https://launchpad.net/ubuntu/+archive/test-rebuild-20210805-impish/+build/21946007 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-ppc64el-008 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:00:19 UTC 2021 ppc64le Buildd toolchain package versions: launchpad-buildd_200~495~ubuntu18.04.1 python3-lpbuildd_200~495~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.8 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 2 Sep 22:02:38 ntpdate[1940]: adjust time server 10.211.37.1 offset 0.284906 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=impish --arch=ppc64el PACKAGEBUILD-21946007 --image-type chroot /home/buildd/filecache-default/24da345c42c7b7d23c5463cf41fef66fd18cba1d Creating target for build PACKAGEBUILD-21946007 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=impish --arch=ppc64el PACKAGEBUILD-21946007 Starting target for build PACKAGEBUILD-21946007 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=impish --arch=ppc64el PACKAGEBUILD-21946007 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish main' 'deb http://ftpmaster.internal/ubuntu impish main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-21946007 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=impish --arch=ppc64el PACKAGEBUILD-21946007 Adding trusted keys to build-PACKAGEBUILD-21946007 Warning: apt-key is deprecated. Manage keyring files in trusted.gpg.d instead (see apt-key(8)). OK Warning: apt-key is deprecated. Manage keyring files in trusted.gpg.d instead (see apt-key(8)). /etc/apt/trusted.gpg -------------------- pub rsa1024 2009-10-22 [SC] 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid [ unknown] Launchpad Toolchain builds /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-cdimage.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 8439 38DF 228D 22F7 B374 2BC0 D94A A3F0 EFE2 1092 uid [ unknown] Ubuntu CD Image Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2018-archive.gpg ------------------------------------------------------ pub rsa4096 2018-09-17 [SC] F6EC B376 2474 EDA9 D21B 7022 8719 20D1 991B C93C uid [ unknown] Ubuntu Archive Automatic Signing Key (2018) RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=impish --arch=ppc64el PACKAGEBUILD-21946007 Updating target for build PACKAGEBUILD-21946007 Get:1 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish InRelease [17.5 kB] Get:2 http://ftpmaster.internal/ubuntu impish InRelease [269 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main ppc64el Packages [31.7 kB] Get:4 http://ftpmaster.internal/ubuntu impish/main ppc64el Packages [1360 kB] Get:5 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main Translation-en [11.9 kB] Get:6 http://ftpmaster.internal/ubuntu impish/main Translation-en [513 kB] Get:7 http://ftpmaster.internal/ubuntu impish/restricted ppc64el Packages [4096 B] Get:8 http://ftpmaster.internal/ubuntu impish/restricted Translation-en [12.5 kB] Get:9 http://ftpmaster.internal/ubuntu impish/universe ppc64el Packages [13.3 MB] Get:10 http://ftpmaster.internal/ubuntu impish/universe Translation-en [5464 kB] Get:11 http://ftpmaster.internal/ubuntu impish/multiverse ppc64el Packages [174 kB] Get:12 http://ftpmaster.internal/ubuntu impish/multiverse Translation-en [108 kB] Fetched 21.2 MB in 6s (3677 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: g++-10 libstdc++-10-dev Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: cpp-11 g++-11 gcc-11 libexpat1 libgcc-11-dev libmpdec3 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libstdc++-11-dev media-types python3 python3-minimal python3-psutil python3.9 python3.9-minimal The following packages will be upgraded: advancecomp apt base-files base-passwd bash binutils binutils-common binutils-powerpc64le-linux-gnu bsdutils build-essential cpp cpp-10 dash debconf diffutils dpkg dpkg-dev e2fsprogs findutils g++ g++-10 gcc gcc-10 gcc-10-base gcc-11-base gpg gpg-agent gpgconf gpgv gzip libapparmor1 libapt-pkg6.0 libasan6 libassuan0 libatomic1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libctf-nobfd0 libctf0 libdb5.3 libdevmapper1.02.1 libdpkg-perl libext2fs2 libgcc-10-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgssapi-krb5-2 libhogweed6 libidn2-0 libisl23 libitm1 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblsan0 liblz4-1 liblzma5 libmount1 libnettle8 libnsl-dev libnsl2 libpam-modules libpam-modules-bin libpam-runtime libpam0g libperl5.32 libprocps8 libquadmath0 libreadline8 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++-10-dev libstdc++6 libsystemd0 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login logsave lto-disabled-list mount openssl passwd perl perl-base perl-modules-5.32 pinentry-curses pkgbinarymangler procps readline-common systemd systemd-sysv systemd-timesyncd sysvinit-utils usrmerge util-linux xz-utils zlib1g 116 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. Need to get 252 MB of archives. After this operation, 491 MB of additional disk space will be used. Get:1 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main ppc64el libc6-dev ppc64el 2.34-0ubuntu1~ppa5 [2025 kB] Get:2 http://ftpmaster.internal/ubuntu impish/main ppc64el libcrypt-dev ppc64el 1:4.4.18-4ubuntu1 [131 kB] Get:3 http://ftpmaster.internal/ubuntu impish/main ppc64el libnsl-dev ppc64el 1.3.0-2 [73.4 kB] Get:4 http://ftpmaster.internal/ubuntu impish/main ppc64el libcrypt1 ppc64el 1:4.4.18-4ubuntu1 [97.1 kB] Get:5 http://ftpmaster.internal/ubuntu impish/main ppc64el libnsl2 ppc64el 1.3.0-2 [43.7 kB] Get:6 http://ftpmaster.internal/ubuntu impish/main ppc64el libasan6 ppc64el 11.2.0-1ubuntu2 [2309 kB] Get:7 http://ftpmaster.internal/ubuntu impish/main ppc64el libubsan1 ppc64el 11.2.0-1ubuntu2 [952 kB] Get:8 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main ppc64el libc-dev-bin ppc64el 2.34-0ubuntu1~ppa5 [21.3 kB] Get:9 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main ppc64el linux-libc-dev ppc64el 5.13.0-14.14 [1210 kB] Get:10 http://ftpmaster.internal/ubuntu impish/main ppc64el libtsan0 ppc64el 11.2.0-1ubuntu2 [2281 kB] Get:11 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main ppc64el libc6 ppc64el 2.34-0ubuntu1~ppa5 [3225 kB] Get:12 http://ftpmaster.internal/ubuntu impish/main ppc64el libquadmath0 ppc64el 11.2.0-1ubuntu2 [166 kB] Get:13 http://ftpmaster.internal/ubuntu impish/main ppc64el liblsan0 ppc64el 11.2.0-1ubuntu2 [996 kB] Get:14 http://ftpmaster.internal/ubuntu impish/main ppc64el libitm1 ppc64el 11.2.0-1ubuntu2 [33.0 kB] Get:15 http://ftpmaster.internal/ubuntu impish/main ppc64el libgomp1 ppc64el 11.2.0-1ubuntu2 [130 kB] Get:16 http://ftpmaster.internal/ubuntu impish/main ppc64el gcc-11-base ppc64el 11.2.0-1ubuntu2 [21.5 kB] Get:17 http://ftpmaster.internal/ubuntu impish/main ppc64el libgcc-s1 ppc64el 11.2.0-1ubuntu2 [34.5 kB] Get:18 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main ppc64el libc-bin ppc64el 2.34-0ubuntu1~ppa5 [1060 kB] Get:19 http://ftpmaster.internal/ubuntu impish/main ppc64el libcc1-0 ppc64el 11.2.0-1ubuntu2 [47.7 kB] Get:20 http://ftpmaster.internal/ubuntu impish/main ppc64el libatomic1 ppc64el 11.2.0-1ubuntu2 [10.7 kB] Get:21 http://ftpmaster.internal/ubuntu impish/main ppc64el libstdc++6 ppc64el 11.2.0-1ubuntu2 [759 kB] Get:22 http://ftpmaster.internal/ubuntu impish/main ppc64el base-files ppc64el 11.1ubuntu3 [61.1 kB] Get:23 http://ftpmaster.internal/ubuntu impish/main ppc64el bash ppc64el 5.1-3ubuntu1 [833 kB] Get:24 http://ftpmaster.internal/ubuntu impish/main ppc64el bsdutils ppc64el 1:2.36.1-8ubuntu1 [86.5 kB] Get:25 http://ftpmaster.internal/ubuntu impish/main ppc64el libperl5.32 ppc64el 5.32.1-3ubuntu3 [4822 kB] Get:26 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main ppc64el dpkg ppc64el 1.20.9ubuntu13 [1322 kB] Get:27 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main ppc64el g++ ppc64el 4:11.2.0-1ubuntu1 [1408 B] Get:28 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main ppc64el gcc ppc64el 4:11.2.0-1ubuntu1 [5152 B] Get:29 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main ppc64el cpp ppc64el 4:11.2.0-1ubuntu1 [27.7 kB] Get:30 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main ppc64el dpkg-dev all 1.20.9ubuntu13 [938 kB] Get:31 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main ppc64el libdpkg-perl all 1.20.9ubuntu13 [235 kB] Get:32 http://ftpmaster.internal/ubuntu impish/main ppc64el perl ppc64el 5.32.1-3ubuntu3 [227 kB] Get:33 http://ftpmaster.internal/ubuntu impish/main ppc64el perl-base ppc64el 5.32.1-3ubuntu3 [1830 kB] Get:34 http://ftpmaster.internal/ubuntu impish/main ppc64el perl-modules-5.32 all 5.32.1-3ubuntu3 [2945 kB] Get:35 http://ftpmaster.internal/ubuntu impish/main ppc64el libdb5.3 ppc64el 5.3.28+dfsg1-0.8ubuntu1 [719 kB] Get:36 http://ftpmaster.internal/ubuntu impish/main ppc64el zlib1g ppc64el 1:1.2.11.dfsg-2ubuntu7 [72.2 kB] Get:37 http://ftpmaster.internal/ubuntu impish/main ppc64el debconf all 1.5.77 [121 kB] Get:38 http://ftpmaster.internal/ubuntu impish/main ppc64el dash ppc64el 0.5.11+git20210120+802ebd4-1 [101 kB] Get:39 http://ftpmaster.internal/ubuntu impish/main ppc64el diffutils ppc64el 1:3.7-5ubuntu1 [213 kB] Get:40 http://ftpmaster.internal/ubuntu impish/main ppc64el findutils ppc64el 4.8.0-1ubuntu2 [382 kB] Get:41 http://ftpmaster.internal/ubuntu impish/main ppc64el gzip ppc64el 1.10-4ubuntu1 [103 kB] Get:42 http://ftpmaster.internal/ubuntu impish/main ppc64el login ppc64el 1:4.8.1-1ubuntu9 [226 kB] Get:43 http://ftpmaster.internal/ubuntu impish/main ppc64el util-linux ppc64el 2.36.1-8ubuntu1 [1080 kB] Get:44 http://ftpmaster.internal/ubuntu impish/main ppc64el base-passwd ppc64el 3.5.51 [50.1 kB] Get:45 http://ftpmaster.internal/ubuntu impish/main ppc64el sysvinit-utils ppc64el 2.96-7ubuntu1 [21.4 kB] Get:46 http://ftpmaster.internal/ubuntu impish/main ppc64el libgcrypt20 ppc64el 1.8.7-5ubuntu1 [484 kB] Get:47 http://ftpmaster.internal/ubuntu impish/main ppc64el liblz4-1 ppc64el 1.9.3-2 [66.7 kB] Get:48 http://ftpmaster.internal/ubuntu impish/main ppc64el liblzma5 ppc64el 5.2.5-2 [113 kB] Get:49 http://ftpmaster.internal/ubuntu impish/main ppc64el systemd-sysv ppc64el 248.3-1ubuntu3 [10.5 kB] Get:50 http://ftpmaster.internal/ubuntu impish/main ppc64el systemd-timesyncd ppc64el 248.3-1ubuntu3 [32.0 kB] Get:51 http://ftpmaster.internal/ubuntu impish/main ppc64el libapparmor1 ppc64el 3.0.3-0ubuntu1 [44.1 kB] Get:52 http://ftpmaster.internal/ubuntu impish/main ppc64el libaudit-common all 1:3.0-2ubuntu2 [4788 B] Get:53 http://ftpmaster.internal/ubuntu impish/main ppc64el libaudit1 ppc64el 1:3.0-2ubuntu2 [43.2 kB] Get:54 http://ftpmaster.internal/ubuntu impish/main ppc64el libnettle8 ppc64el 3.7.3-1 [181 kB] Get:55 http://ftpmaster.internal/ubuntu impish/main ppc64el libhogweed6 ppc64el 3.7.3-1 [198 kB] Get:56 http://ftpmaster.internal/ubuntu impish/main ppc64el libidn2-0 ppc64el 2.3.1-1 [53.6 kB] Get:57 http://ftpmaster.internal/ubuntu impish/main ppc64el libgnutls30 ppc64el 3.7.1-4ubuntu1 [915 kB] Get:58 http://ftpmaster.internal/ubuntu impish/main ppc64el libssl1.1 ppc64el 1.1.1j-1ubuntu5 [1585 kB] Get:59 http://ftpmaster.internal/ubuntu impish/main ppc64el libzstd1 ppc64el 1.4.8+dfsg-2.1 [313 kB] Get:60 http://ftpmaster.internal/ubuntu impish/main ppc64el libkmod2 ppc64el 28-1ubuntu4 [52.7 kB] Get:61 http://ftpmaster.internal/ubuntu impish/main ppc64el libblkid1 ppc64el 2.36.1-8ubuntu1 [122 kB] Get:62 http://ftpmaster.internal/ubuntu impish/main ppc64el libmount1 ppc64el 2.36.1-8ubuntu1 [140 kB] Get:63 http://ftpmaster.internal/ubuntu impish/main ppc64el libpam0g ppc64el 1.3.1-5ubuntu8 [67.0 kB] Get:64 http://ftpmaster.internal/ubuntu impish/main ppc64el mount ppc64el 2.36.1-8ubuntu1 [117 kB] Get:65 http://ftpmaster.internal/ubuntu impish/main ppc64el systemd ppc64el 248.3-1ubuntu3 [4926 kB] Get:66 http://ftpmaster.internal/ubuntu impish/main ppc64el libsystemd0 ppc64el 248.3-1ubuntu3 [382 kB] Get:67 http://ftpmaster.internal/ubuntu impish/main ppc64el libudev1 ppc64el 248.3-1ubuntu3 [96.4 kB] Get:68 http://ftpmaster.internal/ubuntu impish/main ppc64el libapt-pkg6.0 ppc64el 2.3.7 [1020 kB] Get:69 http://ftpmaster.internal/ubuntu impish/main ppc64el gpgv ppc64el 2.2.20-1ubuntu4 [156 kB] Get:70 http://ftpmaster.internal/ubuntu impish/main ppc64el apt ppc64el 2.3.7 [1427 kB] Get:71 http://ftpmaster.internal/ubuntu impish/main ppc64el libpam-modules-bin ppc64el 1.3.1-5ubuntu8 [49.5 kB] Get:72 http://ftpmaster.internal/ubuntu impish/main ppc64el libpam-modules ppc64el 1.3.1-5ubuntu8 [317 kB] Get:73 http://ftpmaster.internal/ubuntu impish/main ppc64el logsave ppc64el 1.46.2-1ubuntu2 [12.0 kB] Get:74 http://ftpmaster.internal/ubuntu impish/main ppc64el libext2fs2 ppc64el 1.46.2-1ubuntu2 [224 kB] Get:75 http://ftpmaster.internal/ubuntu impish/main ppc64el e2fsprogs ppc64el 1.46.2-1ubuntu2 [591 kB] Get:76 http://ftpmaster.internal/ubuntu impish/main ppc64el libpython3.9-minimal ppc64el 3.9.6-1 [753 kB] Get:77 http://ftpmaster.internal/ubuntu impish/main ppc64el libexpat1 ppc64el 2.3.0-1 [78.8 kB] Get:78 http://ftpmaster.internal/ubuntu impish/main ppc64el python3.9-minimal ppc64el 3.9.6-1 [1834 kB] Get:79 http://ftpmaster.internal/ubuntu impish/main ppc64el python3-minimal ppc64el 3.9.4-1 [23.8 kB] Get:80 http://ftpmaster.internal/ubuntu impish/main ppc64el media-types all 4.0.0 [22.2 kB] Get:81 http://ftpmaster.internal/ubuntu impish/main ppc64el libmpdec3 ppc64el 2.5.1-2 [97.3 kB] Get:82 http://ftpmaster.internal/ubuntu impish/main ppc64el readline-common all 8.1-2 [54.1 kB] Get:83 http://ftpmaster.internal/ubuntu impish/main ppc64el libreadline8 ppc64el 8.1-2 [151 kB] Get:84 http://ftpmaster.internal/ubuntu impish/main ppc64el libsqlite3-0 ppc64el 3.35.5-1 [641 kB] Get:85 http://ftpmaster.internal/ubuntu impish/main ppc64el libuuid1 ppc64el 2.36.1-8ubuntu1 [26.4 kB] Get:86 http://ftpmaster.internal/ubuntu impish/main ppc64el libpython3.9-stdlib ppc64el 3.9.6-1 [1671 kB] Get:87 http://ftpmaster.internal/ubuntu impish/main ppc64el python3.9 ppc64el 3.9.6-1 [426 kB] Get:88 http://ftpmaster.internal/ubuntu impish/main ppc64el libpython3-stdlib ppc64el 3.9.4-1 [6984 B] Get:89 http://ftpmaster.internal/ubuntu impish/main ppc64el python3 ppc64el 3.9.4-1 [22.2 kB] Get:90 http://ftpmaster.internal/ubuntu impish/main ppc64el libcom-err2 ppc64el 1.46.2-1ubuntu2 [11.2 kB] Get:91 http://ftpmaster.internal/ubuntu impish/main ppc64el libpam-runtime all 1.3.1-5ubuntu8 [38.7 kB] Get:92 http://ftpmaster.internal/ubuntu impish/main ppc64el libsmartcols1 ppc64el 2.36.1-8ubuntu1 [59.4 kB] Get:93 http://ftpmaster.internal/ubuntu impish/main ppc64el passwd ppc64el 1:4.8.1-1ubuntu9 [838 kB] Get:94 http://ftpmaster.internal/ubuntu impish/main ppc64el libk5crypto3 ppc64el 1.18.3-6 [120 kB] Get:95 http://ftpmaster.internal/ubuntu impish/main ppc64el libkrb5support0 ppc64el 1.18.3-6 [37.2 kB] Get:96 http://ftpmaster.internal/ubuntu impish/main ppc64el libkrb5-3 ppc64el 1.18.3-6 [434 kB] Get:97 http://ftpmaster.internal/ubuntu impish/main ppc64el libgssapi-krb5-2 ppc64el 1.18.3-6 [183 kB] Get:98 http://ftpmaster.internal/ubuntu impish/main ppc64el libprocps8 ppc64el 2:3.3.17-5ubuntu3 [40.6 kB] Get:99 http://ftpmaster.internal/ubuntu impish/main ppc64el libss2 ppc64el 1.46.2-1ubuntu2 [12.4 kB] Get:100 http://ftpmaster.internal/ubuntu impish/main ppc64el procps ppc64el 2:3.3.17-5ubuntu3 [405 kB] Get:101 http://ftpmaster.internal/ubuntu impish/main ppc64el usrmerge all 25ubuntu1 [53.5 kB] Get:102 http://ftpmaster.internal/ubuntu impish/main ppc64el libdevmapper1.02.1 ppc64el 2:1.02.175-2.1ubuntu1 [158 kB] Get:103 http://ftpmaster.internal/ubuntu impish/main ppc64el openssl ppc64el 1.1.1j-1ubuntu5 [665 kB] Get:104 http://ftpmaster.internal/ubuntu impish/main ppc64el xz-utils ppc64el 5.2.5-2 [87.0 kB] Get:105 http://ftpmaster.internal/ubuntu impish/main ppc64el advancecomp ppc64el 2.1-2.1ubuntu1 [231 kB] Get:106 http://ftpmaster.internal/ubuntu impish/main ppc64el libctf0 ppc64el 2.37-1ubuntu1 [111 kB] Get:107 http://ftpmaster.internal/ubuntu impish/main ppc64el libctf-nobfd0 ppc64el 2.37-1ubuntu1 [110 kB] Get:108 http://ftpmaster.internal/ubuntu impish/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.37-1ubuntu1 [2019 kB] Get:109 http://ftpmaster.internal/ubuntu impish/main ppc64el binutils ppc64el 2.37-1ubuntu1 [3170 B] Get:110 http://ftpmaster.internal/ubuntu impish/main ppc64el libbinutils ppc64el 2.37-1ubuntu1 [676 kB] Get:111 http://ftpmaster.internal/ubuntu impish/main ppc64el binutils-common ppc64el 2.37-1ubuntu1 [52.6 kB] Get:112 http://ftpmaster.internal/ubuntu impish/main ppc64el libisl23 ppc64el 0.24-1 [719 kB] Get:113 http://ftpmaster.internal/ubuntu impish/main ppc64el cpp-11 ppc64el 11.2.0-1ubuntu2 [46.1 MB] Get:114 http://ftpmaster.internal/ubuntu impish/main ppc64el libgcc-11-dev ppc64el 11.2.0-1ubuntu2 [1491 kB] Get:115 http://ftpmaster.internal/ubuntu impish/main ppc64el gcc-11 ppc64el 11.2.0-1ubuntu2 [53.6 MB] Get:116 http://ftpmaster.internal/ubuntu impish/main ppc64el libstdc++-11-dev ppc64el 11.2.0-1ubuntu2 [2195 kB] Get:117 http://ftpmaster.internal/ubuntu impish/main ppc64el g++-11 ppc64el 11.2.0-1ubuntu2 [50.8 MB] Get:118 http://ftpmaster.internal/ubuntu impish/main ppc64el lto-disabled-list all 16 [12.5 kB] Get:119 http://ftpmaster.internal/ubuntu impish/main ppc64el python3-psutil ppc64el 5.8.0-1 [154 kB] Get:120 http://ftpmaster.internal/ubuntu impish/main ppc64el build-essential ppc64el 12.9ubuntu1 [4744 B] Get:121 http://ftpmaster.internal/ubuntu impish/universe ppc64el g++-10 ppc64el 10.3.0-6ubuntu1 [9410 kB] Get:122 http://ftpmaster.internal/ubuntu impish/universe ppc64el gcc-10 ppc64el 10.3.0-6ubuntu1 [16.5 MB] Get:123 http://ftpmaster.internal/ubuntu impish/main ppc64el libstdc++-10-dev ppc64el 10.3.0-6ubuntu1 [1927 kB] Get:124 http://ftpmaster.internal/ubuntu impish/main ppc64el libgcc-10-dev ppc64el 10.3.0-6ubuntu1 [1456 kB] Get:125 http://ftpmaster.internal/ubuntu impish/universe ppc64el cpp-10 ppc64el 10.3.0-6ubuntu1 [8188 kB] Get:126 http://ftpmaster.internal/ubuntu impish/main ppc64el gcc-10-base ppc64el 10.3.0-6ubuntu1 [21.5 kB] Get:127 http://ftpmaster.internal/ubuntu impish/main ppc64el libassuan0 ppc64el 2.5.5-1 [42.5 kB] Get:128 http://ftpmaster.internal/ubuntu impish/main ppc64el pinentry-curses ppc64el 1.1.1-1 [34.3 kB] Get:129 http://ftpmaster.internal/ubuntu impish/main ppc64el gpg ppc64el 2.2.20-1ubuntu4 [567 kB] Get:130 http://ftpmaster.internal/ubuntu impish/main ppc64el gpgconf ppc64el 2.2.20-1ubuntu4 [97.8 kB] Get:131 http://ftpmaster.internal/ubuntu impish/main ppc64el gpg-agent ppc64el 2.2.20-1ubuntu4 [215 kB] Get:132 http://ftpmaster.internal/ubuntu impish/main ppc64el pkgbinarymangler all 148 [32.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 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Setting up libitm1:ppc64el (11.2.0-1ubuntu2) ... Setting up libkmod2:ppc64el (28-1ubuntu4) ... Setting up libtsan0:ppc64el (11.2.0-1ubuntu2) ... Setting up libctf0:ppc64el (2.37-1ubuntu1) ... Setting up pinentry-curses (1.1.1-1) ... Setting up cpp-11 (11.2.0-1ubuntu2) ... Setting up pkgbinarymangler (148) ... Setting up libgcc-10-dev:ppc64el (10.3.0-6ubuntu1) ... Setting up libreadline8:ppc64el (8.1-2) ... Setting up e2fsprogs (1.46.2-1ubuntu2) ... Setting up perl (5.32.1-3ubuntu3) ... Setting up libdpkg-perl (1.20.9ubuntu13) ... Setting up libgcc-11-dev:ppc64el (11.2.0-1ubuntu2) ... Setting up cpp (4:11.2.0-1ubuntu1) ... Setting up procps (2:3.3.17-5ubuntu3) ... update-alternatives: warning: alternative /usr/bin/w.procps (part of link group w) doesn't exist; removing from list of alternatives update-alternatives: warning: /etc/alternatives/w is dangling; it will be updated with best choice Setting up gpgconf (2.2.20-1ubuntu4) ... Setting up libc6-dev:ppc64el (2.34-0ubuntu1~ppa5) ... 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Installing new version of config file /etc/systemd/journald.conf ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/pstore.conf ... Installing new version of config file /etc/systemd/resolved.conf ... Installing new version of config file /etc/systemd/sleep.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up systemd-sysv (248.3-1ubuntu3) ... Processing triggers for libc-bin (2.34-0ubuntu1~ppa5) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-21946007 ppc64el impish -c chroot:build-PACKAGEBUILD-21946007 --arch=ppc64el --dist=impish --nolog vg_1.30.0+ds-1.dsc Initiating build PACKAGEBUILD-21946007 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:00:19 UTC 2021 ppc64le sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-ppc64el-008.buildd +==============================================================================+ | vg 1.30.0+ds-1 (ppc64el) Thu, 02 Sep 2021 22:03:47 +0000 | +==============================================================================+ Package: vg Version: 1.30.0+ds-1 Source Version: 1.30.0+ds-1 Distribution: impish Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-21946007/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- vg_1.30.0+ds-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/vg-QOgKMU/vg-1.30.0+ds' with '<>' I: NOTICE: Log filtering will replace 'build/vg-QOgKMU' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-PEwlxM/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-PEwlxM/apt_archive ./ InRelease Get:2 copy:/<>/resolver-PEwlxM/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-PEwlxM/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-PEwlxM/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-PEwlxM/apt_archive ./ Packages [435 B] Fetched 1741 B in 0s (89.3 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: cpp-10 g++-10 gcc-10 gcc-10-base libgcc-10-dev libstdc++-10-dev Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 652 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-PEwlxM/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [652 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 652 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14928 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (ppc64el included in amd64 arm64 ppc64el mips64el s390x riscv64 x32 all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), pv, bsdmainutils, zlib1g-dev, rs, libffi-dev, bwa, protobuf-compiler, libprotoc-dev, libprotobuf-dev, libjansson-dev, libbz2-dev, libncurses5-dev, automake, libtool, jq, samtools, unzip, librdf0-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, 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, tabix, xxd, libsmithwaterman-dev, libdivsufsort-dev, libtsl-hopscotch-map-dev, libvcflib-dev (>= 1.0.1), libvcflib-tools, libhts-dev, help2man, python3:any, libsimde-dev Filtered Build-Depends: debhelper-compat (= 13), pv, bsdmainutils, zlib1g-dev, rs, libffi-dev, bwa, protobuf-compiler, libprotoc-dev, libprotobuf-dev, libjansson-dev, libbz2-dev, libncurses5-dev, automake, libtool, jq, samtools, unzip, librdf0-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, 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, tabix, xxd, libsmithwaterman-dev, libdivsufsort-dev, libtsl-hopscotch-map-dev, libvcflib-dev (>= 1.0.1), libvcflib-tools, libhts-dev, help2man, python3:any, libsimde-dev dpkg-deb: building package 'sbuild-build-depends-vg-dummy' in '/<>/resolver-PEwlxM/apt_archive/sbuild-build-depends-vg-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-vg-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-PEwlxM/apt_archive ./ InRelease Get:2 copy:/<>/resolver-PEwlxM/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-PEwlxM/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-PEwlxM/apt_archive ./ Sources [864 B] Get:5 copy:/<>/resolver-PEwlxM/apt_archive ./ Packages [917 B] Fetched 2744 B in 0s (148 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 package was automatically installed and is no longer required: g++-10 Use 'apt autoremove' to remove it. The following additional packages will be installed: autoconf automake autopoint autotools-dev bc bison bsdextrautils bsdmainutils bwa cmake cmake-data debhelper debugedit 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 libbackward-cpp-dev libblas3 libblkid-dev libboost-program-options-dev libboost-program-options1.74-dev libboost-program-options1.74.0 libboost1.74-dev libbrotli-dev libbrotli1 libbsd0 libbz2-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdatrie1 libdebhelper-perl libdeflate-dev libdeflate0 libdisorder-dev libdisorder0 libdivsufsort-dev libdivsufsort3 libdw-dev libdw1 libelf-dev libelf1 libexpat1-dev libfastahack-dev libfastahack0 libffi-dev libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig-dev libfontconfig1 libfontconfig1-dev libfreetype-dev libfreetype6 libfreetype6-dev libfribidi0 libgfortran5 libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgmp-dev libgmpxx4ldbl libgraphite2-3 libharfbuzz0b libhts-dev libhts3 libice-dev libice6 libicu-dev libicu67 libjansson-dev libjansson4 libjbig0 libjemalloc-dev libjemalloc2 libjpeg-turbo8 libjpeg8 libjq1 libjsoncpp24 liblapack3 libldap-2.5-0 liblocale-gettext-perl libltdl7 liblz4-dev liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmd0 libmhash2 libmount-dev libncurses-dev libncurses5-dev libnghttp2-14 libonig5 libosp5 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix2 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpixman-1-dev libpng-dev libprotobuf-dev libprotobuf-lite23 libprotobuf23 libprotoc-dev libprotoc23 libpsl5 libpthread-stubs0-dev libraptor2-0 libraptor2-dev librasqal3 librasqal3-dev librdf0 librdf0-dev librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libselinux1-dev libsepol1-dev libsigsegv2 libsimde-dev libsm-dev libsm6 libsmithwaterman-dev libsmithwaterman0 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 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 ncal opensp pkg-config po-debconf protobuf-compiler pv python3-distutils python3-lib2to3 python3-lxml python3-pkg-resources python3-pygments r-base-core r-cran-assertthat r-cran-brio r-cran-callr r-cran-cli r-cran-colorspace r-cran-crayon r-cran-desc r-cran-diffobj r-cran-digest r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-jsonlite r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plyr r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rematch2 r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-waldo r-cran-withr rapidjson-dev raptor2-utils rasqal-utils rs samtools sgml-base sgml-data tabix ucf unzip uuid-dev x11-common x11proto-dev x11proto-xext-dev xdg-utils xml-core xorg-sgml-doctools xsltproc xtrans-dev xxd zip zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc bison-doc calendar whois vacation mailutils cmake-doc ninja-build dh-make docbook-defguide docbook-dsssl psgml dbtoepub docbook-xsl-doc-html | docbook-xsl-doc-pdf | docbook-xsl-doc-text | docbook-xsl-doc docbook-xsl-saxon fop libsaxon-java libxalan2-java libxslthl-java xalan flex-doc gawk-doc gettext-doc libasprintf-dev libgettextpo-dev groff dblatex lrzip binutils-dev libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-serialization1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev libcairo2-doc libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev freetype2-doc libgirepository1.0-dev libglib2.0-doc libgdk-pixbuf2.0-bin | libgdk-pixbuf2.0-dev libxml2-utils gmp-doc libgmp10-doc libmpfr-dev libice-doc icu-doc liblzma-doc ncurses-doc libraptor2-doc librasqal3-doc librdf-storage-postgresql librdf-storage-mysql librdf-storage-sqlite librdf-storage-virtuoso redland-utils librdf-perl python-librdf librdf-ruby libsm-doc tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk r-cran-pracma libx11-doc libxcb-doc libxext-doc m4-doc apparmor less www-browser doc-base libmail-box-perl protobuf-mode-el python3-lxml-dbg python-lxml-doc python3-setuptools python-pygments-doc ttf-bitstream-vera elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-covr r-cran-htmlwidgets r-cran-knitr r-cran-rmarkdown r-cran-prettycode r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-dplyr r-cran-png r-cran-jpeg r-cran-viridis r-cran-unitizer r-cran-hmisc r-cran-maps r-cran-maptools r-cran-multcomp r-cran-rpart r-cran-sf r-cran-svglite r-cran-dbi r-cran-rsqlite r-cran-r.utils r-cran-forcats r-cran-stringr r-cran-magick r-cran-httr r-cran-curl r-cran-getopt r-cran-bit64 r-cran-cpp11 r-cran-bitops r-cran-doparallel r-cran-foreach r-cran-iterators r-cran-itertools r-cran-inline r-cran-dichromat r-cran-mockery r-cran-usethis r-cran-bench r-cran-blob r-cran-formattable r-cran-hms r-cran-htmltools r-cran-purrr r-cran-tidyr r-cran-zeallot rapidjson-doc cwltool sgml-base-doc perlsgml w3-recs Recommended packages: libfl-dev curl | wget | lynx bzip2-doc libarchive-cpio-perl shared-mime-info xdg-user-dirs libldap-common libpng-tools publicsuffix redland-utils libsasl2-modules libltdl-dev libmail-sendmail-perl python3-bs4 python3-html5lib r-recommended r-base-dev r-doc-html r-cran-cliapp r-cran-mockery r-cran-sp r-cran-mapproj r-cran-hexbin r-cran-vdiffr r-cran-quantreg r-cran-xml2 r-cran-lubridate r-cran-domc r-cran-abind r-cran-codetools r-cran-curl r-cran-rmarkdown r-cran-mockr r-cran-bit64 r-cran-hms r-cran-data.table r-cran-rsqlite r-cran-knitr r-cran-dplyr r-cran-generics r-cran-dbi libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bc bison bsdextrautils bsdmainutils bwa cmake cmake-data debhelper debugedit 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 libbackward-cpp-dev libblas3 libblkid-dev libboost-program-options-dev libboost-program-options1.74-dev libboost-program-options1.74.0 libboost1.74-dev libbrotli-dev libbrotli1 libbsd0 libbz2-dev libcairo-gobject2 libcairo-script-interpreter2 libcairo2 libcairo2-dev libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdatrie1 libdebhelper-perl libdeflate-dev libdeflate0 libdisorder-dev libdisorder0 libdivsufsort-dev libdivsufsort3 libdw-dev libdw1 libelf-dev libelf1 libexpat1-dev libfastahack-dev libfastahack0 libffi-dev libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig-dev libfontconfig1 libfontconfig1-dev libfreetype-dev libfreetype6 libfreetype6-dev libfribidi0 libgfortran5 libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgmp-dev libgmpxx4ldbl libgraphite2-3 libharfbuzz0b libhts-dev libhts3 libice-dev libice6 libicu-dev libicu67 libjansson-dev libjansson4 libjbig0 libjemalloc-dev libjemalloc2 libjpeg-turbo8 libjpeg8 libjq1 libjsoncpp24 liblapack3 libldap-2.5-0 liblocale-gettext-perl libltdl7 liblz4-dev liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmd0 libmhash2 libmount-dev libncurses-dev libncurses5-dev libnghttp2-14 libonig5 libosp5 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix2 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpixman-1-dev libpng-dev libprotobuf-dev libprotobuf-lite23 libprotobuf23 libprotoc-dev libprotoc23 libpsl5 libpthread-stubs0-dev libraptor2-0 libraptor2-dev librasqal3 librasqal3-dev librdf0 librdf0-dev librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libselinux1-dev libsepol1-dev libsigsegv2 libsimde-dev libsm-dev libsm6 libsmithwaterman-dev libsmithwaterman0 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 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 ncal opensp pkg-config po-debconf protobuf-compiler pv python3-distutils python3-lib2to3 python3-lxml python3-pkg-resources python3-pygments r-base-core r-cran-assertthat r-cran-brio r-cran-callr r-cran-cli r-cran-colorspace r-cran-crayon r-cran-desc r-cran-diffobj r-cran-digest r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-jsonlite r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plyr r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rematch2 r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-waldo r-cran-withr rapidjson-dev raptor2-utils rasqal-utils rs samtools sbuild-build-depends-vg-dummy sgml-base sgml-data tabix ucf unzip uuid-dev x11-common x11proto-dev x11proto-xext-dev xdg-utils xml-core xorg-sgml-doctools xsltproc xtrans-dev xxd zip zlib1g-dev 0 upgraded, 305 newly installed, 0 to remove and 0 not upgraded. Need to get 150 MB of archives. After this operation, 641 MB of additional disk space will be used. Get:1 copy:/<>/resolver-PEwlxM/apt_archive ./ sbuild-build-depends-vg-dummy 0.invalid.0 [994 B] Get:2 http://ftpmaster.internal/ubuntu impish/main ppc64el liblocale-gettext-perl ppc64el 1.07-4build1 [17.2 kB] Get:3 http://ftpmaster.internal/ubuntu impish/main ppc64el bsdextrautils ppc64el 2.36.1-8ubuntu1 [81.6 kB] Get:4 http://ftpmaster.internal/ubuntu impish/main ppc64el libuchardet0 ppc64el 0.0.7-1 [71.0 kB] Get:5 http://ftpmaster.internal/ubuntu impish/main ppc64el groff-base ppc64el 1.22.4-6 [921 kB] Get:6 http://ftpmaster.internal/ubuntu impish/main ppc64el libpipeline1 ppc64el 1.5.3-1 [29.6 kB] Get:7 http://ftpmaster.internal/ubuntu impish/main ppc64el man-db ppc64el 2.9.4-2 [1185 kB] Get:8 http://ftpmaster.internal/ubuntu impish/main ppc64el libsigsegv2 ppc64el 2.13-1ubuntu1 [14.8 kB] Get:9 http://ftpmaster.internal/ubuntu impish/main ppc64el m4 ppc64el 1.4.18-5 [208 kB] Get:10 http://ftpmaster.internal/ubuntu impish/main ppc64el flex ppc64el 2.6.4-8 [304 kB] Get:11 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http://ftpmaster.internal/ubuntu impish/main ppc64el dh-autoreconf all 20 [16.1 kB] Get:61 http://ftpmaster.internal/ubuntu impish/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] Get:62 http://ftpmaster.internal/ubuntu impish/main ppc64el libsub-override-perl all 0.09-2 [9532 B] Get:63 http://ftpmaster.internal/ubuntu impish/main ppc64el libfile-stripnondeterminism-perl all 1.12.0-1 [17.5 kB] Get:64 http://ftpmaster.internal/ubuntu impish/main ppc64el dh-strip-nondeterminism all 1.12.0-1 [5228 B] Get:65 http://ftpmaster.internal/ubuntu impish/main ppc64el libdw1 ppc64el 0.185-1 [244 kB] Get:66 http://ftpmaster.internal/ubuntu impish/main ppc64el debugedit ppc64el 1:5.0-0ubuntu1 [52.6 kB] Get:67 http://ftpmaster.internal/ubuntu impish/main ppc64el dwz ppc64el 0.14-1 [109 kB] Get:68 http://ftpmaster.internal/ubuntu impish/main ppc64el gettext ppc64el 0.21-4ubuntu3 [895 kB] Get:69 http://ftpmaster.internal/ubuntu impish/main ppc64el intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:70 http://ftpmaster.internal/ubuntu impish/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] Get:71 http://ftpmaster.internal/ubuntu impish/main ppc64el debhelper all 13.3.4ubuntu2 [921 kB] Get:72 http://ftpmaster.internal/ubuntu impish/main ppc64el xml-core all 0.18+nmu1 [21.6 kB] Get:73 http://ftpmaster.internal/ubuntu impish/main ppc64el sgml-data all 2.0.11+nmu1 [171 kB] Get:74 http://ftpmaster.internal/ubuntu impish/universe ppc64el docbook all 4.5-6 [122 kB] Get:75 http://ftpmaster.internal/ubuntu impish/universe ppc64el libosp5 ppc64el 1.5.2-13ubuntu3 [705 kB] Get:76 http://ftpmaster.internal/ubuntu impish/universe ppc64el opensp ppc64el 1.5.2-13ubuntu3 [157 kB] Get:77 http://ftpmaster.internal/ubuntu impish/universe ppc64el docbook-to-man ppc64el 1:2.0.0-45 [89.3 kB] Get:78 http://ftpmaster.internal/ubuntu impish/main ppc64el docbook-xml all 4.5-9 [71.2 kB] Get:79 http://ftpmaster.internal/ubuntu impish/universe ppc64el docbook-xsl all 1.79.2+dfsg-1 [1063 kB] Get:80 http://ftpmaster.internal/ubuntu impish/main ppc64el libasm1 ppc64el 0.185-1 [16.4 kB] Get:81 http://ftpmaster.internal/ubuntu impish/main ppc64el elfutils ppc64el 0.185-1 [437 kB] Get:82 http://ftpmaster.internal/ubuntu impish/universe ppc64el libdisorder0 ppc64el 0.0.2+git20130809.8062ee1-2 [4880 B] Get:83 http://ftpmaster.internal/ubuntu impish/universe ppc64el libfastahack0 ppc64el 1.0.0+dfsg-7 [30.1 kB] Get:84 http://ftpmaster.internal/ubuntu impish/universe ppc64el fastahack ppc64el 1.0.0+dfsg-7 [11.3 kB] Get:85 http://ftpmaster.internal/ubuntu impish/main ppc64el libfreetype6 ppc64el 2.10.4+dfsg-1build1 [424 kB] Get:86 http://ftpmaster.internal/ubuntu impish/main ppc64el fonts-dejavu-core all 2.37-2build1 [1041 kB] Get:87 http://ftpmaster.internal/ubuntu impish/main ppc64el fontconfig-config all 2.13.1-4.2ubuntu3 [28.2 kB] Get:88 http://ftpmaster.internal/ubuntu impish/main ppc64el libfontconfig1 ppc64el 2.13.1-4.2ubuntu3 [150 kB] Get:89 http://ftpmaster.internal/ubuntu impish/main ppc64el fontconfig ppc64el 2.13.1-4.2ubuntu3 [183 kB] Get:90 http://ftpmaster.internal/ubuntu impish/main ppc64el pkg-config ppc64el 0.29.2-1ubuntu1 [49.5 kB] Get:91 http://ftpmaster.internal/ubuntu impish/main ppc64el libxslt1.1 ppc64el 1.1.34-4 [167 kB] Get:92 http://ftpmaster.internal/ubuntu impish/main ppc64el python3-lxml ppc64el 4.6.3+dfsg-0.1 [1021 kB] Get:93 http://ftpmaster.internal/ubuntu impish/main ppc64el python3-pygments all 2.7.1+dfsg-2.1 [639 kB] Get:94 http://ftpmaster.internal/ubuntu impish/main ppc64el xsltproc ppc64el 1.1.34-4 [15.2 kB] Get:95 http://ftpmaster.internal/ubuntu impish/universe ppc64el gtk-doc-tools all 1.33.2-1 [320 kB] Get:96 http://ftpmaster.internal/ubuntu impish/universe ppc64el help2man ppc64el 1.48.4 [140 kB] Get:97 http://ftpmaster.internal/ubuntu impish/main ppc64el icu-devtools ppc64el 67.1-6ubuntu2 [200 kB] Get:98 http://ftpmaster.internal/ubuntu impish/main ppc64el libonig5 ppc64el 6.9.6-1.1 [172 kB] Get:99 http://ftpmaster.internal/ubuntu impish/main ppc64el libjq1 ppc64el 1.6-2.1ubuntu1 [132 kB] Get:100 http://ftpmaster.internal/ubuntu impish/main ppc64el jq ppc64el 1.6-2.1ubuntu1 [51.7 kB] Get:101 http://ftpmaster.internal/ubuntu impish/universe ppc64el libbackward-cpp-dev all 1.5-2 [31.8 kB] Get:102 http://ftpmaster.internal/ubuntu impish/main ppc64el libblas3 ppc64el 3.9.0-3ubuntu2 [121 kB] Get:103 http://ftpmaster.internal/ubuntu impish/main ppc64el libboost1.74-dev ppc64el 1.74.0-8ubuntu2 [9509 kB] Get:104 http://ftpmaster.internal/ubuntu impish/main ppc64el libboost-program-options1.74.0 ppc64el 1.74.0-8ubuntu2 [330 kB] Get:105 http://ftpmaster.internal/ubuntu impish/main ppc64el libboost-program-options1.74-dev ppc64el 1.74.0-8ubuntu2 [363 kB] Get:106 http://ftpmaster.internal/ubuntu impish/main ppc64el libboost-program-options-dev ppc64el 1.74.0.3ubuntu5 [3364 B] Get:107 http://ftpmaster.internal/ubuntu impish/main ppc64el libbrotli-dev ppc64el 1.0.9-2build2 [313 kB] Get:108 http://ftpmaster.internal/ubuntu impish/main ppc64el libbz2-dev ppc64el 1.0.8-4ubuntu3 [45.0 kB] Get:109 http://ftpmaster.internal/ubuntu impish/main ppc64el libpixman-1-0 ppc64el 0.40.0-1build2 [268 kB] Get:110 http://ftpmaster.internal/ubuntu impish/main ppc64el libxcb-render0 ppc64el 1.14-3ubuntu1 [15.6 kB] Get:111 http://ftpmaster.internal/ubuntu impish/main ppc64el libxcb-shm0 ppc64el 1.14-3ubuntu1 [5892 B] Get:112 http://ftpmaster.internal/ubuntu impish/main ppc64el libxrender1 ppc64el 1:0.9.10-1build2 [21.0 kB] Get:113 http://ftpmaster.internal/ubuntu impish/main ppc64el libcairo2 ppc64el 1.16.0-5ubuntu1 [697 kB] Get:114 http://ftpmaster.internal/ubuntu impish/main ppc64el libcairo-gobject2 ppc64el 1.16.0-5ubuntu1 [17.5 kB] Get:115 http://ftpmaster.internal/ubuntu impish/main ppc64el liblzo2-2 ppc64el 2.10-2build1 [73.2 kB] Get:116 http://ftpmaster.internal/ubuntu impish/main ppc64el libcairo-script-interpreter2 ppc64el 1.16.0-5ubuntu1 [69.3 kB] Get:117 http://ftpmaster.internal/ubuntu impish/main ppc64el libexpat1-dev ppc64el 2.3.0-1 [125 kB] Get:118 http://ftpmaster.internal/ubuntu impish/main ppc64el zlib1g-dev ppc64el 1:1.2.11.dfsg-2ubuntu7 [177 kB] Get:119 http://ftpmaster.internal/ubuntu impish/main ppc64el libpng-dev ppc64el 1.6.37-3build3 [218 kB] Get:120 http://ftpmaster.internal/ubuntu impish/main ppc64el libfreetype-dev ppc64el 2.10.4+dfsg-1build1 [585 kB] Get:121 http://ftpmaster.internal/ubuntu impish/main ppc64el libfreetype6-dev ppc64el 2.10.4+dfsg-1build1 [9828 B] Get:122 http://ftpmaster.internal/ubuntu impish/main ppc64el uuid-dev ppc64el 2.36.1-8ubuntu1 [40.5 kB] Get:123 http://ftpmaster.internal/ubuntu impish/main ppc64el libfontconfig-dev ppc64el 2.13.1-4.2ubuntu3 [174 kB] Get:124 http://ftpmaster.internal/ubuntu impish/main ppc64el libfontconfig1-dev ppc64el 2.13.1-4.2ubuntu3 [2028 B] Get:125 http://ftpmaster.internal/ubuntu impish/main ppc64el xorg-sgml-doctools all 1:1.11-1.1 [10.9 kB] Get:126 http://ftpmaster.internal/ubuntu impish/main ppc64el x11proto-dev all 2020.1-1 [594 kB] Get:127 http://ftpmaster.internal/ubuntu impish/main ppc64el libxau-dev ppc64el 1:1.0.9-1build3 [9916 B] Get:128 http://ftpmaster.internal/ubuntu impish/main ppc64el libxdmcp-dev ppc64el 1:1.1.3-0ubuntu3 [27.0 kB] Get:129 http://ftpmaster.internal/ubuntu impish/main ppc64el xtrans-dev all 1.4.0-1 [68.9 kB] Get:130 http://ftpmaster.internal/ubuntu impish/main ppc64el libpthread-stubs0-dev ppc64el 0.4-1 [5388 B] Get:131 http://ftpmaster.internal/ubuntu impish/main ppc64el libxcb1-dev ppc64el 1.14-3ubuntu1 [88.7 kB] Get:132 http://ftpmaster.internal/ubuntu impish/main ppc64el libx11-dev ppc64el 2:1.7.2-1 [851 kB] Get:133 http://ftpmaster.internal/ubuntu impish/main ppc64el libxrender-dev ppc64el 1:0.9.10-1build2 [28.3 kB] Get:134 http://ftpmaster.internal/ubuntu impish/main ppc64el x11proto-xext-dev all 2020.1-1 [2620 B] Get:135 http://ftpmaster.internal/ubuntu impish/main ppc64el libxext-dev ppc64el 2:1.3.4-0ubuntu3 [91.5 kB] Get:136 http://ftpmaster.internal/ubuntu impish/main ppc64el x11-common all 1:7.7+22ubuntu1 [22.3 kB] Get:137 http://ftpmaster.internal/ubuntu impish/main ppc64el libice6 ppc64el 2:1.0.10-1 [44.9 kB] Get:138 http://ftpmaster.internal/ubuntu impish/main ppc64el libsm6 ppc64el 2:1.2.3-1 [17.6 kB] Get:139 http://ftpmaster.internal/ubuntu impish/main ppc64el libice-dev ppc64el 2:1.0.10-1 [53.9 kB] Get:140 http://ftpmaster.internal/ubuntu impish/main ppc64el libsm-dev ppc64el 2:1.2.3-1 [19.3 kB] Get:141 http://ftpmaster.internal/ubuntu impish/main ppc64el libpixman-1-dev ppc64el 0.40.0-1build2 [298 kB] Get:142 http://ftpmaster.internal/ubuntu impish/main ppc64el libxcb-render0-dev ppc64el 1.14-3ubuntu1 [19.4 kB] Get:143 http://ftpmaster.internal/ubuntu impish/main ppc64el libxcb-shm0-dev ppc64el 1.14-3ubuntu1 [7048 B] Get:144 http://ftpmaster.internal/ubuntu impish/main ppc64el libffi-dev ppc64el 3.4~20200819gead65ca871-0ubuntu5 [60.6 kB] Get:145 http://ftpmaster.internal/ubuntu impish/main ppc64el libglib2.0-bin ppc64el 2.68.3-1ubuntu1 [90.1 kB] Get:146 http://ftpmaster.internal/ubuntu impish/main ppc64el python3-lib2to3 all 3.9.5-0ubuntu3 [76.2 kB] Get:147 http://ftpmaster.internal/ubuntu impish/main ppc64el python3-distutils all 3.9.5-0ubuntu3 [142 kB] Get:148 http://ftpmaster.internal/ubuntu impish/main ppc64el libglib2.0-dev-bin ppc64el 2.68.3-1ubuntu1 [117 kB] Get:149 http://ftpmaster.internal/ubuntu impish/main ppc64el libblkid-dev ppc64el 2.36.1-8ubuntu1 [222 kB] Get:150 http://ftpmaster.internal/ubuntu impish/main ppc64el libsepol1-dev ppc64el 3.1-1ubuntu1 [390 kB] Get:151 http://ftpmaster.internal/ubuntu impish/main ppc64el libpcre2-16-0 ppc64el 10.36-2ubuntu5 [199 kB] Get:152 http://ftpmaster.internal/ubuntu impish/main ppc64el libpcre2-32-0 ppc64el 10.36-2ubuntu5 [190 kB] Get:153 http://ftpmaster.internal/ubuntu impish/main ppc64el libpcre2-posix2 ppc64el 10.36-2ubuntu5 [6256 B] Get:154 http://ftpmaster.internal/ubuntu impish/main ppc64el libpcre2-dev ppc64el 10.36-2ubuntu5 [674 kB] Get:155 http://ftpmaster.internal/ubuntu impish/main ppc64el libselinux1-dev ppc64el 3.1-3build1 [167 kB] Get:156 http://ftpmaster.internal/ubuntu impish/main ppc64el libmount-dev ppc64el 2.36.1-8ubuntu1 [14.5 kB] Get:157 http://ftpmaster.internal/ubuntu impish/main ppc64el libpcre16-3 ppc64el 2:8.39-13build3 [163 kB] Get:158 http://ftpmaster.internal/ubuntu impish/main ppc64el libpcre32-3 ppc64el 2:8.39-13build3 [156 kB] Get:159 http://ftpmaster.internal/ubuntu impish/main ppc64el libpcrecpp0v5 ppc64el 2:8.39-13build3 [16.6 kB] Get:160 http://ftpmaster.internal/ubuntu impish/main ppc64el libpcre3-dev ppc64el 2:8.39-13build3 [551 kB] Get:161 http://ftpmaster.internal/ubuntu impish/main ppc64el libglib2.0-dev ppc64el 2.68.3-1ubuntu1 [2018 kB] Get:162 http://ftpmaster.internal/ubuntu impish/main ppc64el libcairo2-dev ppc64el 1.16.0-5ubuntu1 [777 kB] Get:163 http://ftpmaster.internal/ubuntu impish/main ppc64el libcurl3-gnutls ppc64el 7.74.0-1.2ubuntu4 [345 kB] Get:164 http://ftpmaster.internal/ubuntu impish/main ppc64el libcurl4-gnutls-dev ppc64el 7.74.0-1.2ubuntu4 [426 kB] Get:165 http://ftpmaster.internal/ubuntu impish/main ppc64el libdatrie1 ppc64el 0.2.13-1ubuntu2 [21.4 kB] Get:166 http://ftpmaster.internal/ubuntu impish/main ppc64el libdeflate0 ppc64el 1.7-1ubuntu2 [49.5 kB] Get:167 http://ftpmaster.internal/ubuntu impish/main ppc64el libdeflate-dev ppc64el 1.7-1ubuntu2 [43.3 kB] Get:168 http://ftpmaster.internal/ubuntu impish/universe ppc64el libdisorder-dev ppc64el 0.0.2+git20130809.8062ee1-2 [4108 B] Get:169 http://ftpmaster.internal/ubuntu impish/universe ppc64el libdivsufsort3 ppc64el 2.0.1-5 [46.2 kB] Get:170 http://ftpmaster.internal/ubuntu impish/universe ppc64el libdivsufsort-dev ppc64el 2.0.1-5 [11.0 kB] Get:171 http://ftpmaster.internal/ubuntu impish/main ppc64el libelf-dev ppc64el 0.185-1 [68.5 kB] Get:172 http://ftpmaster.internal/ubuntu impish/main ppc64el liblzma-dev ppc64el 5.2.5-2 [169 kB] Get:173 http://ftpmaster.internal/ubuntu impish/main ppc64el libdw-dev ppc64el 0.185-1 [314 kB] Get:174 http://ftpmaster.internal/ubuntu impish/universe ppc64el libfastahack-dev ppc64el 1.0.0+dfsg-7 [31.3 kB] Get:175 http://ftpmaster.internal/ubuntu impish/universe ppc64el libfml0 ppc64el 0.1+git20190320.b499514-1 [79.9 kB] Get:176 http://ftpmaster.internal/ubuntu impish/universe ppc64el libfml-dev ppc64el 0.1+git20190320.b499514-1 [93.3 kB] Get:177 http://ftpmaster.internal/ubuntu impish/main ppc64el libgfortran5 ppc64el 11.2.0-1ubuntu2 [507 kB] Get:178 http://ftpmaster.internal/ubuntu impish/main ppc64el libgmpxx4ldbl ppc64el 2:6.2.1+dfsg-1ubuntu2 [9212 B] Get:179 http://ftpmaster.internal/ubuntu impish/main ppc64el libgmp-dev ppc64el 2:6.2.1+dfsg-1ubuntu2 [328 kB] Get:180 http://ftpmaster.internal/ubuntu impish/main ppc64el libgraphite2-3 ppc64el 1.3.14-1 [73.3 kB] Get:181 http://ftpmaster.internal/ubuntu impish/main ppc64el libharfbuzz0b ppc64el 2.7.4-1ubuntu1 [433 kB] Get:182 http://ftpmaster.internal/ubuntu impish/universe ppc64el libhts3 ppc64el 1.11-4 [433 kB] Get:183 http://ftpmaster.internal/ubuntu impish/universe ppc64el libhts-dev ppc64el 1.11-4 [3961 kB] Get:184 http://ftpmaster.internal/ubuntu impish/main ppc64el libicu-dev ppc64el 67.1-6ubuntu2 [9982 kB] Get:185 http://ftpmaster.internal/ubuntu impish/main ppc64el libjansson4 ppc64el 2.13.1-1.1build1 [34.6 kB] Get:186 http://ftpmaster.internal/ubuntu impish/main ppc64el libjansson-dev ppc64el 2.13.1-1.1build1 [46.3 kB] Get:187 http://ftpmaster.internal/ubuntu impish/universe ppc64el libjemalloc2 ppc64el 5.2.1-3 [190 kB] Get:188 http://ftpmaster.internal/ubuntu impish/main ppc64el libjpeg-turbo8 ppc64el 2.0.6-0ubuntu2 [156 kB] Get:189 http://ftpmaster.internal/ubuntu impish/main ppc64el libjpeg8 ppc64el 8c-2ubuntu8 [2146 B] Get:190 http://ftpmaster.internal/ubuntu impish/main ppc64el liblapack3 ppc64el 3.9.0-3ubuntu2 [1739 kB] Get:191 http://ftpmaster.internal/ubuntu impish/main ppc64el libltdl7 ppc64el 2.4.6-15 [44.5 kB] Get:192 http://ftpmaster.internal/ubuntu impish/main ppc64el libmhash2 ppc64el 0.9.9.9-9 [111 kB] Get:193 http://ftpmaster.internal/ubuntu impish/main ppc64el libncurses-dev ppc64el 6.2+20201114-2build1 [418 kB] Get:194 http://ftpmaster.internal/ubuntu impish/main ppc64el libncurses5-dev ppc64el 6.2+20201114-2build1 [996 B] Get:195 http://ftpmaster.internal/ubuntu impish/main ppc64el libthai-data all 0.1.28-4 [134 kB] Get:196 http://ftpmaster.internal/ubuntu impish/main ppc64el libthai0 ppc64el 0.1.28-4 [19.6 kB] Get:197 http://ftpmaster.internal/ubuntu impish/main ppc64el libpango-1.0-0 ppc64el 1.48.7+ds1-2 [219 kB] Get:198 http://ftpmaster.internal/ubuntu impish/main ppc64el libpangoft2-1.0-0 ppc64el 1.48.7+ds1-2 [57.9 kB] Get:199 http://ftpmaster.internal/ubuntu impish/main ppc64el libpangocairo-1.0-0 ppc64el 1.48.7+ds1-2 [38.6 kB] Get:200 http://ftpmaster.internal/ubuntu impish/main ppc64el libpaper1 ppc64el 1.1.28 [13.2 kB] Get:201 http://ftpmaster.internal/ubuntu impish/main ppc64el libpaper-utils ppc64el 1.1.28 [8688 B] Get:202 http://ftpmaster.internal/ubuntu impish/main ppc64el libprotobuf-lite23 ppc64el 3.12.4-1ubuntu2 [188 kB] Get:203 http://ftpmaster.internal/ubuntu impish/main ppc64el libprotobuf23 ppc64el 3.12.4-1ubuntu2 [796 kB] Get:204 http://ftpmaster.internal/ubuntu impish/main ppc64el libprotoc23 ppc64el 3.12.4-1ubuntu2 [633 kB] Get:205 http://ftpmaster.internal/ubuntu impish/main ppc64el libyajl2 ppc64el 2.1.0-3 [22.9 kB] Get:206 http://ftpmaster.internal/ubuntu impish/main ppc64el libraptor2-0 ppc64el 2.0.15-0ubuntu2 [179 kB] Get:207 http://ftpmaster.internal/ubuntu impish/main ppc64el libxml2-dev ppc64el 2.9.10+dfsg-6.7 [787 kB] Get:208 http://ftpmaster.internal/ubuntu impish/main ppc64el libxslt1-dev ppc64el 1.1.34-4 [219 kB] Get:209 http://ftpmaster.internal/ubuntu impish/main ppc64el libyajl-dev ppc64el 2.1.0-3 [29.1 kB] Get:210 http://ftpmaster.internal/ubuntu impish/main ppc64el libraptor2-dev ppc64el 2.0.15-0ubuntu2 [235 kB] Get:211 http://ftpmaster.internal/ubuntu impish/main ppc64el librasqal3 ppc64el 0.9.33-0.1 [194 kB] Get:212 http://ftpmaster.internal/ubuntu impish/main ppc64el librasqal3-dev ppc64el 0.9.33-0.1 [258 kB] Get:213 http://ftpmaster.internal/ubuntu impish/main ppc64el librdf0 ppc64el 1.0.17-1.1ubuntu1 [108 kB] Get:214 http://ftpmaster.internal/ubuntu impish/main ppc64el librdf0-dev ppc64el 1.0.17-1.1ubuntu1 [253 kB] Get:215 http://ftpmaster.internal/ubuntu impish/universe ppc64el libsimde-dev all 0.7.2-4 [258 kB] Get:216 http://ftpmaster.internal/ubuntu impish/universe ppc64el libsmithwaterman0 ppc64el 0.0+git20160702.2610e25-11 [42.0 kB] Get:217 http://ftpmaster.internal/ubuntu impish/universe ppc64el libsmithwaterman-dev ppc64el 0.0+git20160702.2610e25-11 [46.1 kB] Get:218 http://ftpmaster.internal/ubuntu impish/universe ppc64el libsparsehash-dev all 2.0.3-2 [71.7 kB] Get:219 http://ftpmaster.internal/ubuntu impish/universe ppc64el libssw0 ppc64el 1.1-13 [21.0 kB] Get:220 http://ftpmaster.internal/ubuntu impish/universe ppc64el libssw-dev ppc64el 1.1-13 [23.3 kB] Get:221 http://ftpmaster.internal/ubuntu impish/universe ppc64el libtabixpp0 ppc64el 1.1.0-4ubuntu1 [9608 B] Get:222 http://ftpmaster.internal/ubuntu impish/universe ppc64el libtabixpp-dev ppc64el 1.1.0-4ubuntu1 [7744 B] Get:223 http://ftpmaster.internal/ubuntu impish/main ppc64el libtcl8.6 ppc64el 8.6.11+dfsg-1 [1021 kB] Get:224 http://ftpmaster.internal/ubuntu impish/main ppc64el libjbig0 ppc64el 2.1-3.1build1 [26.9 kB] Get:225 http://ftpmaster.internal/ubuntu impish/main ppc64el libwebp6 ppc64el 0.6.1-2.1 [255 kB] Get:226 http://ftpmaster.internal/ubuntu impish/main ppc64el libtiff5 ppc64el 4.3.0-1 [206 kB] Get:227 http://ftpmaster.internal/ubuntu impish/main ppc64el libxft2 ppc64el 2.3.3-0ubuntu3 [47.6 kB] Get:228 http://ftpmaster.internal/ubuntu impish/main ppc64el libxss1 ppc64el 1:1.2.3-1 [8964 B] Get:229 http://ftpmaster.internal/ubuntu impish/main ppc64el libtk8.6 ppc64el 8.6.11-2 [800 kB] Get:230 http://ftpmaster.internal/ubuntu impish/universe ppc64el libtsl-hopscotch-map-dev all 2.3.0-1 [36.5 kB] Get:231 http://ftpmaster.internal/ubuntu impish/universe ppc64el libvcflib1 ppc64el 1.0.2+dfsg-2 [154 kB] Get:232 http://ftpmaster.internal/ubuntu impish/universe ppc64el libvcflib-dev ppc64el 1.0.2+dfsg-2 [82.9 kB] Get:233 http://ftpmaster.internal/ubuntu impish/main ppc64el zip ppc64el 3.0-12 [169 kB] Get:234 http://ftpmaster.internal/ubuntu impish/main ppc64el unzip ppc64el 6.0-26ubuntu1 [174 kB] Get:235 http://ftpmaster.internal/ubuntu impish/main ppc64el xdg-utils all 1.1.3-2ubuntu2 [61.5 kB] Get:236 http://ftpmaster.internal/ubuntu impish/main ppc64el libxt6 ppc64el 1:1.2.0-1 [174 kB] Get:237 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-base-core ppc64el 4.0.4-1build1 [25.3 MB] Get:238 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-littler ppc64el 0.3.12-1 [82.6 kB] Get:239 http://ftpmaster.internal/ubuntu impish/universe ppc64el littler all 0.3.12-1 [2380 B] Get:240 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-pkgkitten all 0.2.1-1 [24.8 kB] Get:241 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-rcpp ppc64el 1.0.6-1 [1950 kB] Get:242 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-plyr ppc64el 1.8.6-2build1 [832 kB] Get:243 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-digest ppc64el 0.6.27-1 [183 kB] Get:244 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-glue ppc64el 1.4.2-1 [134 kB] Get:245 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-gtable all 0.3.0+dfsg-2build1 [138 kB] Get:246 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-brio ppc64el 1.1.1-1 [31.6 kB] Get:247 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-ps ppc64el 1.5.0-1 [278 kB] Get:248 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impish/universe ppc64el r-cran-waldo all 0.2.3-2 [79.4 kB] Get:277 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-testthat ppc64el 3.0.1-1 [1447 kB] Get:278 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-isoband ppc64el 0.2.3-2 [1952 kB] Get:279 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-mass ppc64el 7.3-53.1-1 [1120 kB] Get:280 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-lattice ppc64el 0.20-41-1build1 [1121 kB] Get:281 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-nlme ppc64el 3.1.152-1 [2235 kB] Get:282 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-matrix ppc64el 1.3-2+really1.3-2-0ubuntu1 [3625 kB] Get:283 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-mgcv ppc64el 1.8-34-1 [3011 kB] Get:284 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-farver ppc64el 2.0.3-1build2 [1339 kB] Get:285 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-labeling all 0.4.2-1 [62.6 kB] Get:286 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-colorspace ppc64el 2.0-0+dfsg-1 [1535 kB] Get:287 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-munsell all 0.5.0-2build1 [208 kB] Get:288 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-rcolorbrewer all 1.1-2-3 [54.6 kB] Get:289 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-viridislite all 0.3.0-4 [58.9 kB] Get:290 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-scales all 1.1.1-1build1 [486 kB] Get:291 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-ggplot2 all 3.3.3+dfsg-1 [3122 kB] Get:292 http://ftpmaster.internal/ubuntu impish/universe ppc64el r-cran-gridbase all 0.4-7-5build1 [163 kB] Get:293 http://ftpmaster.internal/ubuntu impish/universe ppc64el libvcflib-tools ppc64el 1.0.2+dfsg-2 [714 kB] Get:294 http://ftpmaster.internal/ubuntu impish/main ppc64el pv ppc64el 1.6.6-1 [49.1 kB] Get:295 http://ftpmaster.internal/ubuntu impish/universe ppc64el rapidjson-dev all 1.1.0+dfsg2-7 [95.0 kB] Get:296 http://ftpmaster.internal/ubuntu impish/main ppc64el raptor2-utils ppc64el 2.0.15-0ubuntu2 [13.8 kB] Get:297 http://ftpmaster.internal/ubuntu impish/main ppc64el rasqal-utils ppc64el 0.9.33-0.1 [18.9 kB] Get:298 http://ftpmaster.internal/ubuntu impish/universe ppc64el rs ppc64el 20200313-1 [16.9 kB] Get:299 http://ftpmaster.internal/ubuntu impish/universe ppc64el samtools ppc64el 1.11-1 [590 kB] Get:300 http://ftpmaster.internal/ubuntu impish/universe ppc64el tabix ppc64el 1.11-4 [401 kB] Get:301 http://ftpmaster.internal/ubuntu impish/universe ppc64el libjemalloc-dev ppc64el 5.2.1-3 [362 kB] Get:302 http://ftpmaster.internal/ubuntu impish/main ppc64el liblz4-dev ppc64el 1.9.3-2 [90.8 kB] Get:303 http://ftpmaster.internal/ubuntu impish/main ppc64el libprotobuf-dev ppc64el 3.12.4-1ubuntu2 [1307 kB] Get:304 http://ftpmaster.internal/ubuntu impish/main ppc64el libprotoc-dev ppc64el 3.12.4-1ubuntu2 [1002 kB] Get:305 http://ftpmaster.internal/ubuntu impish/universe ppc64el protobuf-compiler ppc64el 3.12.4-1ubuntu2 [28.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 150 MB in 11s (13.6 MB/s) Selecting previously unselected package liblocale-gettext-perl. 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Setting up libncurses-dev:ppc64el (6.2+20201114-2build1) ... Setting up libpsl5:ppc64el (0.21.0-1.2) ... Setting up libboost1.74-dev:ppc64el (1.74.0-8ubuntu2) ... Setting up libpixman-1-dev:ppc64el (0.40.0-1build2) ... Setting up bsdextrautils (2.36.1-8ubuntu1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libpcre16-3:ppc64el (2:8.39-13build3) ... Setting up libicu67:ppc64el (67.1-6ubuntu2) ... Setting up libdatrie1:ppc64el (0.2.13-1ubuntu2) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up ncal (12.1.7+nmu3ubuntu1) ... Setting up gawk (1:5.1.0-1build1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:ppc64el (2.68.3-1ubuntu1) ... No schema files found: doing nothing. Setting up bwa (0.7.17-6) ... Setting up libboost-program-options1.74.0:ppc64el (1.74.0-8ubuntu2) ... Setting up unzip (6.0-26ubuntu1) ... Setting up libdebhelper-perl (13.3.4ubuntu2) ... Setting up libbrotli1:ppc64el (1.0.9-2build2) ... Setting up libyajl2:ppc64el (2.1.0-3) ... Setting up x11-common (1:7.7+22ubuntu1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libsmithwaterman0 (0.0+git20160702.2610e25-11) ... Setting up libnghttp2-14:ppc64el (1.43.0-1) ... Setting up libmagic1:ppc64el (1:5.39-3) ... Setting up libsepol1-dev:ppc64el (3.1-1ubuntu1) ... Setting up libdeflate0:ppc64el (1.7-1ubuntu2) ... Setting up bc (1.07.1-2build2) ... Setting up gettext-base (0.21-4ubuntu3) ... Setting up m4 (1.4.18-5) ... Setting up liblzo2-2:ppc64el (2.10-2build1) ... Setting up libprotobuf23:ppc64el (3.12.4-1ubuntu2) ... Setting up file (1:5.39-3) ... Setting up libjemalloc2:ppc64el (5.2.1-3) ... Setting up libffi-dev:ppc64el (3.4~20200819gead65ca871-0ubuntu5) ... Setting up libsparsehash-dev (2.0.3-2) ... Setting up libpthread-stubs0-dev:ppc64el (0.4-1) ... Setting up libfml0:ppc64el (0.1+git20190320.b499514-1) ... 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Setting up libblas3:ppc64el (3.9.0-3ubuntu2) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode Setting up libglib2.0-data (2.68.3-1ubuntu1) ... Setting up libgmpxx4ldbl:ppc64el (2:6.2.1+dfsg-1ubuntu2) ... Setting up libuv1:ppc64el (1.40.0-2) ... Setting up libexpat1-dev:ppc64el (2.3.0-1) ... Setting up libfreetype6:ppc64el (2.10.4+dfsg-1build1) ... Setting up libboost-program-options-dev:ppc64el (1.74.0.3ubuntu5) ... Setting up libx11-data (2:1.7.2-1) ... Setting up librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build2) ... Setting up uuid-dev:ppc64el (2.36.1-8ubuntu1) ... Setting up libprotoc23:ppc64el (3.12.4-1ubuntu2) ... Setting up libtsl-hopscotch-map-dev (2.3.0-1) ... Setting up libfribidi0:ppc64el (1.0.8-2ubuntu1) ... Setting up bsdmainutils (12.1.7+nmu3ubuntu1) ... Setting up libpcre32-3:ppc64el (2:8.39-13build3) ... 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Setting up libmd0:ppc64el (1.0.3-3build1) ... Setting up pv (1.6.6-1) ... Setting up librhash0:ppc64el (1.4.1-2) ... Setting up libuchardet0:ppc64el (0.0.7-1) ... Setting up libncurses5-dev:ppc64el (6.2+20201114-2build1) ... Setting up bison (2:3.7.6+dfsg-1build1) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up libsub-override-perl (0.09-2) ... Setting up libharfbuzz0b:ppc64el (2.7.4-1ubuntu1) ... Setting up libthai-data (0.1.28-4) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up sgml-base (1.30) ... Setting up cmake-data (3.18.4-2ubuntu2) ... Setting up libdivsufsort3:ppc64el (2.0.1-5) ... Setting up libbsd0:ppc64el (0.11.3-1ubuntu2) ... Setting up python3-lib2to3 (3.9.5-0ubuntu3) ... Setting up libdeflate-dev:ppc64el (1.7-1ubuntu2) ... Setting up tabix (1.11-4) ... Setting up libelf1:ppc64el (0.185-1) ... Setting up libssw0:ppc64el (1.1-13) ... Setting up libicu-dev:ppc64el (67.1-6ubuntu2) ... Setting up libxml2:ppc64el (2.9.10+dfsg-6.7) ... Setting up xdg-utils (1.1.3-2ubuntu2) ... Setting up libjansson-dev:ppc64el (2.13.1-1.1build1) ... Setting up libonig5:ppc64el (6.9.6-1.1) ... Setting up liblocale-gettext-perl (1.07-4build1) ... Setting up libbrotli-dev:ppc64el (1.0.9-2build2) ... Setting up libdivsufsort-dev:ppc64el (2.0.1-5) ... Setting up rs (20200313-1) ... Setting up libbz2-dev:ppc64el (1.0.8-4ubuntu3) ... Setting up libjpeg8:ppc64el (8c-2ubuntu8) ... Setting up automake (1:1.16.4-1ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3-distutils (3.9.5-0ubuntu3) ... Setting up x11proto-dev (2020.1-1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libglib2.0-dev-bin (2.68.3-1ubuntu1) ... Setting up libblkid-dev:ppc64el (2.36.1-8ubuntu1) ... Setting up libpaper1:ppc64el (1.1.28) ... Creating config file /etc/papersize with new version Setting up libice6:ppc64el (2:1.0.10-1) ... Setting up libdw1:ppc64el (0.185-1) ... Setting up libxdmcp6:ppc64el (1:1.1.3-0ubuntu3) ... Setting up flex (2.6.4-8) ... Setting up liblapack3:ppc64el (3.9.0-3ubuntu2) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode Setting up libxcb1:ppc64el (1.14-3ubuntu1) ... Setting up gettext (0.21-4ubuntu3) ... Setting up libfml-dev:ppc64el (0.1+git20190320.b499514-1) ... Setting up libgmp-dev:ppc64el (2:6.2.1+dfsg-1ubuntu2) ... Setting up libxau-dev:ppc64el (1:1.0.9-1build3) ... Setting up libpcre2-dev:ppc64el (10.36-2ubuntu5) ... Setting up protobuf-compiler (3.12.4-1ubuntu2) ... Setting up libice-dev:ppc64el (2:1.0.10-1) ... Setting up libssw-dev:ppc64el (1.1-13) ... Setting up libtool (2.4.6-15) ... Setting up libarchive13:ppc64el (3.4.3-2) ... 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Setting up libelf-dev:ppc64el (0.185-1) ... Setting up libsmithwaterman-dev (0.0+git20160702.2610e25-11) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up x11proto-xext-dev (2020.1-1) ... Setting up dwz (0.14-1) ... Setting up libprotoc-dev:ppc64el (3.12.4-1ubuntu2) ... Setting up groff-base (1.22.4-6) ... Setting up xml-core (0.18+nmu1) ... Setting up jq (1.6-2.1ubuntu1) ... Setting up libxslt1.1:ppc64el (1.1.34-4) ... Setting up debugedit (1:5.0-0ubuntu1) ... Setting up libcurl4:ppc64el (7.74.0-1.2ubuntu4) ... Setting up libx11-6:ppc64el (2:1.7.2-1) ... Setting up libasm1:ppc64el (0.185-1) ... Setting up libtiff5:ppc64el (4.3.0-1) ... Setting up libfontconfig1:ppc64el (2.13.1-4.2ubuntu3) ... Setting up libsm6:ppc64el (2:1.2.3-1) ... Setting up libmount-dev:ppc64el (2.36.1-8ubuntu1) ... Setting up elfutils (0.185-1) ... Setting up fontconfig (2.13.1-4.2ubuntu3) ... Regenerating fonts cache... done. Setting up libxcb1-dev:ppc64el (1.14-3ubuntu1) ... Setting up libxslt1-dev:ppc64el (1.1.34-4) ... Setting up libxrender1:ppc64el (1:0.9.10-1build2) ... Setting up libsm-dev:ppc64el (2:1.2.3-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:ppc64el (1.48.7+ds1-2) ... Setting up xsltproc (1.1.34-4) ... Setting up libx11-dev:ppc64el (2:1.7.2-1) ... Setting up libxext6:ppc64el (2:1.3.4-0ubuntu3) ... Setting up libcurl3-gnutls:ppc64el (7.74.0-1.2ubuntu4) ... Setting up libcurl4-gnutls-dev:ppc64el (7.74.0-1.2ubuntu4) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libdw-dev:ppc64el (0.185-1) ... Setting up libcairo2:ppc64el (1.16.0-5ubuntu1) ... Setting up libfreetype6-dev:ppc64el (2.10.4+dfsg-1build1) ... Setting up libxcb-shm0-dev:ppc64el (1.14-3ubuntu1) ... Setting up libglib2.0-dev:ppc64el (2.68.3-1ubuntu1) ... Setting up libxcb-render0-dev:ppc64el (1.14-3ubuntu1) ... Setting up libxt6:ppc64el (1:1.2.0-1) ... Setting up libxext-dev:ppc64el (2:1.3.4-0ubuntu3) ... Setting up python3-lxml:ppc64el (4.6.3+dfsg-0.1) ... Setting up cmake (3.18.4-2ubuntu2) ... Setting up libcairo-gobject2:ppc64el (1.16.0-5ubuntu1) ... Setting up libxss1:ppc64el (1:1.2.3-1) ... Setting up libpangoft2-1.0-0:ppc64el (1.48.7+ds1-2) ... Setting up libxrender-dev:ppc64el (1:0.9.10-1build2) ... Setting up libpangocairo-1.0-0:ppc64el (1.48.7+ds1-2) ... Setting up libcairo-script-interpreter2:ppc64el (1.16.0-5ubuntu1) ... Setting up libxft2:ppc64el (2.3.3-0ubuntu3) ... Setting up libhts3:ppc64el (1.11-4) ... Setting up libfontconfig-dev:ppc64el (2.13.1-4.2ubuntu3) ... Setting up libtk8.6:ppc64el (8.6.11-2) ... Setting up libraptor2-0:ppc64el (2.0.15-0ubuntu2) ... Setting up raptor2-utils (2.0.15-0ubuntu2) ... Setting up libhts-dev:ppc64el (1.11-4) ... Setting up debhelper (13.3.4ubuntu2) ... Setting up samtools (1.11-1) ... Setting up r-base-core (4.0.4-1build1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.4.0-1) ... Setting up r-cran-gtable (0.3.0+dfsg-2build1) ... Setting up r-cran-labeling (0.4.2-1) ... Setting up r-cran-lattice (0.20-41-1build1) ... Setting up r-cran-ps (1.5.0-1) ... Setting up r-cran-nlme (3.1.152-1) ... Setting up r-cran-farver (2.0.3-1build2) ... Setting up r-cran-viridislite (0.3.0-4) ... Setting up libtabixpp0:ppc64el (1.1.0-4ubuntu1) ... Setting up libraptor2-dev (2.0.15-0ubuntu2) ... Setting up libcairo2-dev:ppc64el (1.16.0-5ubuntu1) ... Setting up r-cran-r6 (2.5.0-1) ... Setting up r-cran-pkgkitten (0.2.1-1) ... Setting up r-cran-magrittr (2.0.1-1) ... Setting up r-cran-littler (0.3.12-1) ... Setting up r-cran-rcpp (1.0.6-1) ... Setting up r-cran-brio (1.1.1-1) ... Setting up r-cran-diffobj (0.3.2-1) ... Setting up r-cran-rlang (0.4.10-1ubuntu1) ... Setting up libfontconfig1-dev:ppc64el (2.13.1-4.2ubuntu3) ... Setting up r-cran-gridbase (0.4-7-5build1) ... Setting up r-cran-assertthat (0.2.1-2build1) ... Setting up littler (0.3.12-1) ... Setting up r-cran-withr (2.4.1-1) ... Setting up r-cran-processx (3.4.5-1) ... Setting up r-cran-praise (1.0.0-4build1) ... Setting up r-cran-digest (0.6.27-1) ... Setting up librasqal3:ppc64el (0.9.33-0.1) ... Setting up r-cran-evaluate (0.14-2build1) ... Setting up r-cran-prettyunits (1.1.1-2build1) ... Setting up r-cran-fansi (0.4.2-1) ... Setting up r-cran-mass (7.3-53.1-1) ... Setting up librasqal3-dev (0.9.33-0.1) ... Setting up r-cran-glue (1.4.2-1) ... Setting up r-cran-cli (2.3.0-1) ... Setting up r-cran-lifecycle (0.2.0-2build1) ... Setting up r-cran-rprojroot (2.0.2-1) ... Setting up r-cran-jsonlite (1.7.2+dfsg-1) ... Setting up r-cran-rstudioapi (0.13-1) ... Setting up r-cran-pkgconfig (2.0.3-2build1) ... Setting up r-cran-utf8 (1.1.4-2) ... Setting up r-cran-colorspace (2.0-0+dfsg-1) ... Setting up librdf0:ppc64el (1.0.17-1.1ubuntu1) ... Setting up r-cran-plyr (1.8.6-2build1) ... Setting up r-cran-rcolorbrewer (1.1-2-3) ... Setting up r-cran-matrix (1.3-2+really1.3-2-0ubuntu1) ... Setting up librdf0-dev (1.0.17-1.1ubuntu1) ... Setting up libvcflib1:ppc64el (1.0.2+dfsg-2) ... Setting up r-cran-mgcv (1.8-34-1) ... Setting up libtabixpp-dev:ppc64el (1.1.0-4ubuntu1) ... Setting up libvcflib-dev:ppc64el (1.0.2+dfsg-2) ... Setting up r-cran-ellipsis (0.3.1-1build1) ... Setting up rasqal-utils (0.9.33-0.1) ... Setting up r-cran-callr (3.5.1-1) ... Setting up r-cran-desc (1.2.0-3build1) ... Setting up r-cran-munsell (0.5.0-2build1) ... Setting up r-cran-scales (1.1.1-1build1) ... Setting up r-cran-pkgbuild (1.2.0-1) ... Setting up r-cran-vctrs (0.3.6-1) ... Setting up r-cran-pillar (1.4.7-1) ... Setting up r-cran-pkgload (1.1.0-1) ... Setting up r-cran-tibble (3.0.6+dfsg-1) ... Setting up r-cran-rematch2 (2.1.2-2build1) ... Setting up r-cran-waldo (0.2.3-2) ... Setting up r-cran-testthat (3.0.1-1) ... Setting up r-cran-isoband (0.2.3-2) ... Setting up r-cran-ggplot2 (3.3.3+dfsg-1) ... Setting up libvcflib-tools (1.0.2+dfsg-2) ... Processing triggers for libc-bin (2.34-0ubuntu1~ppa5) ... Processing triggers for sgml-base (1.30) ... Setting up docbook-xsl (1.79.2+dfsg-1) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.30) ... Setting up docbook-xml (4.5-9) ... Setting up docbook (4.5-6) ... Processing triggers for sgml-base (1.30) ... Setting up docbook-to-man (1:2.0.0-45) ... Setting up gtk-doc-tools (1.33.2-1) ... Setting up sbuild-build-depends-vg-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-154-generic ppc64el (ppc64le) Toolchain package versions: binutils_2.37-1ubuntu1 dpkg-dev_1.20.9ubuntu13 g++-10_10.3.0-6ubuntu1 g++-11_11.2.0-1ubuntu2 gcc-10_10.3.0-6ubuntu1 gcc-11_11.2.0-1ubuntu2 libc6-dev_2.34-0ubuntu1~ppa5 libstdc++-10-dev_10.3.0-6ubuntu1 libstdc++-11-dev_11.2.0-1ubuntu2 libstdc++6_11.2.0-1ubuntu2 linux-libc-dev_5.13.0-14.14 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu1 apt_2.3.7 autoconf_2.69-14 automake_1:1.16.4-1ubuntu1 autopoint_0.21-4ubuntu3 autotools-dev_20180224.1+nmu1 base-files_11.1ubuntu3 base-passwd_3.5.51 bash_5.1-3ubuntu1 bc_1.07.1-2build2 binutils_2.37-1ubuntu1 binutils-common_2.37-1ubuntu1 binutils-powerpc64le-linux-gnu_2.37-1ubuntu1 bison_2:3.7.6+dfsg-1build1 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libraptor2-0_2.0.15-0ubuntu2 libraptor2-dev_2.0.15-0ubuntu2 librasqal3_0.9.33-0.1 librasqal3-dev_0.9.33-0.1 librdf0_1.0.17-1.1ubuntu1 librdf0-dev_1.0.17-1.1ubuntu1 libreadline8_8.1-2 librhash0_1.4.1-2 librtmp1_2.4+20151223.gitfa8646d.1-2build2 libsasl2-2_2.1.27+dfsg-2.1build1 libsasl2-modules-db_2.1.27+dfsg-2.1build1 libseccomp2_2.5.1-1ubuntu1 libselinux1_3.1-3build1 libselinux1-dev_3.1-3build1 libsemanage-common_3.1-1ubuntu1 libsemanage1_3.1-1ubuntu1 libsepol1_3.1-1ubuntu1 libsepol1-dev_3.1-1ubuntu1 libsigsegv2_2.13-1ubuntu1 libsimde-dev_0.7.2-4 libsm-dev_2:1.2.3-1 libsm6_2:1.2.3-1 libsmartcols1_2.36.1-8ubuntu1 libsmithwaterman-dev_0.0+git20160702.2610e25-11 libsmithwaterman0_0.0+git20160702.2610e25-11 libsparsehash-dev_2.0.3-2 libsqlite3-0_3.35.5-1 libss2_1.46.2-1ubuntu2 libssh-4_0.9.6-1 libssl1.1_1.1.1j-1ubuntu5 libssw-dev_1.1-13 libssw0_1.1-13 libstdc++-10-dev_10.3.0-6ubuntu1 libstdc++-11-dev_11.2.0-1ubuntu2 libstdc++6_11.2.0-1ubuntu2 libsub-override-perl_0.09-2 libsystemd0_248.3-1ubuntu3 libtabixpp-dev_1.1.0-4ubuntu1 libtabixpp0_1.1.0-4ubuntu1 libtasn1-6_4.16.0-2 libtcl8.6_8.6.11+dfsg-1 libthai-data_0.1.28-4 libthai0_0.1.28-4 libtiff5_4.3.0-1 libtinfo6_6.2+20201114-2build1 libtirpc-common_1.3.1-1build1 libtirpc-dev_1.3.1-1build1 libtirpc3_1.3.1-1build1 libtk8.6_8.6.11-2 libtool_2.4.6-15 libtsan0_11.2.0-1ubuntu2 libtsl-hopscotch-map-dev_2.3.0-1 libubsan1_11.2.0-1ubuntu2 libuchardet0_0.0.7-1 libudev1_248.3-1ubuntu3 libunistring2_0.9.10-4 libuuid1_2.36.1-8ubuntu1 libuv1_1.40.0-2 libvcflib-dev_1.0.2+dfsg-2 libvcflib-tools_1.0.2+dfsg-2 libvcflib1_1.0.2+dfsg-2 libwebp6_0.6.1-2.1 libx11-6_2:1.7.2-1 libx11-data_2:1.7.2-1 libx11-dev_2:1.7.2-1 libxau-dev_1:1.0.9-1build3 libxau6_1:1.0.9-1build3 libxcb-render0_1.14-3ubuntu1 libxcb-render0-dev_1.14-3ubuntu1 libxcb-shm0_1.14-3ubuntu1 libxcb-shm0-dev_1.14-3ubuntu1 libxcb1_1.14-3ubuntu1 libxcb1-dev_1.14-3ubuntu1 libxdmcp-dev_1:1.1.3-0ubuntu3 libxdmcp6_1:1.1.3-0ubuntu3 libxext-dev_2:1.3.4-0ubuntu3 libxext6_2:1.3.4-0ubuntu3 libxft2_2.3.3-0ubuntu3 libxml2_2.9.10+dfsg-6.7 libxml2-dev_2.9.10+dfsg-6.7 libxrender-dev_1:0.9.10-1build2 libxrender1_1:0.9.10-1build2 libxslt1-dev_1.1.34-4 libxslt1.1_1.1.34-4 libxss1_1:1.2.3-1 libxt6_1:1.2.0-1 libxxhash0_0.8.0-2 libyajl-dev_2.1.0-3 libyajl2_2.1.0-3 libzstd1_1.4.8+dfsg-2.1 linux-libc-dev_5.13.0-14.14 littler_0.3.12-1 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu9 logsave_1.46.2-1ubuntu2 lsb-base_11.1.0ubuntu2 lto-disabled-list_16 m4_1.4.18-5 make_4.3-4ubuntu1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.36.1-8ubuntu1 ncal_12.1.7+nmu3ubuntu1 ncurses-base_6.2+20201114-2build1 ncurses-bin_6.2+20201114-2build1 opensp_1.5.2-13ubuntu3 openssl_1.1.1j-1ubuntu5 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu9 patch_2.7.6-7 perl_5.32.1-3ubuntu3 perl-base_5.32.1-3ubuntu3 perl-modules-5.32_5.32.1-3ubuntu3 pinentry-curses_1.1.1-1 pkg-config_0.29.2-1ubuntu1 pkgbinarymangler_148 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 procps_2:3.3.17-5ubuntu3 protobuf-compiler_3.12.4-1ubuntu2 pv_1.6.6-1 python3_3.9.4-1 python3-distutils_3.9.5-0ubuntu3 python3-lib2to3_3.9.5-0ubuntu3 python3-lxml_4.6.3+dfsg-0.1 python3-minimal_3.9.4-1 python3-pkg-resources_52.0.0-4 python3-psutil_5.8.0-1 python3-pygments_2.7.1+dfsg-2.1 python3.9_3.9.6-1 python3.9-minimal_3.9.6-1 r-base-core_4.0.4-1build1 r-cran-assertthat_0.2.1-2build1 r-cran-brio_1.1.1-1 r-cran-callr_3.5.1-1 r-cran-cli_2.3.0-1 r-cran-colorspace_2.0-0+dfsg-1 r-cran-crayon_1.4.0-1 r-cran-desc_1.2.0-3build1 r-cran-diffobj_0.3.2-1 r-cran-digest_0.6.27-1 r-cran-ellipsis_0.3.1-1build1 r-cran-evaluate_0.14-2build1 r-cran-fansi_0.4.2-1 r-cran-farver_2.0.3-1build2 r-cran-ggplot2_3.3.3+dfsg-1 r-cran-glue_1.4.2-1 r-cran-gridbase_0.4-7-5build1 r-cran-gtable_0.3.0+dfsg-2build1 r-cran-isoband_0.2.3-2 r-cran-jsonlite_1.7.2+dfsg-1 r-cran-labeling_0.4.2-1 r-cran-lattice_0.20-41-1build1 r-cran-lifecycle_0.2.0-2build1 r-cran-littler_0.3.12-1 r-cran-magrittr_2.0.1-1 r-cran-mass_7.3-53.1-1 r-cran-matrix_1.3-2+really1.3-2-0ubuntu1 r-cran-mgcv_1.8-34-1 r-cran-munsell_0.5.0-2build1 r-cran-nlme_3.1.152-1 r-cran-pillar_1.4.7-1 r-cran-pkgbuild_1.2.0-1 r-cran-pkgconfig_2.0.3-2build1 r-cran-pkgkitten_0.2.1-1 r-cran-pkgload_1.1.0-1 r-cran-plyr_1.8.6-2build1 r-cran-praise_1.0.0-4build1 r-cran-prettyunits_1.1.1-2build1 r-cran-processx_3.4.5-1 r-cran-ps_1.5.0-1 r-cran-r6_2.5.0-1 r-cran-rcolorbrewer_1.1-2-3 r-cran-rcpp_1.0.6-1 r-cran-rematch2_2.1.2-2build1 r-cran-rlang_0.4.10-1ubuntu1 r-cran-rprojroot_2.0.2-1 r-cran-rstudioapi_0.13-1 r-cran-scales_1.1.1-1build1 r-cran-testthat_3.0.1-1 r-cran-tibble_3.0.6+dfsg-1 r-cran-utf8_1.1.4-2 r-cran-vctrs_0.3.6-1 r-cran-viridislite_0.3.0-4 r-cran-waldo_0.2.3-2 r-cran-withr_2.4.1-1 rapidjson-dev_1.1.0+dfsg2-7 raptor2-utils_2.0.15-0ubuntu2 rasqal-utils_0.9.33-0.1 readline-common_8.1-2 rpcsvc-proto_1.4.2-0ubuntu4 rs_20200313-1 samtools_1.11-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-vg-dummy_0.invalid.0 sed_4.7-1ubuntu1 sensible-utils_0.0.14 sgml-base_1.30 sgml-data_2.0.11+nmu1 systemd_248.3-1ubuntu3 systemd-sysv_248.3-1ubuntu3 systemd-timesyncd_248.3-1ubuntu3 sysvinit-utils_2.96-7ubuntu1 tabix_1.11-4 tar_1.34+dfsg-1build1 tzdata_2021a-1ubuntu1 ubuntu-keyring_2021.03.26 ucf_3.0043 unzip_6.0-26ubuntu1 usrmerge_25ubuntu1 util-linux_2.36.1-8ubuntu1 uuid-dev_2.36.1-8ubuntu1 x11-common_1:7.7+22ubuntu1 x11proto-dev_2020.1-1 x11proto-xext-dev_2020.1-1 xdg-utils_1.1.3-2ubuntu2 xml-core_0.18+nmu1 xorg-sgml-doctools_1:1.11-1.1 xsltproc_1.1.34-4 xtrans-dev_1.4.0-1 xxd_2:8.2.2434-3ubuntu1 xz-utils_5.2.5-2 zip_3.0-12 zlib1g_1:1.2.11.dfsg-2ubuntu7 zlib1g-dev_1:1.2.11.dfsg-2ubuntu7 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Wed Jan 27 12:04:08 2021 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./vg_1.30.0+ds-1.dsc dpkg-source: info: extracting vg in /<>/vg-1.30.0+ds dpkg-source: info: unpacking vg_1.30.0+ds.orig.tar.xz dpkg-source: info: unpacking vg_1.30.0+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc-10 dpkg-source: info: applying use_packaged_libdeflate dpkg-source: info: applying use_packaged_jemalloc dpkg-source: info: applying use_packaged_libbackward-cpp 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 dpkg-source: info: applying fix-handlegraph Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-21946007 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-21946007 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-21946007 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage.pl: info: source package vg dpkg-buildpackage.pl: info: source version 1.30.0+ds-1 dpkg-buildpackage.pl: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage.pl: info: host architecture ppc64el debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/vg-1.30.0+ds' find /<>/vg-1.30.0+ds/include/ -type f -a '!' -name vg_git_version.hpp -delete dh_auto_clean || true make -j4 clean make[2]: Entering directory '/<>/vg-1.30.0+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-1.30.0+ds/deps/sonLib' cd C && make clean cd externalTools && make clean make[4]: Entering directory '/<>/vg-1.30.0+ds/deps/sonLib/C' make[4]: Entering directory '/<>/vg-1.30.0+ds/deps/sonLib/externalTools' rm -rf ../bin ../lib cd cutest && make clean make[4]: Leaving directory '/<>/vg-1.30.0+ds/deps/sonLib/C' make[5]: Entering directory '/<>/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make clean make[5]: Entering directory '/<>/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -rf ./obj/*.o make[5]: Leaving directory '/<>/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' rm -f ../../lib/cuTest.a ../../lib/CuTest.h make[5]: Leaving directory '/<>/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' make[4]: Leaving directory '/<>/vg-1.30.0+ds/deps/sonLib/externalTools' rm -f ./bin/sonLib_daemonize.py make[3]: Leaving directory '/<>/vg-1.30.0+ds/deps/sonLib' cd ./deps && cd gcsa2 && make clean make[3]: Entering directory '/<>/vg-1.30.0+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-1.30.0+ds/deps/gcsa2' make[2]: *** [Makefile:691: clean] Error 2 make[2]: Leaving directory '/<>/vg-1.30.0+ds' dh_auto_clean: error: make -j4 clean returned exit code 2 make[1]: Leaving directory '/<>/vg-1.30.0+ds' debian/rules override_dh_clean make[1]: Entering directory '/<>/vg-1.30.0+ds' rm -Rf ./deps/DYNAMIC/build/CMakeFiles dh_clean make[1]: Leaving directory '/<>/vg-1.30.0+ds' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a debian/rules override_dh_autoreconf make[1]: Entering directory '/<>/vg-1.30.0+ds' dh_autoreconf --sourcedirectory=/<>/vg-1.30.0+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-1.30.0+ds' dh_auto_configure -a debian/rules override_dh_auto_build-arch make[1]: Entering directory '/<>/vg-1.30.0+ds' mkdir -p /<>/vg-1.30.0+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-1.30.0+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 -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp" ./install.sh /<>/vg-1.30.0+ds . ./source_me.sh && cd deps/libhandlegraph && CXXFLAGS="-O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2" cmake -DCMAKE_VERBOSE_MAKEFILE=ON . && make && cp libhandlegraph.a /<>/vg-1.30.0+ds/lib && cp -r src/include/handlegraph /<>/vg-1.30.0+ds/include . ./source_me.sh && cd deps/gssw && make && cp lib/* /<>/vg-1.30.0+ds/lib/ && cp obj/* /<>/vg-1.30.0+ds/obj && cp src/*.h /<>/vg-1.30.0+ds/include . ./source_me.sh && cd ./deps/sonLib && kyotoTycoonLib="" make && cp lib/sonLib.a /<>/vg-1.30.0+ds/lib/libsonlib.a && mkdir -p /<>/vg-1.30.0+ds/include/sonLib && cp lib/*.h /<>/vg-1.30.0+ds/include/sonLib make[3]: Entering directory '/<>/vg-1.30.0+ds/deps/sonLib' cd externalTools && make all make[4]: Entering directory '/<>/vg-1.30.0+ds/deps/sonLib/externalTools' cd cutest && make all make[5]: Entering directory '/<>/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' make[3]: Entering directory '/<>/vg-1.30.0+ds/deps/gssw' gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.30.0+ds/include -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -c CuTest.c gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -I /<>/vg-1.30.0+ds/include -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g -c -o obj/gssw.o src/gssw.c Library will be installed in '/<>/vg-1.30.0+ds' WARNING: .git/hooks directory does not exists. The pre-commit hook is not installed. CMake Warning (dev) at /usr/share/cmake-3.18/Modules/GNUInstallDirs.cmake:225 (message): Unable to determine default CMAKE_INSTALL_LIBDIR directory because no target architecture is known. Please enable at least one language before including GNUInstallDirs. Call Stack (most recent call first): CMakeLists.txt:5 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- The CXX compiler identification is GNU 11.2.0 ar rc cuTest.a *.o ranlib cuTest.a rm -f *.o mv cuTest.a ../../lib/ cp CuTest.h ../../lib/ make[5]: Leaving directory '/<>/vg-1.30.0+ds/deps/sonLib/externalTools/cutest' cd quicktree_1.1 && make all CC="gcc -std=c99" make[5]: Entering directory '/<>/vg-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' gcc -std=c99 -I /<>/vg-1.30.0+ds/include -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/align.o ./src/align.c -- Detecting C compiler ABI info - done -- The C compiler identification is GNU 11.2.0 -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info gcc -std=c99 -I /<>/vg-1.30.0+ds/include -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/cluster.o ./src/cluster.c -- Detecting CXX compiler ABI info - done -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting CXX compile features - done libhandlegraph is root project or external_project -- Configuring done -- Detecting C compiler ABI info -- Generating done -- Build files have been written to: /<>/vg-1.30.0+ds/deps/libhandlegraph make[3]: Entering directory '/<>/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -S/<>/vg-1.30.0+ds/deps/libhandlegraph -B/<>/vg-1.30.0+ds/deps/libhandlegraph --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles /<>/vg-1.30.0+ds/deps/libhandlegraph//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/depend make[5]: Entering directory '/<>/vg-1.30.0+ds/deps/libhandlegraph' cd /<>/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.30.0+ds/deps/libhandlegraph /<>/vg-1.30.0+ds/deps/libhandlegraph /<>/vg-1.30.0+ds/deps/libhandlegraph /<>/vg-1.30.0+ds/deps/libhandlegraph /<>/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_objs.dir/DependInfo.cmake --color= gcc -std=c99 -I /<>/vg-1.30.0+ds/include -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/distancemat.o ./src/distancemat.c Scanning dependencies of target handlegraph_objs make[5]: Leaving directory '/<>/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_objs.dir/build.make CMakeFiles/handlegraph_objs.dir/build make[5]: Entering directory '/<>/vg-1.30.0+ds/deps/libhandlegraph' [ 3%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/deletable_handle_graph.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/deletable_handle_graph.cpp -- Detecting C compiler ABI info - done ./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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Compiler is recent enough to support C++11. -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG gcc -std=c99 -I /<>/vg-1.30.0+ds/include -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/options.o ./src/options.c -- Performing Test HAVE_GCC_STD=C__11__WALL__WEXTRA__DNDEBUG - Success -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS gcc -std=c99 -I /<>/vg-1.30.0+ds/include -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/util.o ./src/util.c gcc -std=c99 -I /<>/vg-1.30.0+ds/include -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/sequence.o ./src/sequence.c -- Performing Test HAVE_GCC_O3__FFAST_MATH__FUNROLL_LOOPS - Success -- Performing Test HAVE_CXA_DEMANGLE gcc -std=c99 -I /<>/vg-1.30.0+ds/include -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/quicktree.o ./src/quicktree.c [ 6%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/handle_graph.cpp gcc -std=c99 -I /<>/vg-1.30.0+ds/include -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/buildtree.o ./src/buildtree.c -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success -- Could NOT find Git (missing: GIT_EXECUTABLE) CMake Warning at CMakeLists.txt:105 (message): git not found. Cloning of submodules will not work. -- Looking for C++ include cstdio gcc -std=c99 -I /<>/vg-1.30.0+ds/include -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -I./include -O3 -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o ./obj/tree.o ./src/tree.c -- Looking for C++ include cstdio - found -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) ./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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -- Configuring done [ 9%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/mutable_handle_graph.cpp -- Generating done -- Build files have been written to: /<>/vg-1.30.0+ds/deps/sdsl-lite/build make[3]: Entering directory '/<>/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/vg-1.30.0+ds/deps/sdsl-lite -B/<>/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 sdsl make[4]: Entering directory '/<>/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/vg-1.30.0+ds/deps/sdsl-lite -B/<>/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 7 make -f CMakeFiles/Makefile2 lib/CMakeFiles/sdsl.dir/all make[5]: Entering directory '/<>/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[6]: Entering directory '/<>/vg-1.30.0+ds/deps/sdsl-lite/build' cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.30.0+ds/deps/sdsl-lite /<>/vg-1.30.0+ds/deps/sdsl-lite/lib /<>/vg-1.30.0+ds/deps/sdsl-lite/build /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= Scanning dependencies of target sdsl make[6]: Leaving directory '/<>/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[6]: Entering directory '/<>/vg-1.30.0+ds/deps/sdsl-lite/build' [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bits.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/bits.cpp [ 12%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/path_handle_graph.cpp In file included from /usr/include/string.h:519, from src/gssw.c:37: In function ‘strncpy’, inlined from ‘gssw_node_create’ at src/gssw.c:4958:5: /usr/include/powerpc64le-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ src/gssw.c: In function ‘gssw_node_create’: src/gssw.c:4954:19: note: length computed here 4954 | int32_t len = strlen(seq); | ^~~~~~~~~~~ gcc -std=c99 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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-1.30.0+ds/deps/sonLib/externalTools/quicktree_1.1' make[4]: Leaving directory '/<>/vg-1.30.0+ds/deps/sonLib/externalTools' cd C && make all make[4]: Entering directory '/<>/vg-1.30.0+ds/deps/sonLib/C' cp inc/avl.h ../lib/avl.h.tmp mv ../lib/avl.h.tmp ../lib/avl.h [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp cp inc/bioioC.h ../lib/bioioC.h.tmp mv ../lib/bioioC.h.tmp ../lib/bioioC.h cp inc/commonC.h ../lib/commonC.h.tmp mv ../lib/commonC.h.tmp ../lib/commonC.h cp inc/fastCMaths.h ../lib/fastCMaths.h.tmp mv ../lib/fastCMaths.h.tmp ../lib/fastCMaths.h cp inc/hashTableC.h ../lib/hashTableC.h.tmp mv ../lib/hashTableC.h.tmp ../lib/hashTableC.h cp inc/hashTableC_itr.h ../lib/hashTableC_itr.h.tmp mv ../lib/hashTableC_itr.h.tmp ../lib/hashTableC_itr.h cp inc/hashTablePrivateC.h ../lib/hashTablePrivateC.h.tmp mv ../lib/hashTablePrivateC.h.tmp ../lib/hashTablePrivateC.h cp inc/jsmn.h ../lib/jsmn.h.tmp mv ../lib/jsmn.h.tmp ../lib/jsmn.h cp inc/pairwiseAlignment.h ../lib/pairwiseAlignment.h.tmp mv ../lib/pairwiseAlignment.h.tmp ../lib/pairwiseAlignment.h cp inc/sonLib.h ../lib/sonLib.h.tmp mv ../lib/sonLib.h.tmp ../lib/sonLib.h cp inc/sonLibAlign.h ../lib/sonLibAlign.h.tmp mv ../lib/sonLibAlign.h.tmp ../lib/sonLibAlign.h cp inc/sonLibCache.h ../lib/sonLibCache.h.tmp mv ../lib/sonLibCache.h.tmp ../lib/sonLibCache.h cp inc/sonLibCommon.h ../lib/sonLibCommon.h.tmp mv ../lib/sonLibCommon.h.tmp ../lib/sonLibCommon.h cp inc/sonLibCompression.h ../lib/sonLibCompression.h.tmp mv ../lib/sonLibCompression.h.tmp ../lib/sonLibCompression.h cp inc/sonLibConnectivity.h ../lib/sonLibConnectivity.h.tmp mv ../lib/sonLibConnectivity.h.tmp ../lib/sonLibConnectivity.h cp inc/sonLibEulerTour.h ../lib/sonLibEulerTour.h.tmp mv ../lib/sonLibEulerTour.h.tmp ../lib/sonLibEulerTour.h cp inc/sonLibExcept.h ../lib/sonLibExcept.h.tmp mv ../lib/sonLibExcept.h.tmp ../lib/sonLibExcept.h cp inc/sonLibFile.h ../lib/sonLibFile.h.tmp mv ../lib/sonLibFile.h.tmp ../lib/sonLibFile.h cp inc/sonLibHash.h ../lib/sonLibHash.h.tmp mv ../lib/sonLibHash.h.tmp ../lib/sonLibHash.h cp inc/sonLibKVDatabase.h ../lib/sonLibKVDatabase.h.tmp mv ../lib/sonLibKVDatabase.h.tmp ../lib/sonLibKVDatabase.h cp inc/sonLibKVDatabaseConf.h ../lib/sonLibKVDatabaseConf.h.tmp mv ../lib/sonLibKVDatabaseConf.h.tmp ../lib/sonLibKVDatabaseConf.h cp inc/sonLibList.h ../lib/sonLibList.h.tmp mv ../lib/sonLibList.h.tmp ../lib/sonLibList.h cp inc/sonLibMath.h ../lib/sonLibMath.h.tmp mv ../lib/sonLibMath.h.tmp ../lib/sonLibMath.h cp inc/sonLibNaiveConnectivity.h ../lib/sonLibNaiveConnectivity.h.tmp mv ../lib/sonLibNaiveConnectivity.h.tmp ../lib/sonLibNaiveConnectivity.h cp inc/sonLibRandom.h ../lib/sonLibRandom.h.tmp mv ../lib/sonLibRandom.h.tmp ../lib/sonLibRandom.h cp inc/sonLibSet.h ../lib/sonLibSet.h.tmp mv ../lib/sonLibSet.h.tmp ../lib/sonLibSet.h cp inc/sonLibSortedSet.h ../lib/sonLibSortedSet.h.tmp mv ../lib/sonLibSortedSet.h.tmp ../lib/sonLibSortedSet.h cp inc/sonLibString.h ../lib/sonLibString.h.tmp mv ../lib/sonLibString.h.tmp ../lib/sonLibString.h cp inc/sonLibTreap.h ../lib/sonLibTreap.h.tmp mv ../lib/sonLibTreap.h.tmp ../lib/sonLibTreap.h cp inc/sonLibTree.h ../lib/sonLibTree.h.tmp mv ../lib/sonLibTree.h.tmp ../lib/sonLibTree.h cp inc/sonLibTuples.h ../lib/sonLibTuples.h.tmp mv ../lib/sonLibTuples.h.tmp ../lib/sonLibTuples.h cp inc/sonLibTypes.h ../lib/sonLibTypes.h.tmp mv ../lib/sonLibTypes.h.tmp ../lib/sonLibTypes.h cp inc/stGraph.h ../lib/stGraph.h.tmp mv ../lib/stGraph.h.tmp ../lib/stGraph.h cp inc/stJson.h ../lib/stJson.h.tmp mv ../lib/stJson.h.tmp ../lib/stJson.h cp inc/stMatrix.h ../lib/stMatrix.h.tmp mv ../lib/stMatrix.h.tmp ../lib/stMatrix.h cp inc/stPhylogeny.h ../lib/stPhylogeny.h.tmp mv ../lib/stPhylogeny.h.tmp ../lib/stPhylogeny.h cp inc/stPosetAlignment.h ../lib/stPosetAlignment.h.tmp mv ../lib/stPosetAlignment.h.tmp ../lib/stPosetAlignment.h cp inc/stSafeC.h ../lib/stSafeC.h.tmp mv ../lib/stSafeC.h.tmp ../lib/stSafeC.h cp inc/stSpimapLayer.h ../lib/stSpimapLayer.h.tmp mv ../lib/stSpimapLayer.h.tmp ../lib/stSpimapLayer.h cp inc/stThreadPool.h ../lib/stThreadPool.h.tmp mv ../lib/stThreadPool.h.tmp ../lib/stThreadPool.h cp inc/stUnionFind.h ../lib/stUnionFind.h.tmp mv ../lib/stUnionFind.h.tmp ../lib/stUnionFind.h gcc -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall --pedantic -funroll-loops -DNDEBUG -I../externalTools/quicktree_1.1/include/ -I /<>/vg-1.30.0+ds/include -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I /<>/vg-1.30.0+ds/include -I/<>/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -I inc -I ../lib/ -c impl/*.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 16%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/path_position_handle_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/bioioC.c: In function ‘parseInt’: impl/bioioC.c:265:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 265 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:265:15: note: did you mean to dereference the pointer? 265 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseFloat’: impl/bioioC.c:286:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 286 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:286:15: note: did you mean to dereference the pointer? 286 | while(*string != '\0' && !isspace(**string)) { | ^ impl/bioioC.c: In function ‘parseString’: impl/bioioC.c:307:23: warning: comparison between pointer and zero character constant [-Wpointer-compare] 307 | while(*string != '\0' && !isspace(**string)) { | ^~ impl/bioioC.c:307:15: note: did you mean to dereference the pointer? 307 | while(*string != '\0' && !isspace(**string)) { | ^ In file included from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: /<>/vg-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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 | ^~~~ [ 19%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/ranked_handle_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 22%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/serializable.cpp src/gssw.c: In function ‘gssw_dna_scaled_adjusted_qual_matrix’: src/gssw.c:5809:9: note: the layout of aggregates containing vectors with 4-byte alignment has changed in GCC 5 5809 | int8_t* gssw_dna_scaled_adjusted_qual_matrix(int8_t max_score, uint8_t max_qual, int8_t* gap_open_out, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp:1: In static member function ‘static void sdsl::bits::write_int(uint64_t*, uint64_t, uint8_t, uint8_t)’, inlined from ‘static void sdsl::memory_manager::resize(t_vec&, typename t_vec::size_type) [with t_vec = sdsl::int_vector<0>]’ at /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/memory_management.hpp:364:36, inlined from ‘void sdsl::int_vector< >::bit_resize(sdsl::int_vector< >::size_type) [with unsigned char t_width = 0]’ at /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1327:27, inlined from ‘void sdsl::int_vector< >::resize(sdsl::int_vector< >::size_type) [with unsigned char t_width = 0]’ at /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:379:23, inlined from ‘sdsl::int_vector< >::int_vector(sdsl::int_vector< >::size_type, sdsl::int_vector< >::value_type, uint8_t) [with unsigned char t_width = 0]’ at /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:1254:11, inlined from ‘sdsl::excess::impl::impl()’ at /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bp_support_algorithm.hpp:114:46: /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp:460:15: warning: ‘*temp’ may be used uninitialized [-Wmaybe-uninitialized] 460 | *word &= | ~~~~~~^~ 461 | ((bits::all_set << (offset+len)) | bits::lo_set[offset]); // mask 1..10..01..1 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 25%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/snarl_decomposition.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 [ 29%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/trivially_serializable.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 [ 0%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_delta.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C impl/sonLibCompression.c: In function ‘stCompression_compress’: impl/sonLibCompression.c:37:9: warning: ‘LZ4_compress’ is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 37 | int64_t bytesWritten = LZ4_compress(((char*)data) + inputOffset, buffer+(outputOffset+1), subChunk ? ST_LZ4_CHUNK_SIZE : sizeInBytes - inputOffset); | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:697:75: note: declared here 697 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ impl/sonLibCompression.c: In function ‘stCompression_decompress’: impl/sonLibCompression.c:60:13: warning: ‘LZ4_uncompress’ is deprecated: use LZ4_decompress_fast() instead [-Wdeprecated-declarations] 60 | int64_t bytesRead = LZ4_uncompress(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:705:68: note: declared here 705 | LZ4_DEPRECATED("use LZ4_decompress_fast() instead") LZ4LIB_API int LZ4_uncompress (const char* source, char* dest, int outputSize); | ^~~~~~~~~~~~~~ impl/sonLibCompression.c:72:17: warning: ‘LZ4_uncompress_unknownOutputSize’ is deprecated: use LZ4_decompress_safe() instead [-Wdeprecated-declarations] 72 | int64_t bytesWritten = LZ4_uncompress_unknownOutputSize(((char *)compressedData)+inputOffset, | ^~~~~~~ In file included from /usr/include/lz4hc.h:43, from impl/sonLibCompression.c:15: /usr/include/lz4.h:706:68: note: declared here 706 | LZ4_DEPRECATED("use LZ4_decompress_safe() instead") LZ4LIB_API int LZ4_uncompress_unknownOutputSize (const char* source, char* dest, int isize, int maxOutputSize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+ds/include -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wall -O3 -g src/example.c -o bin/gssw_example obj/gssw.o -lm -lz In file included from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_delta::impl::impl()’: /<>/vg-1.30.0+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-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.30.0+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-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.30.0+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-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.30.0+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-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.30.0+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-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.30.0+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-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.30.0+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-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.30.0+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-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.30.0+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-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.30.0+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-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_delta.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.30.0+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-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:1: /<>/vg-1.30.0+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 src/example.c:12: src/gssw.h:340:29: error: unknown type name ‘bool’ 340 | bool score_only); | ^~~~ In file included from src/example.c:12: src/gssw.h:18:1: note: ‘bool’ is defined in header ‘’; did you forget to ‘#include ’? 17 | #include "simde/x86/sse4.1.h" +++ |+#include 18 | In file included from src/example.c:12: src/gssw.h:381:24: error: unknown type name ‘bool’ 381 | bool score_only, | ^~~~ src/gssw.h:381:24: note: ‘bool’ is defined in header ‘’; did you forget to ‘#include ’? src/gssw.h:613:17: error: unknown type name ‘bool’ 613 | bool save_matrixes, | ^~~~ src/gssw.h:613:17: note: ‘bool’ is defined in header ‘’; did you forget to ‘#include ’? src/gssw.h:627:18: error: unknown type name ‘bool’ 627 | bool save_matrixes); | ^~~~ src/gssw.h:627:18: note: ‘bool’ is defined in header ‘’; did you forget to ‘#include ’? src/gssw.h:641:26: error: unknown type name ‘bool’ 641 | bool save_matrixes); | ^~~~ src/gssw.h:641:26: note: ‘bool’ is defined in header ‘’; did you forget to ‘#include ’? src/gssw.h:654:25: error: unknown type name ‘bool’ 654 | bool save_matrixes); | ^~~~ src/gssw.h:654:25: note: ‘bool’ is defined in header ‘’; did you forget to ‘#include ’? src/gssw.h:668:33: error: unknown type name ‘bool’ 668 | bool save_matrixes); | ^~~~ src/gssw.h:668:33: note: ‘bool’ is defined in header ‘’; did you forget to ‘#include ’? src/example.c: In function ‘main’: src/example.c:69:5: warning: implicit declaration of function ‘gssw_graph_fill’; did you mean ‘gssw_graph_print’? [-Wimplicit-function-declaration] 69 | gssw_graph_fill(graph, read_seq, nt_table, mat, gap_open, gap_extension, 0, 0, 15, 2, true); | ^~~~~~~~~~~~~~~ | gssw_graph_print make[3]: *** [Makefile:20: bin/gssw_example] Error 1 make[3]: Leaving directory '/<>/vg-1.30.0+ds/deps/gssw' make[2]: *** [Makefile:455: lib/libgssw.a] Error 2 make[2]: *** Waiting for unfinished jobs.... [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_elias_gamma.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 32%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/types.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/types.cpp [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp [ 35%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/copy_graph.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C In file included from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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 | ^~~~ [ 38%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/append_graph.cpp In file included from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/bits.hpp: In constructor ‘sdsl::coder::elias_gamma::impl::impl()’: /<>/vg-1.30.0+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-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.30.0+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-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.30.0+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-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.30.0+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-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.30.0+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-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.30.0+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-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_elias_gamma.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.30.0+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-1.30.0+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:1: /<>/vg-1.30.0+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-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/coder_fibonacci.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:1: /<>/vg-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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 [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/config.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/config.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 14%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_config.cpp.o -c /<>/vg-1.30.0+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 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 41%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/are_equivalent.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-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_isa.cpp.o -c /<>/vg-1.30.0+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 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-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp In file included from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_isa.hpp:24, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_isa.cpp:4: /<>/vg-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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 [ 45%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/find_tips.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 In file included from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp.hpp:26, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp.cpp:6: /<>/vg-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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 [ 48%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/topological_sort.cpp impl/sonLibTree.c: In function ‘tree_clonetree.isra’: impl/sonLibTree.c:207:16: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 207 | return tree->clientData; | ~~~~^~~~~~~~~~~~ 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-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o -c /<>/vg-1.30.0+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 In file included from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_lcp_helper.hpp:4, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:1: /<>/vg-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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 | ^~~~ [ 51%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/apply_orientations.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C [ 54%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/is_single_stranded.cpp cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C g++ -std=gnu++98 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -Wall -funroll-loops -DNDEBUG -I /<>/vg-1.30.0+ds/include -I/<>/vg-1.30.0+ds/include/dynamic -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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-1.30.0+ds/include -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -o ../bin/sonLibTests.tmp tests/allTests.c tests/sonLib*.c tests/st* ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm -lstdc++ -lpthread -llz4 [ 58%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/count_walks.cpp [ 28%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp [ 61%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/eades_algorithm.cpp In file included from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /<>/vg-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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 | ^~~~ [ 64%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/dagify.cpp In file included from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:26, from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa.hpp:26, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa.cpp:1: /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/util.hpp: In function ‘void sdsl::util::init_support(S&, const X*) [with S = sdsl::select_support_mcl<1, 1>; X = sdsl::int_vector<1>]’: /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/util.hpp:316:6: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 316 | void init_support(S& s, const X* x) | ^~~~~~~~~~~~ [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/construct_sa_se.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp In file included from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/construct_sa_se.hpp:5, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/construct_sa_se.cpp:1: /<>/vg-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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 | ^~~~ [ 67%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/strongly_connected_components.cpp 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-1.30.0+ds/include -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -I inc -I ../lib -I tests -o ../bin/sonLib_kvDatabaseTest.tmp tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c ../lib/sonLib.a ../lib/cuTest.a -lz -lm -lm 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-1.30.0+ds/include -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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-1.30.0+ds/include -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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-1.30.0+ds/deps/sonLib/C' cp sonLib_daemonize.py ./bin/sonLib_daemonize.py chmod +x ./bin/sonLib_daemonize.py make[3]: Leaving directory '/<>/vg-1.30.0+ds/deps/sonLib' [ 70%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/find_shortest_paths.cpp [ 74%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/dijkstra.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp [ 77%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/is_acyclic.cpp [ 80%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/reverse_complement.cpp In file included from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/csa_alphabet_strategy.hpp:50, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp:17: /<>/vg-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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 | ^~~~ [ 83%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/split_strands.cpp [ 87%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/unchop.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/io.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/io.cpp [ 90%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/weakly_connected_components.cpp [ 42%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp [ 93%] Building CXX object CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/g++ -I/<>/vg-1.30.0+ds/deps/libhandlegraph/src/include -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -fPIC -std=gnu++14 -o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o -c /<>/vg-1.30.0+ds/deps/libhandlegraph/src/extend.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/louds_tree.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/memory_management.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/memory_management.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/memory_management.cpp In file included from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp.hpp:26, from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/lcp_support_tree.hpp:4, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp:1: /<>/vg-1.30.0+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 | ^~~~ make[5]: Leaving directory '/<>/vg-1.30.0+ds/deps/libhandlegraph' /<>/vg-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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 | ^~~~ [ 93%] Built target handlegraph_objs make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/depend make[5]: Entering directory '/<>/vg-1.30.0+ds/deps/libhandlegraph' cd /<>/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.30.0+ds/deps/libhandlegraph /<>/vg-1.30.0+ds/deps/libhandlegraph /<>/vg-1.30.0+ds/deps/libhandlegraph /<>/vg-1.30.0+ds/deps/libhandlegraph /<>/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_static.dir/DependInfo.cmake --color= Scanning dependencies of target handlegraph_static make[5]: Leaving directory '/<>/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_static.dir/build.make CMakeFiles/handlegraph_static.dir/build make[5]: Entering directory '/<>/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] 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/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o /usr/bin/ranlib libhandlegraph.a make[5]: Leaving directory '/<>/vg-1.30.0+ds/deps/libhandlegraph' [ 96%] Built target handlegraph_static make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/depend make[5]: Entering directory '/<>/vg-1.30.0+ds/deps/libhandlegraph' cd /<>/vg-1.30.0+ds/deps/libhandlegraph && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.30.0+ds/deps/libhandlegraph /<>/vg-1.30.0+ds/deps/libhandlegraph /<>/vg-1.30.0+ds/deps/libhandlegraph /<>/vg-1.30.0+ds/deps/libhandlegraph /<>/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles/handlegraph_shared.dir/DependInfo.cmake --color= In file included from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/louds_tree.hpp:11, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/louds_tree.cpp:1: /<>/vg-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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 | ^~~~ Scanning dependencies of target handlegraph_shared make[5]: Leaving directory '/<>/vg-1.30.0+ds/deps/libhandlegraph' make -f CMakeFiles/handlegraph_shared.dir/build.make CMakeFiles/handlegraph_shared.dir/build make[5]: Entering directory '/<>/vg-1.30.0+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 -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -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/deletable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/mutable_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/path_position_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/ranked_handle_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/snarl_decomposition.cpp.o CMakeFiles/handlegraph_objs.dir/src/trivially_serializable.cpp.o CMakeFiles/handlegraph_objs.dir/src/types.cpp.o CMakeFiles/handlegraph_objs.dir/src/copy_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/append_graph.cpp.o CMakeFiles/handlegraph_objs.dir/src/are_equivalent.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_tips.cpp.o CMakeFiles/handlegraph_objs.dir/src/topological_sort.cpp.o CMakeFiles/handlegraph_objs.dir/src/apply_orientations.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_single_stranded.cpp.o CMakeFiles/handlegraph_objs.dir/src/count_walks.cpp.o CMakeFiles/handlegraph_objs.dir/src/eades_algorithm.cpp.o CMakeFiles/handlegraph_objs.dir/src/dagify.cpp.o CMakeFiles/handlegraph_objs.dir/src/strongly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/find_shortest_paths.cpp.o CMakeFiles/handlegraph_objs.dir/src/dijkstra.cpp.o CMakeFiles/handlegraph_objs.dir/src/is_acyclic.cpp.o CMakeFiles/handlegraph_objs.dir/src/reverse_complement.cpp.o CMakeFiles/handlegraph_objs.dir/src/split_strands.cpp.o CMakeFiles/handlegraph_objs.dir/src/unchop.cpp.o CMakeFiles/handlegraph_objs.dir/src/weakly_connected_components.cpp.o CMakeFiles/handlegraph_objs.dir/src/extend.cpp.o [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/nn_dict_dynamic.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp make[5]: Leaving directory '/<>/vg-1.30.0+ds/deps/libhandlegraph' [100%] Built target handlegraph_shared make[4]: Leaving directory '/<>/vg-1.30.0+ds/deps/libhandlegraph' /usr/bin/cmake -E cmake_progress_start /<>/vg-1.30.0+ds/deps/libhandlegraph/CMakeFiles 0 make[3]: Leaving directory '/<>/vg-1.30.0+ds/deps/libhandlegraph' [ 57%] Building CXX object lib/CMakeFiles/sdsl.dir/ram_filebuf.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_filebuf.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_filebuf.cpp In file included from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/nn_dict_dynamic.hpp:25, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp:1: /<>/vg-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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/ram_fs.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/ram_fs.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/ram_fs.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/rrr_vector_15.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sd_vector.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sd_vector.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp [ 71%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/sfstream.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/sfstream.cpp In file included from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/rrr_vector_15.hpp:25, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp:1: /<>/vg-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /<>/vg-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/structure_tree.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/structure_tree.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint128_t.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/uint128_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/uint256_t.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/uint256_t.cpp [ 85%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/util.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/util.cpp [100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/g++ -DMODE_TI -I/<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include -I/<>/vg-1.30.0+ds/deps/sdsl-lite/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O3 -ffile-prefix-map=/<>/vg-1.30.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fopenmp -std=c++11 -Wall -Wextra -DNDEBUG -O3 -DNDEBUG -o CMakeFiles/sdsl.dir/wt_helper.cpp.o -c /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp In file included from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/wt_helper.hpp:4, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/wt_helper.cpp:1: /<>/vg-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+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-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/int_vector.hpp:26, from /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/sd_vector.hpp:26, from /<>/vg-1.30.0+ds/deps/sdsl-lite/lib/sd_vector.cpp:1: /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/util.hpp: In function ‘void sdsl::util::init_support(S&, const X*) [with S = sdsl::select_support_mcl<1, 1>; X = sdsl::int_vector<1>]’: /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/../include/sdsl/util.hpp:316:6: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 316 | void init_support(S& s, const X* x) | ^~~~~~~~~~~~ [100%] Linking CXX static library libsdsl.a cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib && /usr/bin/cmake -P CMakeFiles/sdsl.dir/cmake_clean_target.cmake cd /<>/vg-1.30.0+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 make[6]: Leaving directory '/<>/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[5]: Leaving directory '/<>/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make[4]: Leaving directory '/<>/vg-1.30.0+ds/deps/sdsl-lite/build' make[3]: Leaving directory '/<>/vg-1.30.0+ds/deps/sdsl-lite/build' Removing old files rm -rf '/<>/vg-1.30.0+ds/include/sdsl/*' rm -f '/<>/vg-1.30.0+ds/lib/libsdsl*' make[3]: Entering directory '/<>/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -S/<>/vg-1.30.0+ds/deps/sdsl-lite -B/<>/vg-1.30.0+ds/deps/sdsl-lite/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles /<>/vg-1.30.0+ds/deps/sdsl-lite/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[4]: Entering directory '/<>/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/depend make[5]: Entering directory '/<>/vg-1.30.0+ds/deps/sdsl-lite/build' cd /<>/vg-1.30.0+ds/deps/sdsl-lite/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/vg-1.30.0+ds/deps/sdsl-lite /<>/vg-1.30.0+ds/deps/sdsl-lite/lib /<>/vg-1.30.0+ds/deps/sdsl-lite/build /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib /<>/vg-1.30.0+ds/deps/sdsl-lite/build/lib/CMakeFiles/sdsl.dir/DependInfo.cmake --color= make[5]: Leaving directory '/<>/vg-1.30.0+ds/deps/sdsl-lite/build' make -f lib/CMakeFiles/sdsl.dir/build.make lib/CMakeFiles/sdsl.dir/build make[5]: Entering directory '/<>/vg-1.30.0+ds/deps/sdsl-lite/build' make[5]: Nothing to be done for 'lib/CMakeFiles/sdsl.dir/build'. make[5]: Leaving directory '/<>/vg-1.30.0+ds/deps/sdsl-lite/build' [100%] Built target sdsl make[4]: Leaving directory '/<>/vg-1.30.0+ds/deps/sdsl-lite/build' /usr/bin/cmake -E cmake_progress_start /<>/vg-1.30.0+ds/deps/sdsl-lite/build/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[4]: Entering directory '/<>/vg-1.30.0+ds/deps/sdsl-lite/build' make[4]: Nothing to be done for 'preinstall'. make[4]: Leaving directory '/<>/vg-1.30.0+ds/deps/sdsl-lite/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /<>/vg-1.30.0+ds/lib/pkgconfig/sdsl-lite.pc -- Installing: /<>/vg-1.30.0+ds/include/sdsl/bit_vector_il.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/bit_vectors.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/bits.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/bp_support.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/bp_support_algorithm.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/bp_support_g.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/bp_support_gg.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/bp_support_sada.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/coder.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/coder_comma.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/coder_elias_delta.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/coder_elias_gamma.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/coder_fibonacci.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/config.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/construct.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/construct_bwt.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/construct_config.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/construct_isa.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/construct_lcp.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/construct_lcp_helper.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/construct_sa.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/construct_sa_se.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/csa_alphabet_strategy.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/csa_bitcompressed.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/csa_sada.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/csa_sampling_strategy.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/csa_wt.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/cst_fully.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/cst_iterators.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/cst_sada.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/cst_sct3.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/dac_vector.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/enc_vector.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/fast_cache.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/hyb_vector.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/int_vector.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/int_vector_buffer.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/int_vector_io_wrappers.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/int_vector_mapper.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/inv_perm_support.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/io.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/iterators.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/k2_treap.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/k2_treap_algorithm.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/k2_treap_helper.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/k2_tree.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/k2_tree_helper.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/lcp.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/lcp_bitcompressed.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/lcp_byte.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/lcp_dac.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/lcp_support_sada.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/lcp_support_tree.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/lcp_support_tree2.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/lcp_vlc.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/lcp_wt.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/louds_tree.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/memory_management.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/nearest_neighbour_dictionary.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/nn_dict_dynamic.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/qsufsort.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/ram_filebuf.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/ram_fs.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/rank_support.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/rank_support_scan.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/rank_support_v.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/rank_support_v5.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/raster_img.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/rmq_succinct_sada.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/rmq_succinct_sct.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/rmq_support.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/rmq_support_sparse_table.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/rrr_helper.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/rrr_vector.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/rrr_vector_15.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/sd_vector.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/sdsl_concepts.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/select_support.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/select_support_mcl.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/select_support_scan.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/sfstream.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/sorted_int_stack.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/sorted_multi_stack_support.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/sorted_stack_support.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/structure_tree.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/suffix_array_algorithm.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/suffix_array_helper.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/suffix_arrays.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/suffix_tree_algorithm.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/suffix_tree_helper.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/suffix_trees.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/uint128_t.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/uint256_t.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/uintx_t.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/util.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/vectors.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/vlc_vector.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/wavelet_trees.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/wm_int.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/wt_algorithm.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/wt_ap.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/wt_blcd.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/wt_gmr.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/wt_helper.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/wt_huff.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/wt_hutu.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/wt_int.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/wt_pc.hpp -- Installing: /<>/vg-1.30.0+ds/include/sdsl/wt_rlmn.hpp -- Installing: /<>/vg-1.30.0+ds/lib/libsdsl.a make[3]: Leaving directory '/<>/vg-1.30.0+ds/deps/sdsl-lite/build' SUCCESS: sdsl was installed successfully! The sdsl include files are located in '/<>/vg-1.30.0+ds/include'. The library files are located in '/<>/vg-1.30.0+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! make[2]: Leaving directory '/<>/vg-1.30.0+ds' dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true" all test/build_graph bin/shuf returned exit code 2 make[1]: *** [debian/rules:38: override_dh_auto_build-arch] Error 25 make[1]: Leaving directory '/<>/vg-1.30.0+ds' make: *** [debian/rules:22: binary-arch] Error 2 dpkg-buildpackage.pl: error: debian/rules binary-arch subprocess returned exit status 2 === USAGE-SUMMARY BEGIN === SUMMARY: host: bos02-ppc64el-008; CPUs: 4/4; CPU avg: 69%; CPU max: 100%; base memory: 0.5 GB; peak memory: 1.1 GB; total memory: 8.0 GB SUMMARY: swap peak/total: 0.0/0.0 GB; disk start/end/total: 4.4/4.5/58.1 GB; disk delta: 0.1 GB === USAGE-SUMMARY END === -------------------------------------------------------------------------------- Build finished at 2021-09-02T22:05:46Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: ppc64el Build Type: any Build-Space: n/a Build-Time: 52 Distribution: impish Fail-Stage: build Host Architecture: ppc64el Install-Time: 58 Job: vg_1.30.0+ds-1.dsc Machine Architecture: ppc64el Package: vg Package-Time: 119 Source-Version: 1.30.0+ds-1 Space: n/a Status: attempted Version: 1.30.0+ds-1 -------------------------------------------------------------------------------- Finished at 2021-09-02T22:05:46Z Build needed 00:01:59, no disk space E: Build failure (dpkg-buildpackage died) Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=impish --arch=ppc64el PACKAGEBUILD-21946007 Scanning for processes to kill in build PACKAGEBUILD-21946007