Start: 2025-08-12 07:28:27 GMT [trixie] Package: fitgcp Version: 0.0.20150429-5 Installed-Size: 23164 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3:any, python3-scipy, python3-numpy, python3-pysam Description: fitting genome coverage distributions with mixture models Homepage: http://sourceforge.net/projects/fitgcp/ Description-md5: 6d250046a14f2fb020b753ee88032582 Section: science Priority: optional Filename: pool/main/f/fitgcp/fitgcp_0.0.20150429-5_all.deb Size: 3675556 MD5sum: a657acb87dccc3c25bda71f1017cd38e SHA256: 307132bcde037065d1602362f025c2d0fbc968351dd522c3d99b228d8ed5e437 [trixie-next] Package: fitgcp Version: 0.0.20150429-5 Installed-Size: 23164 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3:any, python3-scipy, python3-numpy, python3-pysam Description: fitting genome coverage distributions with mixture models Homepage: http://sourceforge.net/projects/fitgcp/ Description-md5: 6d250046a14f2fb020b753ee88032582 Section: science Priority: optional Filename: pool/main/f/fitgcp/fitgcp_0.0.20150429-5_all.deb Size: 3675556 MD5sum: a657acb87dccc3c25bda71f1017cd38e SHA256: 307132bcde037065d1602362f025c2d0fbc968351dd522c3d99b228d8ed5e437 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 trixie -d trixie-next -B /srv/piuparts.debian.org/slave/refchroot/trixie2next/reference-chroot-metadata.dat --apt fitgcp=0.0.20150429-5 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 1.6.1~202508101417~1.6.0-7-g17c4ea32 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 trixie -d trixie-next -B /srv/piuparts.debian.org/slave/refchroot/trixie2next/reference-chroot-metadata.dat --apt fitgcp=0.0.20150429-5 0m0.0s INFO: Running on: Linux piu-slave-conova-01 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpyuniwnzu 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpyuniwnzu 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/proc'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/dev/pts'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpyuniwnzu/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-get', 'update'] 0m2.4s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [138 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9668 kB] Fetched 9805 kB in 1s (8170 kB/s) Reading package lists... 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-get', 'update'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-get', '-yf', 'dist-upgrade'] 0m3.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-get', '-yf', 'dist-upgrade'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.9s DUMP: 8fc0def95551deb38dc214d6c9cce720 - 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.9s INFO: Running scripts post_setup 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_setup_dummy_users'] 0m4.8s 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 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_setup_dummy_users'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_setup_forbid_home'] 0m4.8s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_setup_forbid_home'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.8s 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' 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_setup_minimize'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_setup_minimize'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_setup_zz_backports'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_setup_zz_backports'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.9s DUMP: install ok installed apt apt 3.0.3 install ok installed base-files base-files 13.8 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b5 install ok installed bsdutils bsdutils 1:2.41-5 install ok installed coreutils coreutils 9.7-3 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 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 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 3.0.3 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 2.41-5 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 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 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 0.280 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 2.41-5 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 2.41-5 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 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 2.41-5 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7 install ok installed libssl3t64:amd64 libssl3t64 3.5.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.7-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.7-1 install ok installed libuuid1:amd64 libuuid1 2.41-5 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+really2.41-5 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 2.41-5 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 3.5.1-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-6 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 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-4 install ok installed util-linux util-linux 2.41-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.9s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/trixie2next/reference-chroot-metadata.dat 0m4.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu'] 0m5.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu'] 0m5.2s INFO: Running scripts is_testable 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/is_testable_uninstallable'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/is_testable_uninstallable'] 0m5.3s INFO: Running scripts pre_test 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_test_exceptions'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_test_exceptions'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_test_root_password'] 0m5.3s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_test_root_password'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-cache', 'show', '--no-all-versions', 'fitgcp'] 0m5.6s DUMP: Package: fitgcp Version: 0.0.20150429-5 Installed-Size: 23164 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3:any, python3-scipy, python3-numpy, python3-pysam Description-en: fitting genome coverage distributions with mixture models Genome coverage, the number of sequencing reads mapped to a position in a genome, is an insightful indicator of irregularities within sequencing experiments. While the average genome coverage is frequently used within algorithms in computational genomics, the complete information available in coverage profiles (i.e. histograms over all coverages) is currently not exploited to its full extent. Thus, biases such as fragmented or erroneous reference genomes often remain unaccounted for. Making this information accessible can improve the quality of sequencing experiments and quantitative analyses. . fitGCP is a framework for fitting mixtures of probability distributions to genome coverage profiles. Besides commonly used distributions, fitGCP uses distributions tailored to account for common artifacts. The mixture models are iteratively fitted based on the Expectation-Maximization algorithm. Description-md5: 6d250046a14f2fb020b753ee88032582 Homepage: http://sourceforge.net/projects/fitgcp/ Section: science Priority: optional Filename: pool/main/f/fitgcp/fitgcp_0.0.20150429-5_all.deb Size: 3675556 MD5sum: a657acb87dccc3c25bda71f1017cd38e SHA256: 307132bcde037065d1602362f025c2d0fbc968351dd522c3d99b228d8ed5e437 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-cache', 'show', '--no-all-versions', 'fitgcp'] 0m5.6s INFO: apt-cache knows about the following packages: fitgcp 0m5.6s INFO: Running scripts pre_install 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_database-server'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_database-server'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_exceptions'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_exceptions'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_extras'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_extras'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-cache', 'policy'] 0m5.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.0,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-cache', 'policy'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-cache', 'policy', 'fitgcp'] 0m5.7s DUMP: fitgcp: Installed: (none) Candidate: 0.0.20150429-5 Version table: 0.0.20150429-5 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-cache', 'policy', 'fitgcp'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-get', '-y', 'install', 'fitgcp'] 0m17.2s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: libblas3 libbrotli1 libcom-err2 libcurl3t64-gnutls libdeflate0 libexpat1 libffi8 libgfortran5 libgnutls30t64 libgssapi-krb5-2 libhts3t64 libhtscodecs2 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap2 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libp11-kit0 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1t64 libtasn1-6 libunistring5 media-types netbase python3 python3-decorator python3-minimal python3-numpy python3-numpy-dev python3-pysam python3-scipy python3.13 python3.13-minimal readline-common Suggested packages: gnutls-bin krb5-doc krb5-user python3-doc python3-tk python3-venv gcc gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc python3.13-venv python3.13-doc binutils binfmt-support readline-doc Recommended packages: ca-certificates krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules g++ | c++-compiler python3-pil python3-pooch python3-yaml The following NEW packages will be installed: fitgcp libblas3 libbrotli1 libcom-err2 libcurl3t64-gnutls libdeflate0 libexpat1 libffi8 libgfortran5 libgnutls30t64 libgssapi-krb5-2 libhts3t64 libhtscodecs2 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap2 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libp11-kit0 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1t64 libtasn1-6 libunistring5 media-types netbase python3 python3-decorator python3-minimal python3-numpy python3-numpy-dev python3-pysam python3-scipy python3.13 python3.13-minimal readline-common 0 upgraded, 49 newly installed, 0 to remove and 0 not upgraded. Need to get 44.2 MB of archives. After this operation, 217 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.5-2 [862 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.5-2 [2224 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.5-1 [27.2 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.5 [12.4 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5+20250216-2 [135 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.5-2 [1956 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.5-2 [757 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.5-1 [10.2 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.5-1 [28.2 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1 [139 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-6 [160 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-6 [2447 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:2.2.4+ds-1 [5096 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.2.1-2 [33.0 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.15.3-1 [16.3 MB] Get:22 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get:32 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.14.1-2 [384 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.23.0+ds-1+b1 [3665 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 fitgcp all 0.0.20150429-5 [3676 kB] Fetched 44.2 MB in 0s (176 MB/s) Selecting previously unselected package libexpat1:amd64. 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.5-2_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.5-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.5-2_amd64.deb ... Unpacking python3.13 (3.13.5-2) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Unpacking fitgcp (0.0.20150429-5) ... Setting up libhtscodecs2:amd64 (1.6.1-2) ... Setting up media-types (13.0.0) ... Setting up libkeyutils1:amd64 (1.6.3-6) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up libcom-err2:amd64 (1.47.2-3+b3) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up libblas3:amd64 (3.12.1-6) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libunistring5:amd64 (1.3-2) ... Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Setting up libncursesw6:amd64 (6.5+20250216-2) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up netbase (6.5) ... Setting up libngtcp2-16:amd64 (1.11.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up readline-common (8.2-6) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up liblapack3:amd64 (3.12.1-6) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libidn2-0:amd64 (2.3.8-2) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up libpython3.13-stdlib:amd64 (3.13.5-2) ... Setting up libpython3-stdlib:amd64 (3.13.5-1) ... Setting up libgnutls30t64:amd64 (3.8.9-3) ... Setting up python3.13 (3.13.5-2) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.5-1) ... Setting up python3-decorator (5.2.1-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up python3-numpy (1:2.2.4+ds-1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up python3-scipy (1.15.3-1) ... Setting up libcurl3t64-gnutls:amd64 (8.14.1-2) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up python3-pysam (0.23.0+ds-1+b1) ... Setting up fitgcp (0.0.20150429-5) ... Processing triggers for libc-bin (2.41-12) ... 0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-get', '-y', 'install', 'fitgcp'] 0m17.2s INFO: Running scripts post_install 0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_install_exceptions'] 0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_install_exceptions'] 0m17.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu'] 0m17.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu'] 0m17.9s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpyuniwnzu to trixie-next 0m17.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main deb http://security.debian.org trixie-security main deb http://deb.debian.org/debian/ trixie-updates main deb http://deb.debian.org/debian/ trixie-proposed-updates main 0m17.9s INFO: Running scripts pre_distupgrade 0m17.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m17.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m17.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_distupgrade_exceptions'] 0m17.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_distupgrade_exceptions'] 0m17.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m18.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m18.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m18.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-get', 'update'] 0m18.8s DUMP: Hit:1 http://deb.debian.org/debian trixie InRelease Get:2 http://security.debian.org trixie-security InRelease [43.4 kB] Get:3 http://deb.debian.org/debian trixie-updates InRelease [47.1 kB] Get:4 http://deb.debian.org/debian trixie-proposed-updates InRelease [55.8 kB] Get:5 http://security.debian.org trixie-security/main amd64 Packages [5304 B] Get:6 http://security.debian.org trixie-security/main Translation-en [6724 B] Get:7 http://deb.debian.org/debian trixie-updates/main amd64 Packages [2432 B] Get:8 http://deb.debian.org/debian trixie-updates/main Translation-en [396 B] Get:9 http://deb.debian.org/debian trixie-proposed-updates/main amd64 Packages [7300 B] Get:10 http://deb.debian.org/debian trixie-proposed-updates/main Translation-en [3288 B] Fetched 172 kB in 0s (1574 kB/s) Reading package lists... 0m18.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-get', 'update'] 0m18.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-get', '-yf', 'dist-upgrade'] 0m19.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-get', '-yf', 'dist-upgrade'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m20.6s DUMP: 5c6a884f0339ba51c78a9d3f50b19f1b - 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-cache', 'show', '--no-all-versions', 'fitgcp'] 0m20.8s DUMP: Package: fitgcp Version: 0.0.20150429-5 Installed-Size: 23164 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3:any, python3-scipy, python3-numpy, python3-pysam Description-en: fitting genome coverage distributions with mixture models Genome coverage, the number of sequencing reads mapped to a position in a genome, is an insightful indicator of irregularities within sequencing experiments. While the average genome coverage is frequently used within algorithms in computational genomics, the complete information available in coverage profiles (i.e. histograms over all coverages) is currently not exploited to its full extent. Thus, biases such as fragmented or erroneous reference genomes often remain unaccounted for. Making this information accessible can improve the quality of sequencing experiments and quantitative analyses. . fitGCP is a framework for fitting mixtures of probability distributions to genome coverage profiles. Besides commonly used distributions, fitGCP uses distributions tailored to account for common artifacts. The mixture models are iteratively fitted based on the Expectation-Maximization algorithm. Description-md5: 6d250046a14f2fb020b753ee88032582 Homepage: http://sourceforge.net/projects/fitgcp/ Section: science Priority: optional Filename: pool/main/f/fitgcp/fitgcp_0.0.20150429-5_all.deb Size: 3675556 MD5sum: a657acb87dccc3c25bda71f1017cd38e SHA256: 307132bcde037065d1602362f025c2d0fbc968351dd522c3d99b228d8ed5e437 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-cache', 'show', '--no-all-versions', 'fitgcp'] 0m20.8s INFO: apt-cache knows about the following packages: fitgcp 0m20.8s INFO: Running scripts pre_install 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_database-server'] 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_database-server'] 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_exceptions'] 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_exceptions'] 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_extras'] 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_extras'] 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-cache', 'policy'] 0m20.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie-proposed-updates/main amd64 Packages release v=13-updates,o=Debian,a=proposed-updates,n=trixie-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian trixie-updates/main amd64 Packages release v=13-updates,o=Debian,a=stable-updates,n=trixie-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org trixie-security/main amd64 Packages release v=13,o=Debian,a=stable-security,n=trixie-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.0,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m20.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-cache', 'policy'] 0m20.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-cache', 'policy', 'fitgcp'] 0m20.9s DUMP: fitgcp: Installed: 0.0.20150429-5 Candidate: 0.0.20150429-5 Version table: *** 0.0.20150429-5 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 100 /var/lib/dpkg/status 0m20.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-cache', 'policy', 'fitgcp'] 0m20.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-get', '-y', 'install', 'fitgcp'] 0m21.4s DUMP: Reading package lists... Building dependency tree... Reading state information... fitgcp is already the newest version (0.0.20150429-5). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m21.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-get', '-y', 'install', 'fitgcp'] 0m21.4s INFO: Running scripts post_install 0m21.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_install_exceptions'] 0m21.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_install_exceptions'] 0m21.4s INFO: Running scripts post_distupgrade 0m21.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m21.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m21.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_distupgrade_exceptions'] 0m21.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_distupgrade_exceptions'] 0m21.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m21.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m21.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m21.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m21.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_distupgrade_zz_backports'] 0m21.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_distupgrade_zz_backports'] 0m21.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu'] 0m22.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu'] 0m22.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu'] 0m23.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu'] 0m23.1s INFO: Running scripts pre_install 0m23.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_database-server'] 0m23.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_database-server'] 0m23.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_exceptions'] 0m23.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_exceptions'] 0m23.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_extras'] 0m23.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_extras'] 0m23.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_foreign_architecture'] 0m23.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_foreign_architecture'] 0m23.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m23.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m23.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-cache', 'policy'] 0m23.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie-proposed-updates/main amd64 Packages release v=13-updates,o=Debian,a=proposed-updates,n=trixie-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian trixie-updates/main amd64 Packages release v=13-updates,o=Debian,a=stable-updates,n=trixie-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org trixie-security/main amd64 Packages release v=13,o=Debian,a=stable-security,n=trixie-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.0,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m23.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-cache', 'policy'] 0m23.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-cache', 'policy', 'fitgcp'] 0m23.3s DUMP: fitgcp: Installed: 0.0.20150429-5 Candidate: 0.0.20150429-5 Version table: *** 0.0.20150429-5 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 100 /var/lib/dpkg/status 0m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-cache', 'policy', 'fitgcp'] 0m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-get', '-y', 'install', 'fitgcp=0.0.20150429-5'] 0m23.9s DUMP: Reading package lists... Building dependency tree... Reading state information... fitgcp is already the newest version (0.0.20150429-5). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-get', '-y', 'install', 'fitgcp=0.0.20150429-5'] 0m23.9s INFO: Running scripts post_install 0m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_install_exceptions'] 0m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_install_exceptions'] 0m24.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu'] 0m24.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu'] 0m24.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', '-ac', '--ignore-obsolete'] 0m26.5s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', '-ac', '--ignore-obsolete'] 0m26.5s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m26.5s DUMP: 0.15.9~deb12u1 0m26.5s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m26.5s INFO: Running adequate version 0.15.9~deb12u1 now. 0m26.5s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'fitgcp'] 0m26.6s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'fitgcp'] 0m26.6s INFO: Running scripts pre_remove 0m26.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m26.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m26.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m26.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m26.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m28.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m28.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m28.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m28.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m28.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m28.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_remove_exceptions'] 0m28.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/pre_remove_exceptions'] 0m28.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m28.4s DUMP: install ok installed apt apt 3.0.3 install ok installed base-files base-files 13.8 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b5 install ok installed bsdutils bsdutils 1:2.41-5 install ok installed coreutils coreutils 9.7-3 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 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 install ok installed findutils findutils 4.10.0-3 install ok installed fitgcp fitgcp 0.0.20150429-5 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 3.0.3 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 libblas3:amd64 libblas3 3.12.1-6 install ok installed libblkid1:amd64 libblkid1 2.41-5 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b7 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 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.2-3+b3 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.14.1-2 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libdeflate0:amd64 libdeflate0 1.23-2 install ok installed libexpat1:amd64 libexpat1 2.7.1-2 install ok installed libffi8:amd64 libffi8 3.4.8-2 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-19 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.9-3 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-5 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed libhts3t64:amd64 libhts3t64 1.21+ds-1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.8-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-6 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-5 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-5 install ok installed liblapack3:amd64 liblapack3 3.12.1-6 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-5 install ok installed libldap2:amd64 libldap2 2.6.10+dfsg-1 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 2.41-5 install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1.1 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.8.0-1 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.11.0-1 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.11.0-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-3 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.13.5-1 install ok installed libpython3.13-minimal:amd64 libpython3.13-minimal 3.13.5-2 install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.5-2 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-6 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b5 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-9 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-9 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 2.41-5 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.5.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.7-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.20.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.7-1 install ok installed libunistring5:amd64 libunistring5 1.3-2 install ok installed libuuid1:amd64 libuuid1 2.41-5 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+really2.41-5 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 media-types media-types 13.0.0 install ok installed mount mount 2.41-5 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 netbase netbase 6.5 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.1-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-6 install ok installed python3 python3 3.13.5-1 install ok installed python3-decorator python3-decorator 5.2.1-2 install ok installed python3-minimal python3-minimal 3.13.5-1 install ok installed python3-numpy python3-numpy 1:2.2.4+ds-1 install ok installed python3-numpy-dev:amd64 python3-numpy-dev 1:2.2.4+ds-1 install ok installed python3-pysam python3-pysam 0.23.0+ds-1+b1 install ok installed python3-scipy python3-scipy 1.15.3-1 install ok installed python3.13 python3.13 3.13.5-2 install ok installed python3.13-minimal python3.13-minimal 3.13.5-2 install ok installed readline-common readline-common 8.2-6 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 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-4 install ok installed util-linux util-linux 2.41-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m28.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m28.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-get', 'remove', '--allow-remove-essential', 'libblas3:amd64', 'libbrotli1:amd64', 'libcom-err2:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'libgnutls30t64:amd64', 'libgssapi-krb5-2:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap2:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libp11-kit0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libunistring5:amd64', 'media-types', 'netbase', 'python3', 'python3-decorator', 'python3-minimal', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-pysam', 'python3-scipy', 'python3.13', 'python3.13-minimal', 'readline-common', 'fitgcp'] 0m30.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: fitgcp libblas3 libbrotli1 libcom-err2 libcurl3t64-gnutls libdeflate0 libexpat1 libffi8 libgfortran5 libgnutls30t64 libgssapi-krb5-2 libhts3t64 libhtscodecs2 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap2 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libp11-kit0 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1t64 libtasn1-6 libunistring5 media-types netbase python3 python3-decorator python3-minimal python3-numpy python3-numpy-dev python3-pysam python3-scipy python3.13 python3.13-minimal readline-common 0 upgraded, 0 newly installed, 49 to remove and 0 not upgraded. After this operation, 217 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 ... 8982 files and directories currently installed.) Removing fitgcp (0.0.20150429-5) ... Removing python3-scipy (1.15.3-1) ... Removing python3-numpy (1:2.2.4+ds-1) ... Removing liblapack3:amd64 (3.12.1-6) ... Removing libblas3:amd64 (3.12.1-6) ... Removing python3-pysam (0.23.0+ds-1+b1) ... Removing libhts3t64:amd64 (1.21+ds-1) ... Removing libcurl3t64-gnutls:amd64 (8.14.1-2) ... Removing libbrotli1:amd64 (1.1.0-2+b7) ... Removing libgssapi-krb5-2:amd64 (1.21.3-5) ... Removing libkrb5-3:amd64 (1.21.3-5) ... Removing libcom-err2:amd64 (1.47.2-3+b3) ... Removing libdeflate0:amd64 (1.23-2) ... Removing python3-decorator (5.2.1-2) ... Removing python3 (3.13.5-1) ... Removing python3.13 (3.13.5-2) ... Removing python3-minimal (3.13.5-1) ... Removing python3.13-minimal (3.13.5-2) ... Removing libexpat1:amd64 (2.7.1-2) ... Removing libpython3-stdlib:amd64 (3.13.5-1) ... Removing libpython3.13-stdlib:amd64 (3.13.5-2) ... find: '/usr/lib/python3': No such file or directory Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Removing libgfortran5:amd64 (14.2.0-19) ... Removing libhtscodecs2:amd64 (1.6.1-2) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... Removing libk5crypto3:amd64 (1.21.3-5) ... Removing libkeyutils1:amd64 (1.6.3-6) ... Removing libkrb5support0:amd64 (1.21.3-5) ... Removing libldap2:amd64 (2.6.10+dfsg-1) ... Removing libncursesw6:amd64 (6.5+20250216-2) ... Removing libnghttp2-14:amd64 (1.64.0-1.1) ... Removing libnghttp3-9:amd64 (1.8.0-1) ... Removing libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Removing libngtcp2-16:amd64 (1.11.0-1) ... Removing libpython3.13-minimal:amd64 (3.13.5-2) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-6) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Removing libssh2-1t64:amd64 (1.11.1-1) ... Removing media-types (13.0.0) ... Removing netbase (6.5) ... Removing python3-numpy-dev:amd64 (1:2.2.4+ds-1) ... Removing readline-common (8.2-6) ... Removing libgnutls30t64:amd64 (3.8.9-3) ... Removing libp11-kit0:amd64 (0.25.5-3) ... Removing libffi8:amd64 (3.4.8-2) ... Removing libidn2-0:amd64 (2.3.8-2) ... Removing libtasn1-6:amd64 (4.20.0-2) ... Removing libunistring5:amd64 (1.3-2) ... Processing triggers for libc-bin (2.41-12) ... 0m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-get', 'remove', '--allow-remove-essential', 'libblas3:amd64', 'libbrotli1:amd64', 'libcom-err2:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'libgnutls30t64:amd64', 'libgssapi-krb5-2:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap2:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libp11-kit0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libunistring5:amd64', 'media-types', 'netbase', 'python3', 'python3-decorator', 'python3-minimal', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-pysam', 'python3-scipy', 'python3.13', 'python3.13-minimal', 'readline-common', 'fitgcp'] 0m30.9s INFO: Running scripts post_remove 0m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_remove_exceptions'] 0m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_remove_exceptions'] 0m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'dpkg', '--purge', 'libblas3:amd64', 'libbrotli1:amd64', 'libcom-err2:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'libgnutls30t64:amd64', 'libgssapi-krb5-2:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap2:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libp11-kit0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libunistring5:amd64', 'media-types', 'netbase', 'python3', 'python3-decorator', 'python3-minimal', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-pysam', 'python3-scipy', 'python3.13', 'python3.13-minimal', 'readline-common'] 0m31.1s DUMP: dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcom-err2 which isn't installed dpkg: warning: ignoring request to remove libcurl3t64-gnutls which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libffi8 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libgnutls30t64 which isn't installed (Reading database ... 4945 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-5) ... dpkg: warning: ignoring request to remove libhts3t64 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libidn2-0 which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove libldap2 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnghttp3-9 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-16 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-crypto-gnutls8 which isn't installed dpkg: warning: ignoring request to remove libp11-kit0 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.13-minimal:amd64 (3.13.5-2) ... dpkg: warning: ignoring request to remove libpython3.13-stdlib which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-6) ... dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libtasn1-6 which isn't installed dpkg: warning: ignoring request to remove libunistring5 which isn't installed Purging configuration files for media-types (13.0.0) ... Purging configuration files for netbase (6.5) ... Purging configuration files for python3 (3.13.5-1) ... dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed Purging configuration files for python3-numpy (1:2.2.4+ds-1) ... dpkg: warning: ignoring request to remove python3-numpy-dev which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3.13 which isn't installed Purging configuration files for python3.13-minimal (3.13.5-2) ... Purging configuration files for readline-common (8.2-6) ... 0m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'dpkg', '--purge', 'libblas3:amd64', 'libbrotli1:amd64', 'libcom-err2:amd64', 'libcurl3t64-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'libgnutls30t64:amd64', 'libgssapi-krb5-2:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap2:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libp11-kit0:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.13-minimal:amd64', 'libpython3.13-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libunistring5:amd64', 'media-types', 'netbase', 'python3', 'python3-decorator', 'python3-minimal', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-pysam', 'python3-scipy', 'python3.13', 'python3.13-minimal', 'readline-common'] 0m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'dpkg', '--purge', 'fitgcp'] 0m31.1s DUMP: dpkg: warning: ignoring request to remove fitgcp which isn't installed 0m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'dpkg', '--purge', 'fitgcp'] 0m31.1s INFO: Running scripts post_purge 0m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_purge_exceptions'] 0m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_purge_exceptions'] 0m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'dpkg', '--purge', '--pending'] 0m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'dpkg', '--purge', '--pending'] 0m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'dpkg', '--remove', '--pending'] 0m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'dpkg', '--remove', '--pending'] 0m31.1s INFO: Running scripts post_test 0m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_test_exceptions'] 0m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'tmp/scripts/post_test_exceptions'] 0m31.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu'] 0m31.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu'] 0m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'dpkg-divert', '--list'] 0m31.5s 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 0m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'dpkg-divert', '--list'] 0m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-get', 'clean'] 0m31.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu', 'apt-get', 'clean'] 0m31.6s DEBUG: Recording chroot state 0m32.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/dev/shm'] 0m32.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/dev/shm'] 0m32.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/dev/console'] 0m32.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/dev/console'] 0m32.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/dev/ptmx'] 0m32.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/dev/ptmx'] 0m32.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/dev/pts'] 0m32.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/dev/pts'] 0m32.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/proc'] 0m32.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu/proc'] 0m32.6s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu'] 0m32.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpyuniwnzu'] 0m32.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpyuniwnzu 0m32.6s INFO: PASS: Upgrading between Debian distributions. 0m32.6s INFO: PASS: All tests. 0m32.6s INFO: piuparts run ends. ret=0 End: 2025-08-12 07:29:00 GMT