wstat: 0 Tests: 2 Failed: 1) Failed test: 2 t/31_vg_add.t (Wstat: 0 Tests: 9 Failed: 2) Failed tests: 8-9 t/32_vg_snarls.t (Wstat: 0 Tests: 9 Failed: 4) Failed tests: 1-4 t/36_vg_annotate.t (Wstat: 0 Tests: 7 Failed: 1) Failed test: 7 Files=49, Tests=626, 425 wallclock secs ( 0.74 usr 0.21 sys + 447.44 cusr 126.12 csys = 574.51 CPU) Result: FAIL make[1]: *** [debian/rules:59: override_dh_auto_test-arch] Error 1 make[1]: Leaving directory '/<>/vg-1.22.0+ds' make: *** [debian/rules:17: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20200412-0845 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build-Space: 5256564 Build-Time: 4390 Distribution: focal Fail-Stage: build Host Architecture: arm64 Install-Time: 138 Job: vg_1.22.0+ds-1.dsc Machine Architecture: arm64 Package: vg Package-Time: 4539 Source-Version: 1.22.0+ds-1 Space: 5256564 Status: attempted Version: 1.22.0+ds-1 -------------------------------------------------------------------------------- Finished at 20200412-0845 Build needed 01:15:39, 5256564k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-18984357 Scanning for processes to kill in build PACKAGEBUILD-18984357