Start: 2025-06-19 06:44:12 GMT [stable] Package: bcftools Version: 1.16-1 Installed-Size: 2423 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libhts3 (>= 1.16) Recommends: perl Suggests: python3, python3-numpy, python3-matplotlib, texlive-latex-recommended Description: genomic variant calling and manipulation of VCF/BCF files Homepage: https://samtools.github.io/bcftools/ Description-md5: 2de6efc9fd60536b3eed1acdf68063bd Tag: implemented-in::c, role::program Section: science Priority: optional Filename: pool/main/b/bcftools/bcftools_1.16-1_amd64.deb Size: 692188 MD5sum: 43f2a7e1906a51f1f67be2b45bb79719 SHA256: d6ae8a3e98b601014bfca11184a3b8da1c9a3c003967b71655da8ef7b8d5edf1 [testing] Package: bcftools Version: 1.21-1 Installed-Size: 2716 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libhts3t64 (>= 1.17) Recommends: perl, python3-gffutils, python3-matplotlib Suggests: python3, python3-numpy, texlive-latex-recommended Description: genomic variant calling and manipulation of VCF/BCF files Homepage: https://samtools.github.io/bcftools/ Description-md5: 2de6efc9fd60536b3eed1acdf68063bd Tag: implemented-in::c, role::program Section: science Priority: optional Filename: pool/main/b/bcftools/bcftools_1.21-1_amd64.deb Size: 783620 MD5sum: 426ae4ab62b2fd8e268186c35f81be66 SHA256: 764405ce5c48f8779313753b0f3c9d791b46081a7d2f88a019e96691019c902b [sid] Package: bcftools Version: 1.21-1 Installed-Size: 2716 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libhts3t64 (>= 1.17) Recommends: perl, python3-gffutils, python3-matplotlib Suggests: python3, python3-numpy, texlive-latex-recommended Description: genomic variant calling and manipulation of VCF/BCF files Homepage: https://samtools.github.io/bcftools/ Description-md5: 2de6efc9fd60536b3eed1acdf68063bd Tag: implemented-in::c, role::program Section: science Priority: optional Filename: pool/main/b/bcftools/bcftools_1.21-1_amd64.deb Size: 783620 MD5sum: 426ae4ab62b2fd8e268186c35f81be66 SHA256: 764405ce5c48f8779313753b0f3c9d791b46081a7d2f88a019e96691019c902b 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/bookworm-merged-usr_amd64.tar.gz -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt bcftools=1.21-1 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/bookworm-merged-usr_amd64.tar.gz -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt bcftools=1.21-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-35-amd64 #1 SMP Debian 5.10.237-1 (2025-05-19) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpco1e0rqm 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpco1e0rqm 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm/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/tmpco1e0rqm/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/tmpco1e0rqm/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm 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/tmpco1e0rqm/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'apt-get', 'update'] 0m0.7s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'apt-get', 'update'] 0m0.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'apt-get', '-yf', 'dist-upgrade'] 0m0.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m0.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'apt-get', '-yf', 'dist-upgrade'] 0m0.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.1s DUMP: 9ec3d089399c2f7b28e5238096956c7d - 0m1.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.1s INFO: Running scripts post_setup 0m1.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/post_setup_dummy_users'] 0m1.5s 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 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/post_setup_dummy_users'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/post_setup_forbid_home'] 0m1.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/post_setup_forbid_home'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/post_setup_force-unsafe-io'] 0m1.6s 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' 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/post_setup_force-unsafe-io'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/post_setup_minimize'] 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/post_setup_minimize'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/post_setup_squeeze-backports'] 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/post_setup_squeeze-backports'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/post_setup_zz_backports'] 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/post_setup_zz_backports'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m1.6s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u11 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b8 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u3 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u2 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14+deb12u1 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u10 install ok installed libc6:amd64 libc6 2.36-9+deb12u10 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4+deb12u1 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14+deb12u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-1 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u3 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+deb12u3 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14+deb12u1 install ok installed libsystemd0:amd64 libsystemd0 252.36-1~deb12u1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2+deb12u1 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.36-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u3 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+deb12u1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+deb12u3 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+deb12u1 install ok installed perl-base perl-base 5.36.0-7+deb12u2 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2025b-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u3 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u3 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m1.6s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat 0m1.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm'] 0m1.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm'] 0m1.8s INFO: Running scripts is_testable 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/is_testable_uninstallable'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/is_testable_uninstallable'] 0m1.8s INFO: Running scripts pre_test 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_test_exceptions'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_test_exceptions'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_test_root_password'] 0m1.8s DUMP: New password: Retype new password: passwd: password updated successfully 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_test_root_password'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'apt-cache', 'show', '--no-all-versions', 'bcftools'] 0m1.9s DUMP: Package: bcftools Version: 1.16-1 Installed-Size: 2423 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libhts3 (>= 1.16) Recommends: perl Suggests: python3, python3-numpy, python3-matplotlib, texlive-latex-recommended Description-en: genomic variant calling and manipulation of VCF/BCF files BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Description-md5: 2de6efc9fd60536b3eed1acdf68063bd Homepage: https://samtools.github.io/bcftools/ Tag: implemented-in::c, role::program Section: science Priority: optional Filename: pool/main/b/bcftools/bcftools_1.16-1_amd64.deb Size: 692188 MD5sum: 43f2a7e1906a51f1f67be2b45bb79719 SHA256: d6ae8a3e98b601014bfca11184a3b8da1c9a3c003967b71655da8ef7b8d5edf1 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'apt-cache', 'show', '--no-all-versions', 'bcftools'] 0m1.9s INFO: apt-cache knows about the following packages: bcftools 0m1.9s INFO: Running scripts pre_install 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_install_database-server'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_install_database-server'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_install_exceptions'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_install_exceptions'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_install_extras'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_install_extras'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_install_foreign_architecture'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_install_foreign_architecture'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'apt-cache', 'policy'] 0m2.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.11,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'apt-cache', 'policy'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'apt-cache', 'policy', 'bcftools'] 0m2.0s DUMP: bcftools: Installed: (none) Candidate: 1.16-1 Version table: 1.16-1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'apt-cache', 'policy', 'bcftools'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'apt-get', '-y', 'install', 'bcftools'] 0m2.9s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: libbrotli1 libcurl3-gnutls libdeflate0 libgssapi-krb5-2 libhts3 libhtscodecs2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 libnghttp2-14 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1 libssl3 Suggested packages: python3 python3-numpy python3-matplotlib texlive-latex-recommended krb5-doc krb5-user Recommended packages: perl ca-certificates krb5-locales libldap-common publicsuffix libsasl2-modules The following NEW packages will be installed: bcftools libbrotli1 libcurl3-gnutls libdeflate0 libgssapi-krb5-2 libhts3 libhtscodecs2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 libnghttp2-14 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1 libssl3 0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded. Need to get 5179 kB of archives. After this operation, 15.4 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u3 [32.8 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u3 [78.9 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:5 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.16-1~deb12u1 [2026 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u3 [332 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u3 [135 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u2 [73.0 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-10+deb12u12 [386 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 bcftools amd64 1.16-1 [692 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 5179 kB in 0s (48.0 MB/s) Selecting previously unselected package libbrotli1:amd64. (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 ... 6093 files and directories currently installed.) Preparing to unpack .../00-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../01-libkrb5support0_1.20.1-2+deb12u3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-2+deb12u3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../02-libk5crypto3_1.20.1-2+deb12u3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-2+deb12u3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../03-libkeyutils1_1.6.3-2_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-2) ... Selecting previously unselected package libssl3:amd64. Preparing to unpack .../04-libssl3_3.0.16-1~deb12u1_amd64.deb ... Unpacking libssl3:amd64 (3.0.16-1~deb12u1) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../05-libkrb5-3_1.20.1-2+deb12u3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-2+deb12u3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../06-libgssapi-krb5-2_1.20.1-2+deb12u3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-2+deb12u3) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../07-libsasl2-modules-db_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../08-libsasl2-2_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../09-libldap-2.5-0_2.5.13+dfsg-5_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../10-libnghttp2-14_1.52.0-1+deb12u2_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.52.0-1+deb12u2) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../11-libpsl5_0.21.2-1_amd64.deb ... Unpacking libpsl5:amd64 (0.21.2-1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../12-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../13-libssh2-1_1.10.0-3+b1_amd64.deb ... Unpacking libssh2-1:amd64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../14-libcurl3-gnutls_7.88.1-10+deb12u12_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.88.1-10+deb12u12) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../15-libdeflate0_1.14-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.14-1) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../16-libhtscodecs2_1.3.0-4_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.3.0-4) ... Selecting previously unselected package libhts3:amd64. Preparing to unpack .../17-libhts3_1.16+ds-3_amd64.deb ... Unpacking libhts3:amd64 (1.16+ds-3) ... Selecting previously unselected package bcftools. Preparing to unpack .../18-bcftools_1.16-1_amd64.deb ... Unpacking bcftools (1.16-1) ... Setting up libhtscodecs2:amd64 (1.3.0-4) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libssl3:amd64 (3.0.16-1~deb12u1) ... Setting up libnghttp2-14:amd64 (1.52.0-1+deb12u2) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u3) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u3) ... Setting up libcurl3-gnutls:amd64 (7.88.1-10+deb12u12) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up bcftools (1.16-1) ... Processing triggers for libc-bin (2.36-9+deb12u10) ... 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'apt-get', '-y', 'install', 'bcftools'] 0m2.9s INFO: Running scripts post_install 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/post_install_exceptions'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/post_install_exceptions'] 0m2.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm'] 0m3.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm'] 0m3.1s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpco1e0rqm to testing 0m3.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m3.1s INFO: Running scripts pre_distupgrade 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_distupgrade_exceptions'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_distupgrade_exceptions'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'apt-get', 'update'] 60m3.2s ERROR: Terminating command due to excessive runtime 60m3.7s DUMP: ***** Command was terminated after exceeding runtime limit (3600 s) ***** 60m3.7s ERROR: Command failed (status=-15): ['chroot', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm', 'apt-get', 'update'] ***** Command was terminated after exceeding runtime limit (3600 s) ***** 60m3.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm/dev/shm'] 60m3.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm/dev/shm'] 60m3.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm/dev/console'] 60m3.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm/dev/console'] 60m3.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm/dev/ptmx'] 60m3.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm/dev/ptmx'] 60m3.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm/dev/pts'] 60m3.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm/dev/pts'] 60m3.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm/proc'] 60m3.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm/proc'] 60m3.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm'] 60m4.0s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpco1e0rqm'] 60m4.0s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpco1e0rqm 60m4.0s ERROR: piuparts run ends. ret=1 End: 2025-06-19 07:44:16 GMT