Start: 2022-10-31 03:35:00 GMT [testing] Package: toppic-common Source: toppic Version: 1.3.0+dfsg1-4 Installed-Size: 24344 Maintainer: The Debichem Group Architecture: all Depends: fonts-font-awesome, fonts-freefont-ttf, libjs-filesaver, libjs-bootstrap4, libjs-popper.js, libjs-jquery-ui, node-jquery Description: Top-down proteoform identification and characterization (common data) Homepage: http://proteomics.informatics.iupui.edu/software/toppic/index.html Description-md5: bbae5ecb9fcba93e79d38a482e49ed1b Section: science Priority: optional Filename: pool/main/t/toppic/toppic-common_1.3.0+dfsg1-4_all.deb Size: 5454484 MD5sum: 7232a40072a100c437a8bddeb4c61658 SHA256: 5e75ceaa11b5d3f8ca603fa6cc5b538be542d0df2c06096789f1a1acecc674a0 [sid] Package: toppic-common Source: toppic Version: 1.5.3+dfsg1-1 Installed-Size: 56336 Maintainer: The Debichem Group Architecture: all Depends: fonts-font-awesome, fonts-freefont-ttf, libjs-filesaver, libjs-bootstrap4, libjs-popper.js, libjs-jquery-ui, node-jquery Description: Top-down proteoform identification and characterization (common data) Homepage: http://proteomics.informatics.iupui.edu/software/toppic/index.html Description-md5: 38d72472bf94d4a506454a39f9fd75ae Section: science Priority: optional Filename: pool/main/t/toppic/toppic-common_1.5.3+dfsg1-1_all.deb Size: 18754620 MD5sum: 3295d191cf96b8e41749cb9c91950588 SHA256: 5b9f837825031e99098adbcde59a76d7e58f60a99081a8ff6cdaac47dc2b83c7 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/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt toppic-common=1.5.3+dfsg1-1 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 1.1.5 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/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt toppic-common=1.5.3+dfsg1-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-19-amd64 #1 SMP Debian 5.10.149-2 (2022-10-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpt_kfd5av 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpt_kfd5av 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m1.9s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/proc'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/proc'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/dev/pts'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/dev/pts'] 0m1.9s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/dev/ptmx'] 0m1.9s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/dev/ptmx'] 0m1.9s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/dev/console'] 0m1.9s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/dev/console'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/dev/shm'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/dev/shm'] 0m1.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m2.0s DEBUG: Created policy-rc.d and chmodded it. 0m2.0s DEBUG: Created resolv.conf. 0m2.0s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpt_kfd5av/tmp/scripts/ 0m2.0s INFO: Running scripts post_chroot_unpack 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-get', 'update'] 0m3.9s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [164 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8691 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [5880 kB] Fetched 14.7 MB in 1s (10.5 MB/s) Reading package lists... 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-get', 'update'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-get', '-yf', 'dist-upgrade'] 0m7.4s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following NEW packages will be installed: libperl5.36 perl-modules-5.36 The following packages will be upgraded: bash libc-bin libc6 libffi8 login passwd perl perl-base tzdata 9 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 15.6 MB of archives. After this operation, 47.6 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 bash amd64 5.2-2 [1489 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 login amd64 1:4.12.3+dfsg1-2 [605 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 perl-modules-5.36 all 5.36.0-4 [2815 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libperl5.36 amd64 5.36.0-4 [4211 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 perl amd64 5.36.0-4 [238 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 perl-base amd64 5.36.0-4 [1607 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libc6 amd64 2.35-4 [2738 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libc-bin amd64 2.35-4 [617 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 passwd amd64 1:4.12.3+dfsg1-2 [971 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libffi8 amd64 3.4.4-1 [22.9 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 tzdata all 2022f-1 [278 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 15.6 MB in 0s (146 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 ... 8663 files and directories currently installed.) Preparing to unpack .../archives/bash_5.2-2_amd64.deb ... Unpacking bash (5.2-2) over (5.2~rc2-2) ... Setting up bash (5.2-2) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (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 ... 8663 files and directories currently installed.) Preparing to unpack .../login_1%3a4.12.3+dfsg1-2_amd64.deb ... Unpacking login (1:4.12.3+dfsg1-2) over (1:4.12.3+dfsg1-1) ... Setting up login (1:4.12.3+dfsg1-2) ... (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 ... 8663 files and directories currently installed.) Preparing to unpack .../perl_5.36.0-4_amd64.deb ... Unpacking perl (5.36.0-4) over (5.34.0-5) ... Selecting previously unselected package perl-modules-5.36. Preparing to unpack .../perl-modules-5.36_5.36.0-4_all.deb ... Unpacking perl-modules-5.36 (5.36.0-4) ... Selecting previously unselected package libperl5.36:amd64. Preparing to unpack .../libperl5.36_5.36.0-4_amd64.deb ... Unpacking libperl5.36:amd64 (5.36.0-4) ... Preparing to unpack .../perl-base_5.36.0-4_amd64.deb ... Unpacking perl-base (5.36.0-4) over (5.34.0-5) ... Setting up perl-base (5.36.0-4) ... (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 ... 10589 files and directories currently installed.) Preparing to unpack .../libc6_2.35-4_amd64.deb ... Unpacking libc6:amd64 (2.35-4) over (2.35-3) ... Setting up libc6:amd64 (2.35-4) ... (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 ... 10589 files and directories currently installed.) Preparing to unpack .../libc-bin_2.35-4_amd64.deb ... Unpacking libc-bin (2.35-4) over (2.35-3) ... Setting up libc-bin (2.35-4) ... (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 ... 10590 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.12.3+dfsg1-2_amd64.deb ... Unpacking passwd (1:4.12.3+dfsg1-2) over (1:4.12.3+dfsg1-1) ... Setting up passwd (1:4.12.3+dfsg1-2) ... (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 ... 10590 files and directories currently installed.) Preparing to unpack .../libffi8_3.4.4-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.4-1) over (3.4.2-4) ... Setting up libffi8:amd64 (3.4.4-1) ... (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 ... 10590 files and directories currently installed.) Preparing to unpack .../tzdata_2022f-1_all.deb ... Unpacking tzdata (2022f-1) over (2022e-1) ... Setting up tzdata (2022f-1) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Oct 31 03:35:08 UTC 2022. Universal Time is now: Mon Oct 31 03:35:08 UTC 2022. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up perl-modules-5.36 (5.36.0-4) ... Setting up libperl5.36:amd64 (5.36.0-4) ... Setting up perl (5.36.0-4) ... Processing triggers for libc-bin (2.35-4) ... Processing triggers for debianutils (5.7-0.3) ... 0m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-get', '-yf', 'dist-upgrade'] 0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m8.0s DUMP: 078f4fc4bb0d98d2b45a37f98ed4c208 - 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m8.0s INFO: Running scripts post_setup 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_setup_dummy_users'] 0m8.3s 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 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_setup_dummy_users'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_setup_forbid_home'] 0m8.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_setup_forbid_home'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.4s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_setup_minimize'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_setup_minimize'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_setup_zz_backports'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_setup_zz_backports'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.4s DUMP: install ok installed adduser adduser 3.129 install ok installed apt apt 2.5.3+b1 install ok installed base-files base-files 12.3 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2-2 install ok installed bsdutils bsdutils 1:2.38.1-1.1+b1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.11+git20210903+057cd650a4ed-9 install ok installed debconf debconf 1.5.79 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 5.7-0.3 install ok installed diffutils diffutils 1:3.8-1 install ok installed dpkg dpkg 1.21.9+b1 install ok installed e2fsprogs e2fsprogs 1.46.6~rc1-1+b1 install ok installed findutils findutils 4.9.0-3 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-3 install ok installed gpgv gpgv 2.2.40-1 install ok installed grep grep 3.7-1 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.5.3+b1 install ok installed libattr1:amd64 libattr1 1:2.5.1-1 install ok installed libaudit-common libaudit-common 1:3.0.7-1.1 install ok installed libaudit1:amd64 libaudit1 1:3.0.7-1.1+b1 install ok installed libblkid1:amd64 libblkid1 2.38.1-1.1+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.35-4 install ok installed libc6:amd64 libc6 2.35-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b1 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.6~rc1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.28-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.10 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.264 install ok installed libext2fs2:amd64 libext2fs2 1.46.6~rc1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-2 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-3 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.8-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.45-2 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1 install ok installed libmount1:amd64 libmount1 2.38.1-1.1+b1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-5 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-5 install ok installed libpam-runtime libpam-runtime 1.5.2-5 install ok installed libpam0g:amd64 libpam0g 1.5.2-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.40-1 install ok installed libpcre3:amd64 libpcre3 2:8.39-14 install ok installed libperl5.34:amd64 libperl5.34 5.34.0-5 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b2 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b2 install ok installed libsepol2:amd64 libsepol2 3.4-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-1.1+b1 install ok installed libss2:amd64 libss2 1.46.6~rc1-1+b1 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-3 install ok installed libsystemd0:amd64 libsystemd0 251.6-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libtinfo6:amd64 libtinfo6 6.3+20220423-2 install ok installed libudev1:amd64 libudev1 251.6-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-1.1+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.2+dfsg-1 install ok installed login login 1:4.12.3+dfsg1-2 install ok installed logsave logsave 1.46.6~rc1-1+b1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-1.1+b1 install ok installed ncurses-base ncurses-base 6.3+20220423-2 install ok installed ncurses-bin ncurses-bin 6.3+20220423-2 install ok installed passwd passwd 1:4.12.3+dfsg1-2 install ok installed perl perl 5.36.0-4 install ok installed perl-base perl-base 5.36.0-4 install ok installed perl-modules-5.34 perl-modules-5.34 5.34.0-5 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-4 install ok installed sed sed 4.8-1 install ok installed sysvinit-utils sysvinit-utils 3.05-6 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2022f-1 install ok installed usr-is-merged usr-is-merged 33 install ok installed usrmerge usrmerge 33 install ok installed util-linux util-linux 2.38.1-1.1+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-1.1+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-4.1 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.4s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m8.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av'] 0m8.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av'] 0m8.9s INFO: Running scripts is_testable 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/is_testable_uninstallable'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/is_testable_uninstallable'] 0m8.9s INFO: Running scripts pre_test 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_test_exceptions'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_test_exceptions'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_test_root_password'] 0m9.0s DUMP: New password: Retype new password: passwd: password updated successfully 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_test_root_password'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-cache', 'show', '--no-all-versions', 'toppic-common'] 0m9.1s DUMP: Package: toppic-common Source: toppic Version: 1.3.0+dfsg1-4 Installed-Size: 24344 Maintainer: The Debichem Group Architecture: all Depends: fonts-font-awesome, fonts-freefont-ttf, libjs-filesaver, libjs-bootstrap4, libjs-popper.js, libjs-jquery-ui, node-jquery Description-en: Top-down proteoform identification and characterization (common data) The TopPIC Suite consists of four software tools for the interpretation of top-down mass spectrometry data: TopFD, TopPIC, TopMG, and TopDiff. . -TopFD (Top-down mass spectral Feature Detection) is a software tool for top-down spectral deconvolution and a successor to MS-Deconv. It groups top-down spectral peaks into isotopomer envelopes and converts isotopomer envelopes to monoisotopic neutral masses. In addition, it extracts proteoform features from LC-MS or CE-MS data. . -TopPIC (Top-down mass spectrometry based Proteoform Identification and Characterization) identifies and characterizes proteoforms at the proteome level by searching top-down tandem mass spectra against a protein sequence database. TopPIC is a successor to MS-Align+. It efficiently identifies proteoforms with unexpected alterations, such as mutations and post-translational modifications (PTMs), accurately estimates the statistical significance of identifications, and characterizes reported proteoforms with unknown mass shifts. It uses several techniques, such as indexes, spectral alignment, generation function methods, and the modification identification score (MIScore), to increase the speed, sensitivity, and accuracy. . -TopMG (Top-down mass spectrometry based proteoform identification using Mass Graphs) is a software tool for identifying ultra-modified proteoforms by searching top-down tandem mass spectra against a protein sequence database. It is capable of identifying proteoforms with multiple variable PTMs and unexpected alterations, such as histone proteoforms and phosphorylated ones. It uses mass graphs, which efficiently represent candidate proteoforms with multiple variable PTMs, to increase the speed and sensitivity in proteoform identification. In addition, approximate spectrum-based filtering methods are employed for protein sequence filtering, and a Markov chain Monte Carlo method (TopMCMC) is used for estimating the statistical significance of identifications. . -TopDiff (Top-down mass spectrometry-based identification of Differentially expressed proteoforms) compares the abundances of proteoforms and finds differentially expressed proteoforms by using identifications of top-down mass spectrometry data of several protein samples. . This package ships common data used by the various program in the toppic package. Description-md5: bbae5ecb9fcba93e79d38a482e49ed1b Homepage: http://proteomics.informatics.iupui.edu/software/toppic/index.html Section: science Priority: optional Filename: pool/main/t/toppic/toppic-common_1.3.0+dfsg1-4_all.deb Size: 5454484 MD5sum: 7232a40072a100c437a8bddeb4c61658 SHA256: 5e75ceaa11b5d3f8ca603fa6cc5b538be542d0df2c06096789f1a1acecc674a0 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-cache', 'show', '--no-all-versions', 'toppic-common'] 0m9.1s INFO: apt-cache knows about the following packages: toppic-common 0m9.1s INFO: Running scripts pre_install 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_database-server'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_database-server'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_exceptions'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_exceptions'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_extras'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_extras'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-cache', 'policy'] 0m9.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release o=Debian,a=testing,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-cache', 'policy'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-cache', 'policy', 'toppic-common'] 0m9.3s DUMP: toppic-common: Installed: (none) Candidate: 1.3.0+dfsg1-4 Version table: 1.3.0+dfsg1-4 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-cache', 'policy', 'toppic-common'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-get', '-y', 'install', 'toppic-common'] 0m10.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: fonts-font-awesome fonts-freefont-ttf javascript-common libjs-bootstrap4 libjs-filesaver libjs-jquery libjs-jquery-ui libjs-popper.js node-jquery Suggested packages: apache2 | lighttpd | httpd libjs-jquery-ui-docs Recommended packages: libjs-sizzle The following NEW packages will be installed: fonts-font-awesome fonts-freefont-ttf javascript-common libjs-bootstrap4 libjs-filesaver libjs-jquery libjs-jquery-ui libjs-popper.js node-jquery toppic-common 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. Need to get 9855 kB of archives. After this operation, 42.5 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 fonts-freefont-ttf all 20120503-10 [2552 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 javascript-common all 11+nmu1 [6260 B] Get:4 http://deb.debian.org/debian bookworm/main amd64 libjs-popper.js all 1.16.1+ds-5 [52.0 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 libjs-bootstrap4 all 4.6.1+dfsg1-3 [527 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libjs-filesaver all 2.0.4+dfsg+~2.0.5-1 [9776 B] Get:7 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 node-jquery all 3.6.1+dfsg+~3.5.14-1 [160 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 toppic-common all 1.3.0+dfsg1-4 [5454 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 9855 kB in 0s (93.3 MB/s) Selecting previously unselected package fonts-font-awesome. (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 ... 10592 files and directories currently installed.) Preparing to unpack .../0-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Selecting previously unselected package fonts-freefont-ttf. Preparing to unpack .../1-fonts-freefont-ttf_20120503-10_all.deb ... Unpacking fonts-freefont-ttf (20120503-10) ... Selecting previously unselected package javascript-common. Preparing to unpack .../2-javascript-common_11+nmu1_all.deb ... Unpacking javascript-common (11+nmu1) ... Selecting previously unselected package libjs-popper.js. Preparing to unpack .../3-libjs-popper.js_1.16.1+ds-5_all.deb ... Unpacking libjs-popper.js (1.16.1+ds-5) ... Selecting previously unselected package libjs-bootstrap4. Preparing to unpack .../4-libjs-bootstrap4_4.6.1+dfsg1-3_all.deb ... Unpacking libjs-bootstrap4 (4.6.1+dfsg1-3) ... Selecting previously unselected package libjs-filesaver. Preparing to unpack .../5-libjs-filesaver_2.0.4+dfsg+~2.0.5-1_all.deb ... Unpacking libjs-filesaver (2.0.4+dfsg+~2.0.5-1) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../6-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../7-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... Selecting previously unselected package node-jquery. Preparing to unpack .../8-node-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking node-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package toppic-common. Preparing to unpack .../9-toppic-common_1.3.0+dfsg1-4_all.deb ... Unpacking toppic-common (1.3.0+dfsg1-4) ... Setting up javascript-common (11+nmu1) ... Setting up libjs-popper.js (1.16.1+ds-5) ... Setting up fonts-freefont-ttf (20120503-10) ... Setting up libjs-filesaver (2.0.4+dfsg+~2.0.5-1) ... Setting up libjs-bootstrap4 (4.6.1+dfsg1-3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up node-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up toppic-common (1.3.0+dfsg1-4) ... 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-get', '-y', 'install', 'toppic-common'] 0m10.9s INFO: Running scripts post_install 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_install_exceptions'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_install_exceptions'] 0m10.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av'] 0m11.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av'] 0m11.4s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpt_kfd5av to sid 0m11.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m11.4s INFO: Running scripts pre_distupgrade 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_distupgrade_exceptions'] 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_distupgrade_exceptions'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-get', 'update'] 0m14.4s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [161 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9391 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6937 kB] Fetched 16.5 MB in 2s (7779 kB/s) Reading package lists... 0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-get', 'update'] 0m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-get', '-yf', 'dist-upgrade'] 0m17.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: gcc-12-base grep libgcc-s1 libgpg-error0 liblzma5 libpcre2-8-0 libstdc++6 libsystemd0 libudev1 toppic-common 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 20.8 MB of archives. After this operation, 32.7 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 grep amd64 3.8-3 [421 kB] Get:2 http://deb.debian.org/debian sid/main amd64 gcc-12-base amd64 12.2.0-7 [36.6 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 12.2.0-7 [613 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 12.2.0-7 [49.8 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.46-1 [76.9 kB] Get:6 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.2.7-0.1 [181 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.40-2 [260 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 252~rc3-2 [327 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 252~rc3-2 [105 kB] Get:10 http://deb.debian.org/debian sid/main amd64 toppic-common all 1.5.3+dfsg1-1 [18.8 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 20.8 MB in 0s (160 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 ... 11624 files and directories currently installed.) Preparing to unpack .../archives/grep_3.8-3_amd64.deb ... Unpacking grep (3.8-3) over (3.7-1) ... Setting up grep (3.8-3) ... (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 ... 11626 files and directories currently installed.) Preparing to unpack .../gcc-12-base_12.2.0-7_amd64.deb ... Unpacking gcc-12-base:amd64 (12.2.0-7) over (12.2.0-3) ... Setting up gcc-12-base:amd64 (12.2.0-7) ... (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 ... 11626 files and directories currently installed.) Preparing to unpack .../libstdc++6_12.2.0-7_amd64.deb ... Unpacking libstdc++6:amd64 (12.2.0-7) over (12.2.0-3) ... Setting up libstdc++6:amd64 (12.2.0-7) ... (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 ... 11626 files and directories currently installed.) Preparing to unpack .../libgcc-s1_12.2.0-7_amd64.deb ... Unpacking libgcc-s1:amd64 (12.2.0-7) over (12.2.0-3) ... Setting up libgcc-s1:amd64 (12.2.0-7) ... (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 ... 11626 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.46-1_amd64.deb ... Unpacking libgpg-error0:amd64 (1.46-1) over (1.45-2) ... Setting up libgpg-error0:amd64 (1.46-1) ... (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 ... 11626 files and directories currently installed.) Preparing to unpack .../liblzma5_5.2.7-0.1_amd64.deb ... Unpacking liblzma5:amd64 (5.2.7-0.1) over (5.2.5-2.1) ... Setting up liblzma5:amd64 (5.2.7-0.1) ... (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 ... 11626 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.40-2_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.40-2) over (10.40-1) ... Setting up libpcre2-8-0:amd64 (10.40-2) ... (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 ... 11626 files and directories currently installed.) Preparing to unpack .../libsystemd0_252~rc3-2_amd64.deb ... Unpacking libsystemd0:amd64 (252~rc3-2) over (251.6-1) ... Setting up libsystemd0:amd64 (252~rc3-2) ... (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 ... 11626 files and directories currently installed.) Preparing to unpack .../libudev1_252~rc3-2_amd64.deb ... Unpacking libudev1:amd64 (252~rc3-2) over (251.6-1) ... Setting up libudev1:amd64 (252~rc3-2) ... (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 ... 11626 files and directories currently installed.) Preparing to unpack .../toppic-common_1.5.3+dfsg1-1_all.deb ... Unpacking toppic-common (1.5.3+dfsg1-1) over (1.3.0+dfsg1-4) ... Setting up toppic-common (1.5.3+dfsg1-1) ... Processing triggers for libc-bin (2.35-4) ... 0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-get', '-yf', 'dist-upgrade'] 0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m17.7s DUMP: 619b36976d8f6e82163f8dc5661116a5 - 0m17.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m17.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-cache', 'show', '--no-all-versions', 'toppic-common'] 0m17.9s DUMP: Package: toppic-common Source: toppic Version: 1.5.3+dfsg1-1 Installed-Size: 56336 Maintainer: The Debichem Group Architecture: all Depends: fonts-font-awesome, fonts-freefont-ttf, libjs-filesaver, libjs-bootstrap4, libjs-popper.js, libjs-jquery-ui, node-jquery Description-en: Top-down proteoform identification and characterization (common data) The TopPIC Suite consists of four software tools for the interpretation of top-down mass spectrometry data: TopFD, TopPIC, TopMG, and TopDiff. . -TopFD (Top-down mass spectral Feature Detection) is a software tool for top-down spectral deconvolution and a successor to MS-Deconv. It groups top-down spectral peaks into isotopomer envelopes and converts isotopomer envelopes to monoisotopic neutral masses. In addition, it extracts proteoform features from LC-MS or CE-MS data. . -TopPIC (Top-down mass spectrometry based Proteoform Identification and Characterization) identifies and characterizes proteoforms at the proteome level by searching top-down tandem mass spectra against a protein sequence database. TopPIC is a successor to MS-Align+. It efficiently identifies proteoforms with unexpected alterations, such as mutations and post-translational modifications (PTMs), accurately estimates the statistical significance of identifications, and characterizes reported proteoforms with unknown mass shifts. It uses several techniques, such as indexes, spectral alignment, generation function methods, and the modification identification score (MIScore), to increase the speed, sensitivity, and accuracy. . -TopMG (Top-down mass spectrometry based proteoform identification using Mass Graphs) is a software tool for identifying ultra-modified proteoforms by searching top-down tandem mass spectra against a protein sequence database. It is capable of identifying proteoforms with multiple variable PTMs and unexpected alterations, such as histone proteoforms and phosphorylated ones. It uses mass graphs, which efficiently represent candidate proteoforms with multiple variable PTMs, to increase the speed and sensitivity in proteoform identification. In addition, approximate spectrum-based filtering methods are employed for protein sequence filtering, and a Markov chain Monte Carlo method (TopMCMC) is used for estimating the statistical significance of identifications. . -TopDiff (Top-down mass spectrometry-based identification of Differentially expressed proteoforms) compares the abundances of proteoforms and finds differentially expressed proteoforms by using identifications of top-down mass spectrometry data of several protein samples. . This package ships common data used by the various program in the toppic package and some documentation. Description-md5: 38d72472bf94d4a506454a39f9fd75ae Homepage: http://proteomics.informatics.iupui.edu/software/toppic/index.html Section: science Priority: optional Filename: pool/main/t/toppic/toppic-common_1.5.3+dfsg1-1_all.deb Size: 18754620 MD5sum: 3295d191cf96b8e41749cb9c91950588 SHA256: 5b9f837825031e99098adbcde59a76d7e58f60a99081a8ff6cdaac47dc2b83c7 0m17.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-cache', 'show', '--no-all-versions', 'toppic-common'] 0m17.9s INFO: apt-cache knows about the following packages: toppic-common 0m17.9s INFO: Running scripts pre_install 0m17.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_database-server'] 0m17.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_database-server'] 0m17.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_exceptions'] 0m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_exceptions'] 0m18.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_extras'] 0m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_extras'] 0m18.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-cache', 'policy'] 0m18.1s 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: 0m18.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-cache', 'policy'] 0m18.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-cache', 'policy', 'toppic-common'] 0m18.1s DUMP: toppic-common: Installed: 1.5.3+dfsg1-1 Candidate: 1.5.3+dfsg1-1 Version table: *** 1.5.3+dfsg1-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m18.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-cache', 'policy', 'toppic-common'] 0m18.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-get', '-y', 'install', 'toppic-common'] 0m18.5s DUMP: Reading package lists... Building dependency tree... Reading state information... toppic-common is already the newest version (1.5.3+dfsg1-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-get', '-y', 'install', 'toppic-common'] 0m18.5s INFO: Running scripts post_install 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_install_exceptions'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_install_exceptions'] 0m18.5s INFO: Running scripts post_distupgrade 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_distupgrade_exceptions'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_distupgrade_exceptions'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_distupgrade_zz_backports'] 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_distupgrade_zz_backports'] 0m18.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av'] 0m19.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av'] 0m19.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av'] 0m19.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av'] 0m19.6s INFO: Running scripts pre_install 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_database-server'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_database-server'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_exceptions'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_exceptions'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_extras'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_extras'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-cache', 'policy'] 0m19.7s 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: 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-cache', 'policy'] 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-cache', 'policy', 'toppic-common'] 0m19.7s DUMP: toppic-common: Installed: 1.5.3+dfsg1-1 Candidate: 1.5.3+dfsg1-1 Version table: *** 1.5.3+dfsg1-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-cache', 'policy', 'toppic-common'] 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-get', '-y', 'install', 'toppic-common=1.5.3+dfsg1-1'] 0m20.1s DUMP: Reading package lists... Building dependency tree... Reading state information... toppic-common is already the newest version (1.5.3+dfsg1-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-get', '-y', 'install', 'toppic-common=1.5.3+dfsg1-1'] 0m20.1s INFO: Running scripts post_install 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_install_exceptions'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_install_exceptions'] 0m20.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av'] 0m20.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av'] 0m21.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', '-ac', '--ignore-obsolete'] 0m22.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', '-ac', '--ignore-obsolete'] 0m22.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m22.3s DUMP: 0.15.6 0m22.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m22.3s INFO: Running adequate version 0.15.6 now. 0m22.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'toppic-common'] 0m22.4s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'toppic-common'] 0m22.4s INFO: Running scripts pre_remove 0m22.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m23.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m23.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m23.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m23.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m23.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m23.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_remove_exceptions'] 0m23.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/pre_remove_exceptions'] 0m23.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m23.2s DUMP: install ok installed adduser adduser 3.129 install ok installed apt apt 2.5.3+b1 install ok installed base-files base-files 12.3 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2-2 install ok installed bsdutils bsdutils 1:2.38.1-1.1+b1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.11+git20210903+057cd650a4ed-9 install ok installed debconf debconf 1.5.79 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 5.7-0.3 install ok installed diffutils diffutils 1:3.8-1 install ok installed dpkg dpkg 1.21.9+b1 install ok installed e2fsprogs e2fsprogs 1.46.6~rc1-1+b1 install ok installed findutils findutils 4.9.0-3 install ok installed fonts-font-awesome fonts-font-awesome 5.0.10+really4.7.0~dfsg-4.1 install ok installed fonts-freefont-ttf fonts-freefont-ttf 20120503-10 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-7 install ok installed gpgv gpgv 2.2.40-1 install ok installed grep grep 3.8-3 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed javascript-common javascript-common 11+nmu1 install ok installed libacl1:amd64 libacl1 2.3.1-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.5.3+b1 install ok installed libattr1:amd64 libattr1 1:2.5.1-1 install ok installed libaudit-common libaudit-common 1:3.0.7-1.1 install ok installed libaudit1:amd64 libaudit1 1:3.0.7-1.1+b1 install ok installed libblkid1:amd64 libblkid1 2.38.1-1.1+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.35-4 install ok installed libc6:amd64 libc6 2.35-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b1 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.6~rc1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.28-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.10 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.264 install ok installed libext2fs2:amd64 libext2fs2 1.46.6~rc1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-2 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-7 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.8-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed libjs-bootstrap4 libjs-bootstrap4 4.6.1+dfsg1-3 install ok installed libjs-filesaver libjs-filesaver 2.0.4+dfsg+~2.0.5-1 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.13.2+dfsg-1 install ok installed libjs-popper.js libjs-popper.js 1.16.1+ds-5 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.2.7-0.1 install ok installed libmount1:amd64 libmount1 2.38.1-1.1+b1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-5 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-5 install ok installed libpam-runtime libpam-runtime 1.5.2-5 install ok installed libpam0g:amd64 libpam0g 1.5.2-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.40-2 install ok installed libpcre3:amd64 libpcre3 2:8.39-14 install ok installed libperl5.34:amd64 libperl5.34 5.34.0-5 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b2 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b2 install ok installed libsepol2:amd64 libsepol2 3.4-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-1.1+b1 install ok installed libss2:amd64 libss2 1.46.6~rc1-1+b1 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-7 install ok installed libsystemd0:amd64 libsystemd0 252~rc3-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libtinfo6:amd64 libtinfo6 6.3+20220423-2 install ok installed libudev1:amd64 libudev1 252~rc3-2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-1.1+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.2+dfsg-1 install ok installed login login 1:4.12.3+dfsg1-2 install ok installed logsave logsave 1.46.6~rc1-1+b1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-1.1+b1 install ok installed ncurses-base ncurses-base 6.3+20220423-2 install ok installed ncurses-bin ncurses-bin 6.3+20220423-2 install ok installed node-jquery node-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed passwd passwd 1:4.12.3+dfsg1-2 install ok installed perl perl 5.36.0-4 install ok installed perl-base perl-base 5.36.0-4 install ok installed perl-modules-5.34 perl-modules-5.34 5.34.0-5 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-4 install ok installed sed sed 4.8-1 install ok installed sysvinit-utils sysvinit-utils 3.05-6 install ok installed tar tar 1.34+dfsg-1 install ok installed toppic-common toppic-common 1.5.3+dfsg1-1 install ok installed tzdata tzdata 2022f-1 install ok installed usr-is-merged usr-is-merged 33 install ok installed usrmerge usrmerge 33 install ok installed util-linux util-linux 2.38.1-1.1+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-1.1+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-4.1 0m23.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m23.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-get', 'remove', 'fonts-font-awesome', 'fonts-freefont-ttf', 'javascript-common', 'libjs-bootstrap4', 'libjs-filesaver', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-popper.js', 'node-jquery', 'toppic-common'] 0m24.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: fonts-font-awesome fonts-freefont-ttf javascript-common libjs-bootstrap4 libjs-filesaver libjs-jquery libjs-jquery-ui libjs-popper.js node-jquery toppic-common 0 upgraded, 0 newly installed, 10 to remove and 0 not upgraded. After this operation, 75.3 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 ... 12237 files and directories currently installed.) Removing toppic-common (1.5.3+dfsg1-1) ... Removing fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Removing fonts-freefont-ttf (20120503-10) ... Removing libjs-bootstrap4 (4.6.1+dfsg1-3) ... Removing libjs-popper.js (1.16.1+ds-5) ... Removing javascript-common (11+nmu1) ... Removing libjs-filesaver (2.0.4+dfsg+~2.0.5-1) ... Removing libjs-jquery-ui (1.13.2+dfsg-1) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing node-jquery (3.6.1+dfsg+~3.5.14-1) ... 0m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-get', 'remove', 'fonts-font-awesome', 'fonts-freefont-ttf', 'javascript-common', 'libjs-bootstrap4', 'libjs-filesaver', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-popper.js', 'node-jquery', 'toppic-common'] 0m24.0s INFO: Running scripts post_remove 0m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_remove_exceptions'] 0m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_remove_exceptions'] 0m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'dpkg', '--purge', 'fonts-font-awesome', 'fonts-freefont-ttf', 'javascript-common', 'libjs-bootstrap4', 'libjs-filesaver', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-popper.js', 'node-jquery'] 0m24.1s DUMP: (Reading database ... 10600 files and directories currently installed.) Purging configuration files for fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... dpkg: warning: ignoring request to remove fonts-freefont-ttf which isn't installed Purging configuration files for javascript-common (11+nmu1) ... Purging configuration files for libjs-bootstrap4 (4.6.1+dfsg1-3) ... dpkg: warning: ignoring request to remove libjs-filesaver which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-jquery-ui which isn't installed Purging configuration files for libjs-popper.js (1.16.1+ds-5) ... dpkg: warning: ignoring request to remove node-jquery which isn't installed 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'dpkg', '--purge', 'fonts-font-awesome', 'fonts-freefont-ttf', 'javascript-common', 'libjs-bootstrap4', 'libjs-filesaver', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-popper.js', 'node-jquery'] 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'dpkg', '--purge', 'toppic-common'] 0m24.1s DUMP: dpkg: warning: ignoring request to remove toppic-common which isn't installed 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'dpkg', '--purge', 'toppic-common'] 0m24.1s INFO: Running scripts post_purge 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_purge_exceptions'] 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_purge_exceptions'] 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'dpkg', '--purge', '--pending'] 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'dpkg', '--purge', '--pending'] 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'dpkg', '--remove', '--pending'] 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'dpkg', '--remove', '--pending'] 0m24.1s INFO: Running scripts post_test 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_test_exceptions'] 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'tmp/scripts/post_test_exceptions'] 0m24.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av'] 0m24.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av'] 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'dpkg-divert', '--list'] 0m24.6s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'dpkg-divert', '--list'] 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-get', 'clean'] 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av', 'apt-get', 'clean'] 0m24.6s DEBUG: Recording chroot state 0m26.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/dev/shm'] 0m26.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/dev/shm'] 0m26.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/dev/console'] 0m26.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/dev/console'] 0m26.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/dev/ptmx'] 0m26.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/dev/ptmx'] 0m26.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/dev/pts'] 0m26.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/dev/pts'] 0m26.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/proc'] 0m26.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av/proc'] 0m26.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av'] 0m26.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpt_kfd5av'] 0m26.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpt_kfd5av 0m26.3s INFO: PASS: Upgrading between Debian distributions. 0m26.3s INFO: PASS: All tests. 0m26.3s INFO: piuparts run ends. ret=0 End: 2022-10-31 03:35:27 GMT