Start: 2024-11-03 15:33:51 GMT [testing] Package: hyphy-mpi Source: hyphy Version: 2.5.62+dfsg-1 Installed-Size: 7526 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.38), libcurl3t64-gnutls (>= 7.16.2), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libopenmpi3t64 (>= 4.1.6), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 13.1), zlib1g (>= 1:1.2.11.dfsg), hyphy-common (= 2.5.62+dfsg-1) Description: Hypothesis testing using Phylogenies (MPI version) Homepage: https://hyphy.org/ Description-md5: bf880100fd3d0b8d321965866c6d667b Section: science Priority: optional Filename: pool/main/h/hyphy/hyphy-mpi_2.5.62+dfsg-1_amd64.deb Size: 1537748 MD5sum: 309d83af7bed6055fc252c45dc6c88b2 SHA256: aa33a94db5106efec2245ca25ffadf23a3949dbcb96651c1997faef78cd5c041 [sid] Package: hyphy-mpi Source: hyphy Version: 2.5.63+dfsg-1 Installed-Size: 7402 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.38), libcurl3t64-gnutls (>= 7.16.2), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libopenmpi3t64 (>= 5.0.5), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 5), zlib1g (>= 1:1.2.11.dfsg), hyphy-common (= 2.5.63+dfsg-1) Description: Hypothesis testing using Phylogenies (MPI version) Homepage: https://hyphy.org/ Description-md5: bf880100fd3d0b8d321965866c6d667b Section: science Priority: optional Filename: pool/main/h/hyphy/hyphy-mpi_2.5.63+dfsg-1_amd64.deb Size: 1535132 MD5sum: ef3cb9f2cbec4ec92f561bd83c474db5 SHA256: 33cb113612c7f741d0156f2d527d6fea7f58c9b6390915e50a32d9a1763a8f6f Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt hyphy-mpi=2.5.63+dfsg-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt hyphy-mpi=2.5.63+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp1qivpseq 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp1qivpseq 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/proc'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/proc'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/dev/pts'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/dev/pts'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/dev/ptmx'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/6', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/6', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp1qivpseq/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-get', 'update'] 0m3.5s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [172 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9328 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6239 kB] Fetched 15.7 MB in 2s (7146 kB/s) Reading package lists... 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-get', 'update'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-get', '-yf', 'dist-upgrade'] 0m5.4s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: coreutils libssl3t64 openssl-provider-legacy 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5492 kB of archives. After this operation, 296 kB disk space will be freed. Get:1 http://deb.debian.org/debian trixie/main amd64 coreutils amd64 9.5-1+b1 [2922 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 openssl-provider-legacy amd64 3.3.2-2 [298 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libssl3t64 amd64 3.3.2-2 [2271 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 5492 kB in 0s (64.8 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5166 files and directories currently installed.) Preparing to unpack .../coreutils_9.5-1+b1_amd64.deb ... Unpacking coreutils (9.5-1+b1) over (9.4-3.1) ... Setting up coreutils (9.5-1+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5167 files and directories currently installed.) Preparing to unpack .../openssl-provider-legacy_3.3.2-2_amd64.deb ... Unpacking openssl-provider-legacy (3.3.2-2) over (3.3.2-1) ... Setting up openssl-provider-legacy (3.3.2-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5167 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.3.2-2_amd64.deb ... Unpacking libssl3t64:amd64 (3.3.2-2) over (3.3.2-1) ... Setting up libssl3t64:amd64 (3.3.2-2) ... Processing triggers for libc-bin (2.40-3) ... 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-get', '-yf', 'dist-upgrade'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.2s DUMP: cf7284a76eaf48e14c0a906837d478c9 - 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.2s INFO: Running scripts post_setup 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_setup_dummy_users'] 0m7.1s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_setup_dummy_users'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_setup_forbid_home'] 0m7.1s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_setup_forbid_home'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.2s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_setup_minimize'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_setup_minimize'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_setup_zz_backports'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_setup_zz_backports'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.2s DUMP: install ok installed apt apt 2.9.10 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-9 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-6 install ok installed gpgv gpgv 2.2.44-1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.10 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:3.1.2-4 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-4+b1 install ok installed libblkid1:amd64 libblkid1 2.40.2-9 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.272+b1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2+b1 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-9 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b2 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b2 install ok installed libselinux1:amd64 libselinux1 3.7-3 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-9 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-6 install ok installed libsystemd0:amd64 libsystemd0 256.7-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 256.7-2 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-9 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-9 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-9 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl-base perl-base 5.40.0-6 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-4 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-9 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.2s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m7.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qivpseq'] 0m7.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qivpseq'] 0m7.6s INFO: Running scripts is_testable 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/is_testable_uninstallable'] 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/is_testable_uninstallable'] 0m7.6s INFO: Running scripts pre_test 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_test_exceptions'] 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_test_exceptions'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_test_root_password'] 0m7.7s DUMP: New password: Retype new password: passwd: password updated successfully 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_test_root_password'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-cache', 'show', '--no-all-versions', 'hyphy-mpi'] 0m7.9s DUMP: Package: hyphy-mpi Source: hyphy Version: 2.5.62+dfsg-1 Installed-Size: 7526 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.38), libcurl3t64-gnutls (>= 7.16.2), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libopenmpi3t64 (>= 4.1.6), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 13.1), zlib1g (>= 1:1.2.11.dfsg), hyphy-common (= 2.5.62+dfsg-1) Description-en: Hypothesis testing using Phylogenies (MPI version) HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface) and it can be compiled as a shared library and called from other programming environments such as Python or R. Continued development of HyPhy is currently supported in part by an NIGMS R01 award 1R01GM093939. . This package provides an executable using MPI to do multiprocessing. Description-md5: bf880100fd3d0b8d321965866c6d667b Homepage: https://hyphy.org/ Section: science Priority: optional Filename: pool/main/h/hyphy/hyphy-mpi_2.5.62+dfsg-1_amd64.deb Size: 1537748 MD5sum: 309d83af7bed6055fc252c45dc6c88b2 SHA256: aa33a94db5106efec2245ca25ffadf23a3949dbcb96651c1997faef78cd5c041 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-cache', 'show', '--no-all-versions', 'hyphy-mpi'] 0m7.9s INFO: apt-cache knows about the following packages: hyphy-mpi 0m7.9s INFO: Running scripts pre_install 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_database-server'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_database-server'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_exceptions'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_exceptions'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_extras'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_extras'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-cache', 'policy'] 0m8.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-cache', 'policy'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-cache', 'policy', 'hyphy-mpi'] 0m8.0s DUMP: hyphy-mpi: Installed: (none) Candidate: 2.5.62+dfsg-1 Version table: 2.5.62+dfsg-1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-cache', 'policy', 'hyphy-mpi'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-get', '-y', 'install', 'hyphy-mpi'] 0m34.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: adduser hyphy-common ibverbs-providers libamd-comgr2 libamdhip64-5 libatomic1 libbrotli1 libcurl3t64-gnutls libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libgomp1 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libicu72 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 libllvm17t64 libmunge2 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3t64 libpciaccess0 libpmix2t64 libpsl5t64 libpsm-infinipath1 libpsm2-2 librdmacm1t64 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libucx0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libz3-4 ocl-icd-libopencl1 Suggested packages: liblocale-gettext-perl perl cron quota krb5-doc krb5-user libhwloc-contrib-plugins pciutils opencl-icd Recommended packages: ca-certificates krb5-locales libldap-common publicsuffix libsasl2-modules The following NEW packages will be installed: adduser hyphy-common hyphy-mpi ibverbs-providers libamd-comgr2 libamdhip64-5 libatomic1 libbrotli1 libcurl3t64-gnutls libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libgomp1 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libicu72 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 libllvm17t64 libmunge2 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3t64 libpciaccess0 libpmix2t64 libpsl5t64 libpsm-infinipath1 libpsm2-2 librdmacm1t64 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libucx0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libz3-4 ocl-icd-libopencl1 0 upgraded, 64 newly installed, 0 to remove and 0 not upgraded. Need to get 77.7 MB of archives. After this operation, 331 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 adduser all 3.137 [140 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 hyphy-common all 2.5.62+dfsg-1 [607 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b5 [307 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:7 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.4.0-1+b1 [63.6 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.10.1-2 [360 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-6 [137 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 libnl-3-200 amd64 3.7.0-0.3+b1 [59.4 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-200 amd64 3.7.0-0.3+b1 [182 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 libibverbs1 amd64 52.0-2+b1 [62.2 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 ibverbs-providers amd64 52.0-2+b1 [343 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-6 [9284 B] Get:28 http://deb.debian.org/debian trixie/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 librdmacm1t64 amd64 52.0-2+b1 [70.4 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 libfabric1 amd64 1.17.0-3.1 [631 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 libhwloc15 amd64 2.11.2-1 [164 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 libmunge2 amd64 0.5.15-4+b1 [20.0 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b2 [51.9 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b2 [18.2 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b2 [24.4 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b2 [804 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 libxnvctrl0 amd64 535.171.04-1+b1 [14.2 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b2 [40.2 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libhwloc-plugins amd64 2.11.2-1 [18.1 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libpmix2t64 amd64 5.0.3-2+b1 [662 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.8.12-3.1+b3 [7772 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 libllvm17t64 amd64 1:17.0.6-18 [23.6 MB] Get:51 http://deb.debian.org/debian trixie/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get:52 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get:53 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 libhsa-runtime64-1 amd64 5.7.1-3 [510 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 libamdhip64-5 amd64 5.7.1-5 [8877 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 libibumad3 amd64 52.0-2+b1 [28.2 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 libibmad5 amd64 52.0-2+b1 [43.4 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 libopenmpi3t64 amd64 4.1.6-13.3 [2426 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 hyphy-mpi amd64 2.5.62+dfsg-1 [1538 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 77.7 MB in 20s (3985 kB/s) Selecting previously unselected package adduser. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5171 files and directories currently installed.) Preparing to unpack .../archives/adduser_3.137_all.deb ... Unpacking adduser (3.137) ... Setting up adduser (3.137) ... Selecting previously unselected package hyphy-common. (Reading database ... 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Setting up libedit2:amd64 (3.1-20240808-1) ... Setting up libsqlite3-0:amd64 (3.46.1-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libibumad3:amd64 (52.0-2+b1) ... Setting up libibmad5:amd64 (52.0-2+b1) ... Setting up hyphy-common (2.5.62+dfsg-1) ... Setting up libgomp1:amd64 (14.2.0-6) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up libz3-4:amd64 (4.8.12-3.1+b3) ... Setting up libmunge2:amd64 (0.5.15-4+b1) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhwloc15:amd64 (2.11.2-1) ... Setting up libatomic1:amd64 (14.2.0-6) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libnghttp3-9:amd64 (1.4.0-1+b1) ... Setting up libnuma1:amd64 (2.0.18-1+b1) ... Setting up ocl-icd-libopencl1:amd64 (2.3.2-1+b2) ... Setting up libnl-3-200:amd64 (3.7.0-0.3+b1) ... Setting up libpsm2-2 (11.2.185-2.1) ... Setting up libx11-6:amd64 (2:1.8.7-1+b2) ... Setting up libngtcp2-16:amd64 (1.6.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libdrm-common (2.4.123-1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.3+b1) ... Setting up libxnvctrl0:amd64 (535.171.04-1+b1) ... Setting up libllvm17t64:amd64 (1:17.0.6-18) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libdrm2:amd64 (2.4.123-1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... Setting up libibverbs1:amd64 (52.0-2+b1) ... Setting up ibverbs-providers:amd64 (52.0-2+b1) ... Setting up libcurl3t64-gnutls:amd64 (8.10.1-2) ... Setting up libhwloc-plugins:amd64 (2.11.2-1) ... Setting up libpmix2t64:amd64 (5.0.3-2+b1) ... Setting up librdmacm1t64:amd64 (52.0-2+b1) ... Setting up libhsakmt1:amd64 (5.7.0-1) ... Setting up libfabric1:amd64 (1.17.0-3.1) ... Setting up libhsa-runtime64-1:amd64 (5.7.1-3) ... Setting up libamdhip64-5 (5.7.1-5) ... Setting up libucx0:amd64 (1.17.0+ds-3) ... Setting up libopenmpi3t64:amd64 (4.1.6-13.3) ... Setting up hyphy-mpi (2.5.62+dfsg-1) ... Processing triggers for libc-bin (2.40-3) ... 0m34.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-get', '-y', 'install', 'hyphy-mpi'] 0m34.4s INFO: Running scripts post_install 0m34.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_install_exceptions'] 0m34.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_install_exceptions'] 0m34.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qivpseq'] 0m34.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qivpseq'] 0m34.7s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp1qivpseq to sid 0m34.7s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m34.7s INFO: Running scripts pre_distupgrade 0m34.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m34.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m34.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_distupgrade_exceptions'] 0m34.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_distupgrade_exceptions'] 0m34.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m34.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m34.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m34.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m34.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m34.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m34.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-get', 'update'] 0m37.8s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [202 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.0 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7333 kB] Fetched 17.6 MB in 2s (8023 kB/s) Reading package lists... 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-get', 'update'] 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-get', '-yf', 'dist-upgrade'] 0m40.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: gcc-14-base gpgv hyphy-common hyphy-mpi libatomic1 libaudit-common libaudit1 libdebconfclient0 libgcc-s1 libgomp1 libhsa-runtime64-1 libhsakmt1 libopenmpi3t64 libstdc++6 libsystemd0 libudev1 libx11-6 libx11-data libxau6 tzdata 20 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 7972 kB of archives. After this operation, 1530 kB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 gpgv amd64 2.2.45-2 [219 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-8 [9280 B] Get:3 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.2.0-8 [47.2 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14.2.0-8 [714 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-8 [137 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14.2.0-8 [72.7 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:4.0.1-2 [12.3 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:4.0.1-2 [54.4 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.273 [10.1 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 256.7-3 [382 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 256.7-3 [145 kB] Get:12 http://deb.debian.org/debian sid/main amd64 tzdata all 2024b-3 [255 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libopenmpi3t64 amd64 5.0.5-3 [2007 kB] Get:14 http://deb.debian.org/debian sid/main amd64 hyphy-mpi amd64 2.5.63+dfsg-1 [1535 kB] Get:15 http://deb.debian.org/debian sid/main amd64 hyphy-common all 2.5.63+dfsg-1 [607 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libhsakmt1 amd64 6.1.2+ds-1 [59.8 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libhsa-runtime64-1 amd64 6.1.2-2 [535 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.10-1 [337 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.10-1 [813 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7972 kB in 0s (35.8 MB/s) (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6781 files and directories currently installed.) Preparing to unpack .../libudev1_256.7-3_amd64.deb ... Unpacking libudev1:amd64 (256.7-3) over (256.7-2) ... Setting up libudev1:amd64 (256.7-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6781 files and directories currently installed.) Preparing to unpack .../0-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) over (2024a-4) ... Preparing to unpack .../1-libopenmpi3t64_5.0.5-3_amd64.deb ... Unpacking libopenmpi3t64:amd64 (5.0.5-3) over (4.1.6-13.3) ... Preparing to unpack .../2-hyphy-mpi_2.5.63+dfsg-1_amd64.deb ... Unpacking hyphy-mpi (2.5.63+dfsg-1) over (2.5.62+dfsg-1) ... Preparing to unpack .../3-hyphy-common_2.5.63+dfsg-1_all.deb ... Unpacking hyphy-common (2.5.63+dfsg-1) over (2.5.62+dfsg-1) ... Preparing to unpack .../4-libhsakmt1_6.1.2+ds-1_amd64.deb ... Unpacking libhsakmt1:amd64 (6.1.2+ds-1) over (5.7.0-1) ... Preparing to unpack .../5-libhsa-runtime64-1_6.1.2-2_amd64.deb ... Unpacking libhsa-runtime64-1:amd64 (6.1.2-2) over (5.7.1-3) ... Preparing to unpack .../6-libx11-data_2%3a1.8.10-1_all.deb ... Unpacking libx11-data (2:1.8.10-1) over (2:1.8.7-1) ... Preparing to unpack .../7-libx11-6_2%3a1.8.10-1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.10-1) over (2:1.8.7-1+b2) ... Preparing to unpack .../8-libxau6_1%3a1.0.11-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.11-1) over (1:1.0.9-1+b2) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up hyphy-common (2.5.63+dfsg-1) ... Setting up libgomp1:amd64 (14.2.0-8) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Nov 3 15:34:32 UTC 2024. Universal Time is now: Sun Nov 3 15:34:32 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libx11-data (2:1.8.10-1) ... Setting up libatomic1:amd64 (14.2.0-8) ... Setting up libopenmpi3t64:amd64 (5.0.5-3) ... Setting up libx11-6:amd64 (2:1.8.10-1) ... Setting up libhsakmt1:amd64 (6.1.2+ds-1) ... Setting up hyphy-mpi (2.5.63+dfsg-1) ... Setting up libhsa-runtime64-1:amd64 (6.1.2-2) ... Processing triggers for libc-bin (2.40-3) ... 0m40.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-get', '-yf', 'dist-upgrade'] 0m40.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m41.3s DUMP: b75e36f8faa3cb9863df82394414c8f8 - 0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-cache', 'show', '--no-all-versions', 'hyphy-mpi'] 0m41.5s DUMP: Package: hyphy-mpi Source: hyphy Version: 2.5.63+dfsg-1 Installed-Size: 7402 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.38), libcurl3t64-gnutls (>= 7.16.2), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libopenmpi3t64 (>= 5.0.5), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 5), zlib1g (>= 1:1.2.11.dfsg), hyphy-common (= 2.5.63+dfsg-1) Description-en: Hypothesis testing using Phylogenies (MPI version) HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface) and it can be compiled as a shared library and called from other programming environments such as Python or R. Continued development of HyPhy is currently supported in part by an NIGMS R01 award 1R01GM093939. . This package provides an executable using MPI to do multiprocessing. Description-md5: bf880100fd3d0b8d321965866c6d667b Homepage: https://hyphy.org/ Section: science Priority: optional Filename: pool/main/h/hyphy/hyphy-mpi_2.5.63+dfsg-1_amd64.deb Size: 1535132 MD5sum: ef3cb9f2cbec4ec92f561bd83c474db5 SHA256: 33cb113612c7f741d0156f2d527d6fea7f58c9b6390915e50a32d9a1763a8f6f 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-cache', 'show', '--no-all-versions', 'hyphy-mpi'] 0m41.5s INFO: apt-cache knows about the following packages: hyphy-mpi 0m41.5s INFO: Running scripts pre_install 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_database-server'] 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_database-server'] 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_exceptions'] 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_exceptions'] 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_extras'] 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_extras'] 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_foreign_architecture'] 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_foreign_architecture'] 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-cache', 'policy'] 0m41.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m41.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-cache', 'policy'] 0m41.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-cache', 'policy', 'hyphy-mpi'] 0m41.6s DUMP: hyphy-mpi: Installed: 2.5.63+dfsg-1 Candidate: 2.5.63+dfsg-1 Version table: *** 2.5.63+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m41.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-cache', 'policy', 'hyphy-mpi'] 0m41.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-get', '-y', 'install', 'hyphy-mpi'] 0m42.2s DUMP: Reading package lists... Building dependency tree... Reading state information... hyphy-mpi is already the newest version (2.5.63+dfsg-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m42.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-get', '-y', 'install', 'hyphy-mpi'] 0m42.2s INFO: Running scripts post_install 0m42.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_install_exceptions'] 0m42.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_install_exceptions'] 0m42.2s INFO: Running scripts post_distupgrade 0m42.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m42.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m42.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_distupgrade_exceptions'] 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_distupgrade_exceptions'] 0m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_distupgrade_zz_backports'] 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_distupgrade_zz_backports'] 0m42.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qivpseq'] 0m42.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qivpseq'] 0m42.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qivpseq'] 0m43.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qivpseq'] 0m43.3s INFO: Running scripts pre_install 0m43.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_database-server'] 0m43.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_database-server'] 0m43.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_exceptions'] 0m43.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_exceptions'] 0m43.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_extras'] 0m43.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_extras'] 0m43.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_foreign_architecture'] 0m43.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_foreign_architecture'] 0m43.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m43.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m43.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-cache', 'policy'] 0m43.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m43.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-cache', 'policy'] 0m43.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-cache', 'policy', 'hyphy-mpi'] 0m43.4s DUMP: hyphy-mpi: Installed: 2.5.63+dfsg-1 Candidate: 2.5.63+dfsg-1 Version table: *** 2.5.63+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m43.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-cache', 'policy', 'hyphy-mpi'] 0m43.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-get', '-y', 'install', 'hyphy-mpi=2.5.63+dfsg-1'] 0m44.0s DUMP: Reading package lists... Building dependency tree... Reading state information... hyphy-mpi is already the newest version (2.5.63+dfsg-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m44.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-get', '-y', 'install', 'hyphy-mpi=2.5.63+dfsg-1'] 0m44.0s INFO: Running scripts post_install 0m44.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_install_exceptions'] 0m44.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_install_exceptions'] 0m44.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qivpseq'] 0m44.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qivpseq'] 0m44.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', '-ac', '--ignore-obsolete'] 0m46.5s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', '-ac', '--ignore-obsolete'] 0m46.5s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m46.6s DUMP: 0.15.6 0m46.6s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m46.6s INFO: Running adequate version 0.15.6 now. 0m46.6s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'hyphy-mpi'] 0m46.6s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'hyphy-mpi'] 0m46.6s INFO: Running scripts pre_remove 0m46.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m46.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m46.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m46.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m46.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m48.0s DUMP: UNOWNED SYMLINK /usr/lib/x86_64-linux-gnu/libmpi_usempi_ignore_tkr-gfortranso.40 -> libmpi_usempi_ignore_tkr-gfortran.so.40.30.0 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_remove_exceptions'] 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/pre_remove_exceptions'] 0m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m48.1s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.9.10 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-9 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed hyphy-common hyphy-common 2.5.63+dfsg-1 install ok installed hyphy-mpi hyphy-mpi 2.5.63+dfsg-1 install ok installed ibverbs-providers:amd64 ibverbs-providers 52.0-2+b1 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libamd-comgr2:amd64 libamd-comgr2 6.0+git20231212.4510c28+dfsg-3+b2 install ok installed libamdhip64-5 libamdhip64-5 5.7.1-5 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.10 install ok installed libatomic1:amd64 libatomic1 14.2.0-8 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.1-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.1-2 install ok installed libblkid1:amd64 libblkid1 2.40.2-9 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b5 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.10.1-2 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.273 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.123-1 install ok installed libdrm-common libdrm-common 2.4.123-1 install ok installed libdrm2:amd64 libdrm2 2.4.123-1 install ok installed libedit2:amd64 libedit2 3.1-20240808-1 install ok installed libelf1t64:amd64 libelf1t64 0.192-4 install ok installed libevent-core-2.1-7t64:amd64 libevent-core-2.1-7t64 2.1.12-stable-10+b1 install ok installed libevent-pthreads-2.1-7t64:amd64 libevent-pthreads-2.1-7t64 2.1.12-stable-10+b1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libfabric1:amd64 libfabric1 1.17.0-3.1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2+b1 install ok installed libgomp1:amd64 libgomp1 14.2.0-8 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libhsa-runtime64-1:amd64 libhsa-runtime64-1 6.1.2-2 install ok installed libhsakmt1:amd64 libhsakmt1 6.1.2+ds-1 install ok installed libhwloc-plugins:amd64 libhwloc-plugins 2.11.2-1 install ok installed libhwloc15:amd64 libhwloc15 2.11.2-1 install ok installed libibmad5:amd64 libibmad5 52.0-2+b1 install ok installed libibumad3:amd64 libibumad3 52.0-2+b1 install ok installed libibverbs1:amd64 libibverbs1 52.0-2+b1 install ok installed libicu72:amd64 libicu72 72.1-5+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-4 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.18+dfsg-3+b1 install ok installed libllvm17t64:amd64 libllvm17t64 1:17.0.6-18 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-9 install ok installed libmunge2:amd64 libmunge2 0.5.15-4+b1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.4.0-1+b1 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.6.0-1 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.6.0-1 install ok installed libnl-3-200:amd64 libnl-3-200 3.7.0-0.3+b1 install ok installed libnl-route-3-200:amd64 libnl-route-3-200 3.7.0-0.3+b1 install ok installed libnuma1:amd64 libnuma1 2.0.18-1+b1 install ok installed libopenmpi3t64:amd64 libopenmpi3t64 5.0.5-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpciaccess0:amd64 libpciaccess0 0.17-3+b2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b2 install ok installed libpmix2t64:amd64 libpmix2t64 5.0.3-2+b1 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libpsm-infinipath1 libpsm-infinipath1 3.3+20.604758e7-6.3 install ok installed libpsm2-2 libpsm2-2 11.2.185-2.1 install ok installed librdmacm1t64:amd64 librdmacm1t64 52.0-2+b1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b5 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-8 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-8 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b2 install ok installed libselinux1:amd64 libselinux1 3.7-3 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-9 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 256.7-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libucx0:amd64 libucx0 1.17.0+ds-3 install ok installed libudev1:amd64 libudev1 256.7-3 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-9 install ok installed libx11-6:amd64 libx11-6 2:1.8.10-1 install ok installed libx11-data libx11-data 2:1.8.10-1 install ok installed libxau6:amd64 libxau6 1:1.0.11-1 install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3+b2 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b2 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.1 install ok installed libxnvctrl0:amd64 libxnvctrl0 535.171.04-1+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libz3-4:amd64 libz3-4 4.8.12-3.1+b3 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-9 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-9 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed ocl-icd-libopencl1:amd64 ocl-icd-libopencl1 2.3.2-1+b2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl-base perl-base 5.40.0-6 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-9 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-get', 'remove', 'adduser', 'hyphy-common', 'ibverbs-providers:amd64', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libatomic1:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libfabric1:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'libllvm17t64:amd64', 'libmunge2:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3t64:amd64', 'libpciaccess0:amd64', 'libpmix2t64:amd64', 'libpsl5t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libucx0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libz3-4:amd64', 'ocl-icd-libopencl1:amd64', 'hyphy-mpi'] 0m49.1s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: adduser hyphy-common hyphy-mpi ibverbs-providers libamd-comgr2 libamdhip64-5 libatomic1 libbrotli1 libcurl3t64-gnutls libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libgomp1 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libicu72 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 libllvm17t64 libmunge2 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3t64 libpciaccess0 libpmix2t64 libpsl5t64 libpsm-infinipath1 libpsm2-2 librdmacm1t64 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libucx0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libz3-4 ocl-icd-libopencl1 0 upgraded, 0 newly installed, 64 to remove and 0 not upgraded. After this operation, 329 MB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6627 files and directories currently installed.) Removing hyphy-mpi (2.5.63+dfsg-1) ... Removing libopenmpi3t64:amd64 (5.0.5-3) ... Removing libucx0:amd64 (1.17.0+ds-3) ... Removing libfabric1:amd64 (1.17.0-3.1) ... Removing librdmacm1t64:amd64 (52.0-2+b1) ... Removing hyphy-common (2.5.63+dfsg-1) ... Removing ibverbs-providers:amd64 (52.0-2+b1) ... Removing libamdhip64-5 (5.7.1-5) ... Removing libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Removing libatomic1:amd64 (14.2.0-8) ... Removing libcurl3t64-gnutls:amd64 (8.10.1-2) ... Removing libbrotli1:amd64 (1.1.0-2+b5) ... Removing libhsa-runtime64-1:amd64 (6.1.2-2) ... Removing libhsakmt1:amd64 (6.1.2+ds-1) ... Removing libdrm-amdgpu1:amd64 (2.4.123-1) ... Removing libdrm2:amd64 (2.4.123-1) ... Removing libdrm-common (2.4.123-1) ... Removing libllvm17t64:amd64 (1:17.0.6-18) ... Removing libedit2:amd64 (3.1-20240808-1) ... Removing libelf1t64:amd64 (0.192-4) ... Removing libpmix2t64:amd64 (5.0.3-2+b1) ... Removing libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Removing libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Removing libgomp1:amd64 (14.2.0-8) ... Removing libgssapi-krb5-2:amd64 (1.21.3-3) ... Removing libhwloc-plugins:amd64 (2.11.2-1) ... Removing libhwloc15:amd64 (2.11.2-1) ... Removing libibmad5:amd64 (52.0-2+b1) ... Removing libibumad3:amd64 (52.0-2+b1) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Removing libicu72:amd64 (72.1-5+b1) ... Removing libkrb5-3:amd64 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-4) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Removing libmunge2:amd64 (0.5.15-4+b1) ... Removing libnghttp2-14:amd64 (1.64.0-1) ... Removing libnghttp3-9:amd64 (1.4.0-1+b1) ... Removing libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Removing libngtcp2-16:amd64 (1.6.0-1) ... Removing libpsm2-2 (11.2.185-2.1) ... Removing libnuma1:amd64 (2.0.18-1+b1) ... Removing libpciaccess0:amd64 (0.17-3+b2) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... Removing libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: warning: alternative /usr/lib/libpsm1/libpsm_infinipath.so.1.16 (part of link group libpsm_infinipath.so.1) doesn't exist; removing from list of alternatives update-alternatives: warning: /etc/alternatives/libpsm_infinipath.so.1 is dangling; it will be updated with best choice Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Removing libsqlite3-0:amd64 (3.46.1-1) ... Removing libssh2-1t64:amd64 (1.11.1-1) ... Removing libxnvctrl0:amd64 (535.171.04-1+b1) ... Removing libxext6:amd64 (2:1.3.4-1+b2) ... Removing libx11-6:amd64 (2:1.8.10-1) ... Removing libx11-data (2:1.8.10-1) ... Removing libxcb1:amd64 (1.17.0-2+b1) ... Removing libxau6:amd64 (1:1.0.11-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3+b2) ... Removing libz3-4:amd64 (4.8.12-3.1+b3) ... Removing ocl-icd-libopencl1:amd64 (2.3.2-1+b2) ... Removing libibverbs1:amd64 (52.0-2+b1) ... Removing adduser (3.137) ... Removing libnl-route-3-200:amd64 (3.7.0-0.3+b1) ... Removing libnl-3-200:amd64 (3.7.0-0.3+b1) ... Processing triggers for libc-bin (2.40-3) ... 0m49.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-get', 'remove', 'adduser', 'hyphy-common', 'ibverbs-providers:amd64', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libatomic1:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libfabric1:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'libllvm17t64:amd64', 'libmunge2:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3t64:amd64', 'libpciaccess0:amd64', 'libpmix2t64:amd64', 'libpsl5t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libucx0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libz3-4:amd64', 'ocl-icd-libopencl1:amd64', 'hyphy-mpi'] 0m49.1s INFO: Running scripts post_remove 0m49.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_remove_exceptions'] 0m49.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_remove_exceptions'] 0m49.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'dpkg', '--purge', 'adduser', 'hyphy-common', 'ibverbs-providers:amd64', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libatomic1:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libfabric1:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'libllvm17t64:amd64', 'libmunge2:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3t64:amd64', 'libpciaccess0:amd64', 'libpmix2t64:amd64', 'libpsl5t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libucx0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libz3-4:amd64', 'ocl-icd-libopencl1:amd64'] 0m49.1s DUMP: (Reading database ... 5180 files and directories currently installed.) Purging configuration files for adduser (3.137) ... dpkg: warning: ignoring request to remove hyphy-common which isn't installed Purging configuration files for ibverbs-providers:amd64 (52.0-2+b1) ... dpkg: warning: ignoring request to remove libamd-comgr2 which isn't installed dpkg: warning: ignoring request to remove libamdhip64-5 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcurl3t64-gnutls which isn't installed dpkg: warning: ignoring request to remove libdrm-amdgpu1 which isn't installed dpkg: warning: ignoring request to remove libdrm-common which isn't installed dpkg: warning: ignoring request to remove libdrm2 which isn't installed dpkg: warning: ignoring request to remove libedit2 which isn't installed dpkg: warning: ignoring request to remove libelf1t64 which isn't installed dpkg: warning: ignoring request to remove libevent-core-2.1-7t64 which isn't installed dpkg: warning: ignoring request to remove libevent-pthreads-2.1-7t64 which isn't installed dpkg: warning: ignoring request to remove libfabric1 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-3) ... dpkg: warning: ignoring request to remove libhsa-runtime64-1 which isn't installed dpkg: warning: ignoring request to remove libhsakmt1 which isn't installed dpkg: warning: ignoring request to remove libhwloc-plugins which isn't installed dpkg: warning: ignoring request to remove libhwloc15 which isn't installed dpkg: warning: ignoring request to remove libibmad5 which isn't installed dpkg: warning: ignoring request to remove libibumad3 which isn't installed dpkg: warning: ignoring request to remove libibverbs1 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove libllvm17t64 which isn't installed dpkg: warning: ignoring request to remove libmunge2 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnghttp3-9 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-16 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-crypto-gnutls8 which isn't installed Purging configuration files for libnl-3-200:amd64 (3.7.0-0.3+b1) ... dpkg: warning: ignoring request to remove libnl-route-3-200 which isn't installed dpkg: warning: ignoring request to remove libnuma1 which isn't installed dpkg: warning: ignoring request to remove libopenmpi3t64 which isn't installed dpkg: warning: ignoring request to remove libpciaccess0 which isn't installed dpkg: warning: ignoring request to remove libpmix2t64 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed Purging configuration files for libpsm-infinipath1 (3.3+20.604758e7-6.3) ... dpkg: warning: ignoring request to remove libpsm2-2 which isn't installed dpkg: warning: ignoring request to remove librdmacm1t64 which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libucx0 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxnvctrl0 which isn't installed dpkg: warning: ignoring request to remove libz3-4 which isn't installed dpkg: warning: ignoring request to remove ocl-icd-libopencl1 which isn't installed 0m49.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'dpkg', '--purge', 'adduser', 'hyphy-common', 'ibverbs-providers:amd64', 'libamd-comgr2:amd64', 'libamdhip64-5', 'libatomic1:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libfabric1:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'libllvm17t64:amd64', 'libmunge2:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3t64:amd64', 'libpciaccess0:amd64', 'libpmix2t64:amd64', 'libpsl5t64:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libucx0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libz3-4:amd64', 'ocl-icd-libopencl1:amd64'] 0m49.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'dpkg', '--purge', 'hyphy-mpi'] 0m49.1s DUMP: dpkg: warning: ignoring request to remove hyphy-mpi which isn't installed 0m49.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'dpkg', '--purge', 'hyphy-mpi'] 0m49.1s INFO: Running scripts post_purge 0m49.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_purge_exceptions'] 0m49.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_purge_exceptions'] 0m49.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'dpkg', '--purge', '--pending'] 0m49.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'dpkg', '--purge', '--pending'] 0m49.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'dpkg', '--remove', '--pending'] 0m49.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'dpkg', '--remove', '--pending'] 0m49.2s INFO: Running scripts post_test 0m49.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_test_exceptions'] 0m49.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'tmp/scripts/post_test_exceptions'] 0m49.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qivpseq'] 0m49.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1qivpseq'] 0m49.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'dpkg-divert', '--list'] 0m49.5s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m49.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'dpkg-divert', '--list'] 0m49.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-get', 'clean'] 0m49.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1qivpseq', 'apt-get', 'clean'] 0m49.5s DEBUG: Recording chroot state 0m50.0s INFO: Warning: Package purging left files on system: /usr/lib/x86_64-linux-gnu/libmpi_usempi_ignore_tkr-gfortranso.40 -> libmpi_usempi_ignore_tkr-gfortran.so.40.30.0 not owned 0m50.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/dev/shm'] 0m50.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/dev/shm'] 0m50.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/dev/console'] 0m50.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/dev/console'] 0m50.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/dev/ptmx'] 0m50.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/dev/ptmx'] 0m50.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/dev/pts'] 0m50.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/dev/pts'] 0m50.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/proc'] 0m50.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1qivpseq/proc'] 0m50.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp1qivpseq'] 0m50.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp1qivpseq'] 0m50.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp1qivpseq 0m50.6s INFO: PASS: Upgrading between Debian distributions. 0m50.6s INFO: PASS: All tests. 0m50.6s INFO: piuparts run ends. ret=0 End: 2024-11-03 15:34:42 GMT