Start: 2025-05-01 15:28:27 GMT [testing] Package: pique-doc Source: pique Version: 1.0-7 Installed-Size: 2152 Maintainer: Debian Med Packaging Team Architecture: all Enhances: pique Description: software pipeline for performing genome wide association studies (docs) Multi-Arch: foreign Homepage: https://github.com/tony-travis/PIQUE/ Description-md5: 25721dafac8d6a38338c5fefaed38d0a Section: doc Priority: optional Filename: pool/main/p/pique/pique-doc_1.0-7_all.deb Size: 1927560 MD5sum: 10becd4d24261780d66b348fac490556 SHA256: ba1c88a2c5a5ab2d6d6b3bc20cbffe12972e12be6119afd0e6d654927cf81c8c [sid] Package: pique-doc Source: pique Version: 1.1-1 Installed-Size: 3698 Maintainer: Debian Med Packaging Team Architecture: all Enhances: pique Description: software pipeline for performing genome wide association studies (docs) Multi-Arch: foreign Homepage: https://github.com/tony-travis/PIQUE/ Description-md5: 25721dafac8d6a38338c5fefaed38d0a Section: doc Priority: optional Filename: pool/main/p/pique/pique-doc_1.1-1_all.deb Size: 3520664 MD5sum: 7b9932baf4ca9a6499f176a57bbcd2b8 SHA256: d659fb42b242095e06655f27b5a47d35762348a12b43ad8ad052063c97de88a3 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/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 pique-doc=1.1-1 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 1.5.2~202503162239~1.5.1-10-g345d5865 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/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 pique-doc=1.1-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-34-amd64 #1 SMP Debian 5.10.234-1 (2025-02-24) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp93e7husi 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp93e7husi 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp93e7husi', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp93e7husi', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp93e7husi/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp93e7husi/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp93e7husi/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp93e7husi/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp93e7husi/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp93e7husi/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp93e7husi/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp93e7husi/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmp93e7husi/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmp93e7husi/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp93e7husi/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp93e7husi/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp93e7husi/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-get', 'update'] 0m1.5s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [175 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9684 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6496 kB] Fetched 16.4 MB in 1s (19.7 MB/s) Reading package lists... 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-get', 'update'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: coreutils diffutils libcap2 login.defs passwd 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 4854 kB of archives. After this operation, 3072 B of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 coreutils amd64 9.7-2 [3024 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 diffutils amd64 1:3.10-4 [387 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libcap2 amd64 1:2.75-7 [28.1 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 login.defs all 1:4.17.4-2 [186 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 passwd amd64 1:4.17.4-2 [1229 kB] Fetched 4854 kB in 0s (52.3 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 ... 4937 files and directories currently installed.) Preparing to unpack .../coreutils_9.7-2_amd64.deb ... Unpacking coreutils (9.7-2) over (9.7-1) ... Setting up coreutils (9.7-2) ... (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 ... 4936 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.10-4_amd64.deb ... Unpacking diffutils (1:3.10-4) over (1:3.10-3) ... Setting up diffutils (1:3.10-4) ... (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 ... 4936 files and directories currently installed.) Preparing to unpack .../libcap2_1%3a2.75-7_amd64.deb ... Unpacking libcap2:amd64 (1:2.75-7) over (1:2.75-6) ... Setting up libcap2:amd64 (1:2.75-7) ... (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 ... 4936 files and directories currently installed.) Preparing to unpack .../login.defs_1%3a4.17.4-2_all.deb ... Unpacking login.defs (1:4.17.4-2) over (1:4.17.4-1) ... Preparing to unpack .../passwd_1%3a4.17.4-2_amd64.deb ... Unpacking passwd (1:4.17.4-2) over (1:4.17.4-1) ... Setting up login.defs (1:4.17.4-2) ... Setting up passwd (1:4.17.4-2) ... Processing triggers for libc-bin (2.41-7) ... 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s DUMP: 364e39e5ce97dbbe9cab3634b4a2cd54 - 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s INFO: Running scripts post_setup 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_setup_dummy_users'] 0m2.9s 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 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_setup_dummy_users'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_setup_forbid_home'] 0m2.9s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_setup_forbid_home'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.9s 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' 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_setup_minimize'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_setup_minimize'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_setup_zz_backports'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_setup_zz_backports'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.9s DUMP: install ok installed apt apt 3.0.0 install ok installed base-files base-files 13.7 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2 install ok installed bsdutils bsdutils 1:2.41-4 install ok installed coreutils coreutils 9.7-2 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.22 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.18 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.0 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblkid1:amd64 libblkid1 2.41-4 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 2.41-7 install ok installed libc6:amd64 libc6 2.41-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-7 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.278 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-4 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-4 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3 install ok installed libpam-runtime libpam-runtime 1.7.0-3 install ok installed libpam0g:amd64 libpam0g 1.7.0-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-4 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-3 install ok installed libssl3t64:amd64 libssl3t64 3.5.0-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.5-2 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.5-2 install ok installed libuuid1:amd64 libuuid1 2.41-4 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-4 install ok installed login.defs login.defs 1:4.17.4-2 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41-4 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.0-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-3 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-1 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-2 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.41-4 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.9s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m2.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp93e7husi'] 0m3.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp93e7husi'] 0m3.1s INFO: Running scripts is_testable 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/is_testable_uninstallable'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/is_testable_uninstallable'] 0m3.1s INFO: Running scripts pre_test 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_test_exceptions'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_test_exceptions'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_test_root_password'] 0m3.1s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_test_root_password'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-cache', 'show', '--no-all-versions', 'pique-doc'] 0m3.2s DUMP: Package: pique-doc Source: pique Version: 1.0-7 Installed-Size: 2152 Maintainer: Debian Med Packaging Team Architecture: all Enhances: pique Description-en: software pipeline for performing genome wide association studies (docs) PIQUE is a software pipeline for performing genome wide association studies (GWAS). The main function of PIQUE is to provide ??convenience?? wrappers that allow users to perform GWAS using the popular program EMMAX (Kang et al., 2010) without the need to be familiar with all of the software tools used to generate the required EMMAX input files. PIQUE will also perform a number of quality control steps prior to running EMMAX, ensuring that the various input data files are in the correct format. PIQUE proceeds in two main stages although there are multiple entry and exit points from which the pipeline can be run. The first stage consists of running the ??pique-input?? program, which can read genotype and phenotype information in several different formats and generates all the necessary input files required to run EMMAX. The second step in the pipeline uses the ??pique-run?? program to actually run EMMAX using the files generated by ??pique-input?? (or pre-existing user-supplied input files) to perform the GWAS and output the analysis summary files. . This package contains the documentation as well as example data. Description-md5: 25721dafac8d6a38338c5fefaed38d0a Multi-Arch: foreign Homepage: https://github.com/tony-travis/PIQUE/ Section: doc Priority: optional Filename: pool/main/p/pique/pique-doc_1.0-7_all.deb Size: 1927560 MD5sum: 10becd4d24261780d66b348fac490556 SHA256: ba1c88a2c5a5ab2d6d6b3bc20cbffe12972e12be6119afd0e6d654927cf81c8c 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-cache', 'show', '--no-all-versions', 'pique-doc'] 0m3.2s INFO: apt-cache knows about the following packages: pique-doc 0m3.2s INFO: Running scripts pre_install 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_database-server'] 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_database-server'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_exceptions'] 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_exceptions'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_extras'] 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_extras'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-cache', 'policy'] 0m3.3s 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: 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-cache', 'policy'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-cache', 'policy', 'pique-doc'] 0m3.3s DUMP: pique-doc: Installed: (none) Candidate: 1.0-7 Version table: 1.0-7 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-cache', 'policy', 'pique-doc'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-get', '-y', 'install', 'pique-doc'] 0m4.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: pique-doc 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 1928 kB of archives. After this operation, 2204 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 pique-doc all 1.0-7 [1928 kB] Fetched 1928 kB in 0s (8245 kB/s) Selecting previously unselected package pique-doc. (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 ... 4940 files and directories currently installed.) Preparing to unpack .../pique-doc_1.0-7_all.deb ... Unpacking pique-doc (1.0-7) ... Setting up pique-doc (1.0-7) ... 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-get', '-y', 'install', 'pique-doc'] 0m4.0s INFO: Running scripts post_install 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_install_exceptions'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_install_exceptions'] 0m4.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp93e7husi'] 0m4.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp93e7husi'] 0m4.2s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp93e7husi to sid 0m4.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m4.2s INFO: Running scripts pre_distupgrade 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_distupgrade_exceptions'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_distupgrade_exceptions'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-get', 'update'] 0m6.0s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [205 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.1 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7405 kB] Fetched 17.7 MB in 1s (12.7 MB/s) Reading package lists... 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-get', 'update'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-get', '-yf', 'dist-upgrade'] 0m7.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt libapt-pkg7.0 pique-doc 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 6086 kB of archives. After this operation, 1591 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libapt-pkg7.0 amd64 3.0.1 [1113 kB] Get:2 http://deb.debian.org/debian sid/main amd64 apt amd64 3.0.1 [1452 kB] Get:3 http://deb.debian.org/debian sid/main amd64 pique-doc all 1.1-1 [3521 kB] Fetched 6086 kB in 0s (23.0 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 ... 4954 files and directories currently installed.) Preparing to unpack .../libapt-pkg7.0_3.0.1_amd64.deb ... Unpacking libapt-pkg7.0:amd64 (3.0.1) over (3.0.0) ... Setting up libapt-pkg7.0:amd64 (3.0.1) ... (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 ... 4954 files and directories currently installed.) Preparing to unpack .../archives/apt_3.0.1_amd64.deb ... Unpacking apt (3.0.1) over (3.0.0) ... Setting up apt (3.0.1) ... (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 ... 4954 files and directories currently installed.) Preparing to unpack .../pique-doc_1.1-1_all.deb ... Unpacking pique-doc (1.1-1) over (1.0-7) ... Setting up pique-doc (1.1-1) ... Processing triggers for libc-bin (2.41-7) ... 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-get', '-yf', 'dist-upgrade'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.7s DUMP: 09bc6706828bb99a68347072b317b2a7 - 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-cache', 'show', '--no-all-versions', 'pique-doc'] 0m7.9s DUMP: Package: pique-doc Source: pique Version: 1.1-1 Installed-Size: 3698 Maintainer: Debian Med Packaging Team Architecture: all Enhances: pique Description-en: software pipeline for performing genome wide association studies (docs) PIQUE is a software pipeline for performing genome wide association studies (GWAS). The main function of PIQUE is to provide ??convenience?? wrappers that allow users to perform GWAS using the popular program EMMAX (Kang et al., 2010) without the need to be familiar with all of the software tools used to generate the required EMMAX input files. PIQUE will also perform a number of quality control steps prior to running EMMAX, ensuring that the various input data files are in the correct format. PIQUE proceeds in two main stages although there are multiple entry and exit points from which the pipeline can be run. The first stage consists of running the ??pique-input?? program, which can read genotype and phenotype information in several different formats and generates all the necessary input files required to run EMMAX. The second step in the pipeline uses the ??pique-run?? program to actually run EMMAX using the files generated by ??pique-input?? (or pre-existing user-supplied input files) to perform the GWAS and output the analysis summary files. . This package contains the documentation as well as example data. Description-md5: 25721dafac8d6a38338c5fefaed38d0a Multi-Arch: foreign Homepage: https://github.com/tony-travis/PIQUE/ Section: doc Priority: optional Filename: pool/main/p/pique/pique-doc_1.1-1_all.deb Size: 3520664 MD5sum: 7b9932baf4ca9a6499f176a57bbcd2b8 SHA256: d659fb42b242095e06655f27b5a47d35762348a12b43ad8ad052063c97de88a3 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-cache', 'show', '--no-all-versions', 'pique-doc'] 0m7.9s INFO: apt-cache knows about the following packages: pique-doc 0m7.9s INFO: Running scripts pre_install 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_database-server'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_database-server'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_exceptions'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_exceptions'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_extras'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_extras'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-cache', 'policy'] 0m7.9s 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: 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-cache', 'policy'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-cache', 'policy', 'pique-doc'] 0m7.9s DUMP: pique-doc: Installed: 1.1-1 Candidate: 1.1-1 Version table: *** 1.1-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-cache', 'policy', 'pique-doc'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-get', '-y', 'install', 'pique-doc'] 0m8.2s DUMP: Reading package lists... Building dependency tree... Reading state information... pique-doc is already the newest version (1.1-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-get', '-y', 'install', 'pique-doc'] 0m8.2s INFO: Running scripts post_install 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_install_exceptions'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_install_exceptions'] 0m8.2s INFO: Running scripts post_distupgrade 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_distupgrade_exceptions'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_distupgrade_exceptions'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_distupgrade_zz_backports'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_distupgrade_zz_backports'] 0m8.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp93e7husi'] 0m8.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp93e7husi'] 0m8.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp93e7husi'] 0m8.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp93e7husi'] 0m8.6s INFO: Running scripts pre_install 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_database-server'] 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_database-server'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_exceptions'] 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_exceptions'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_extras'] 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_extras'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-cache', 'policy'] 0m8.6s 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: 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-cache', 'policy'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-cache', 'policy', 'pique-doc'] 0m8.6s DUMP: pique-doc: Installed: 1.1-1 Candidate: 1.1-1 Version table: *** 1.1-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-cache', 'policy', 'pique-doc'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-get', '-y', 'install', 'pique-doc=1.1-1'] 0m8.9s DUMP: Reading package lists... Building dependency tree... Reading state information... pique-doc is already the newest version (1.1-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-get', '-y', 'install', 'pique-doc=1.1-1'] 0m8.9s INFO: Running scripts post_install 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_install_exceptions'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_install_exceptions'] 0m8.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp93e7husi'] 0m9.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp93e7husi'] 0m9.2s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp93e7husi', '-ac', '--ignore-obsolete'] 0m9.5s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp93e7husi', '-ac', '--ignore-obsolete'] 0m9.5s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m9.6s DUMP: 0.15.6 0m9.6s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m9.6s INFO: Running adequate version 0.15.6 now. 0m9.6s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'pique-doc'] 0m9.6s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'pique-doc'] 0m9.6s INFO: Running scripts pre_remove 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_remove_exceptions'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/pre_remove_exceptions'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.9s DUMP: install ok installed apt apt 3.0.1 install ok installed base-files base-files 13.7 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2 install ok installed bsdutils bsdutils 1:2.41-4 install ok installed coreutils coreutils 9.7-2 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.22 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.18 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.1 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblkid1:amd64 libblkid1 2.41-4 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 2.41-7 install ok installed libc6:amd64 libc6 2.41-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-7 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.278 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-4 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-4 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3 install ok installed libpam-runtime libpam-runtime 1.7.0-3 install ok installed libpam0g:amd64 libpam0g 1.7.0-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-4 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-3 install ok installed libssl3t64:amd64 libssl3t64 3.5.0-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.5-2 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.5-2 install ok installed libuuid1:amd64 libuuid1 2.41-4 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-4 install ok installed login.defs login.defs 1:4.17.4-2 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41-4 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.0-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-3 install ok installed pique-doc pique-doc 1.1-1 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-1 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-2 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.41-4 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-get', 'remove', '--allow-remove-essential', 'pique-doc'] 0m10.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: pique-doc 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 3787 kB 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 ... 4956 files and directories currently installed.) Removing pique-doc (1.1-1) ... 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-get', 'remove', '--allow-remove-essential', 'pique-doc'] 0m10.3s INFO: Running scripts post_remove 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_remove_exceptions'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_remove_exceptions'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'dpkg', '--purge', 'pique-doc'] 0m10.3s DUMP: dpkg: warning: ignoring request to remove pique-doc which isn't installed 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'dpkg', '--purge', 'pique-doc'] 0m10.3s INFO: Running scripts post_purge 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_purge_exceptions'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_purge_exceptions'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'dpkg', '--purge', '--pending'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'dpkg', '--purge', '--pending'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'dpkg', '--remove', '--pending'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'dpkg', '--remove', '--pending'] 0m10.3s INFO: Running scripts post_test 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_test_exceptions'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'tmp/scripts/post_test_exceptions'] 0m10.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp93e7husi'] 0m10.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp93e7husi'] 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'dpkg-divert', '--list'] 0m10.5s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged 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 /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 0m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'dpkg-divert', '--list'] 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-get', 'clean'] 0m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp93e7husi', 'apt-get', 'clean'] 0m10.5s DEBUG: Recording chroot state 0m11.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp93e7husi/dev/shm'] 0m11.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp93e7husi/dev/shm'] 0m11.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp93e7husi/dev/console'] 0m11.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp93e7husi/dev/console'] 0m11.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp93e7husi/dev/ptmx'] 0m11.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp93e7husi/dev/ptmx'] 0m11.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp93e7husi/dev/pts'] 0m11.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp93e7husi/dev/pts'] 0m11.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp93e7husi/proc'] 0m11.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp93e7husi/proc'] 0m11.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp93e7husi'] 0m11.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp93e7husi'] 0m11.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp93e7husi 0m11.2s INFO: PASS: Upgrading between Debian distributions. 0m11.2s INFO: PASS: All tests. 0m11.2s INFO: piuparts run ends. ret=0 End: 2025-05-01 15:28:38 GMT