Start: 2022-03-30 06:26:22 GMT [testing] Package: parallel-fastq-dump Version: 0.6.7-2 Installed-Size: 24 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, sra-toolkit Description: parallel fastq-dump wrapper Homepage: https://github.com/rvalieris/parallel-fastq-dump Description-md5: 12a1cac080addde82a2286cafbd92156 Section: science Priority: optional Filename: pool/main/p/parallel-fastq-dump/parallel-fastq-dump_0.6.7-2_amd64.deb Size: 5552 MD5sum: 877d044b1e41cd6445336ebb9c0da419 SHA256: e68596d40c1c184161d38eef62789937134ca5a162b6d96011bfc51ff8963b4c [sid] Package: parallel-fastq-dump Version: 0.6.7-3 Installed-Size: 24 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, sra-toolkit Description: parallel fastq-dump wrapper Homepage: https://github.com/rvalieris/parallel-fastq-dump Description-md5: 12a1cac080addde82a2286cafbd92156 Section: science Priority: optional Filename: pool/main/p/parallel-fastq-dump/parallel-fastq-dump_0.6.7-3_amd64.deb Size: 5616 MD5sum: da2dc8c27b50e6a20548a7bbd6851948 SHA256: 6ba8b32a21be2485b7f02d4ac2ec25291f10256c19b1e2f48d8d6da6cdcdf04f Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt parallel-fastq-dump=0.6.7-3 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.4 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt parallel-fastq-dump=0.6.7-3 0m0.0s INFO: Running on: Linux piu-slave-conova-01 4.19.0-20-amd64 #1 SMP Debian 4.19.235-1 (2022-03-17) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpl6stzco1 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpl6stzco1 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m1.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/proc'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/proc'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/dev/pts'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/dev/pts'] 0m1.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/dev/ptmx'] 0m1.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/dev/ptmx'] 0m1.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/dev/console'] 0m1.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/dev/console'] 0m1.6s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/dev/shm'] 0m1.6s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/dev/shm'] 0m1.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m1.6s DEBUG: Created policy-rc.d and chmodded it. 0m1.6s DEBUG: Created resolv.conf. 0m1.6s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpl6stzco1/tmp/scripts/ 0m1.6s INFO: Running scripts post_chroot_unpack 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-get', 'update'] 0m3.4s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [130 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8363 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [5721 kB] Fetched 14.2 MB in 1s (10.5 MB/s) Reading package lists... 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-get', 'update'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-get', '-yf', 'dist-upgrade'] 0m3.7s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-get', '-yf', 'dist-upgrade'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.2s DUMP: c943e6cba2e673a06c9d63adec894b45 - 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.2s INFO: Running scripts post_setup 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_setup_dummy_users'] 0m4.8s DUMP: useradd warning: dummy1000's uid 1000 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1001's uid 1001 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1002's uid 1002 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1003's uid 1003 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1004's uid 1004 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1005's uid 1005 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1006's uid 1006 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1007's uid 1007 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1008's uid 1008 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1009's uid 1009 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1010's uid 1010 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_setup_dummy_users'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', '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/tmpl6stzco1', 'tmp/scripts/post_setup_forbid_home'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.8s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_setup_minimize'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_setup_minimize'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_setup_zz_backports'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_setup_zz_backports'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.8s DUMP: install ok installed adduser adduser 3.121 install ok installed apt apt 2.4.3 install ok installed base-files base-files 12.2 install ok installed base-passwd base-passwd 3.5.52 install ok installed bash bash 5.1-6 install ok installed bsdutils bsdutils 1:2.37.3-1+b1 install ok installed coreutils coreutils 8.32-4.1 install ok installed dash dash 0.5.11+git20210903+057cd650a4ed-8 install ok installed debconf debconf 1.5.79 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 5.7-0.1 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.21.2 install ok installed e2fsprogs e2fsprogs 1.46.5-2 install ok installed findutils findutils 4.9.0-2 install ok installed gcc-12-base:amd64 gcc-12-base 12-20220319-1 install ok installed gpgv gpgv 2.2.27-3+b1 install ok installed grep grep 3.7-1 install ok installed gzip gzip 1.10-4 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.62 install ok installed libacl1:amd64 libacl1 2.3.1-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.4.3 install ok installed libattr1:amd64 libattr1 1:2.5.1-1 install ok installed libaudit-common libaudit-common 1:3.0.7-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.7-1+b1 install ok installed libblkid1:amd64 libblkid1 2.37.3-1+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5 install ok installed libc-bin libc-bin 2.33-7 install ok installed libc6:amd64 libc6 2.33-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.5-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.27-1.1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.261 install ok installed libext2fs2:amd64 libext2fs2 1.46.5-2 install ok installed libffi8:amd64 libffi8 3.4.2-4 install ok installed libgcc-s1:amd64 libgcc-s1 12-20220319-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.9.4-5 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-3 install ok installed libgnutls30:amd64 libgnutls30 3.7.3-4+b1 install ok installed libgpg-error0:amd64 libgpg-error0 1.43-3 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.19.2-2+b1 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.2-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.19.2-2+b1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.19.2-2+b1 install ok installed libkrb5support0:amd64 libkrb5support0 1.19.2-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2 install ok installed libmount1:amd64 libmount1 2.37.3-1+b1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.0-6 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-11 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-11 install ok installed libpam-runtime libpam-runtime 1.4.0-11 install ok installed libpam0g:amd64 libpam0g 1.4.0-11 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.39-3 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.3-2 install ok installed libselinux1:amd64 libselinux1 3.3-1+b2 install ok installed libsemanage-common libsemanage-common 3.3-1 install ok installed libsemanage2:amd64 libsemanage2 3.3-1+b2 install ok installed libsepol2:amd64 libsepol2 3.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.37.3-1+b1 install ok installed libss2:amd64 libss2 1.46.5-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1n-1 install ok installed libstdc++6:amd64 libstdc++6 12-20220319-1 install ok installed libsystemd0:amd64 libsystemd0 250.4-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.18.0-4 install ok installed libtinfo6:amd64 libtinfo6 6.3-2 install ok installed libtirpc-common libtirpc-common 1.3.2-2 install ok installed libtirpc3:amd64 libtirpc3 1.3.2-2 install ok installed libudev1:amd64 libudev1 250.4-1 install ok installed libunistring2:amd64 libunistring2 1.0-1 install ok installed libuuid1:amd64 libuuid1 2.37.3-1+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.4.9+dfsg-1 install ok installed login login 1:4.11.1+dfsg1-2 install ok installed logsave logsave 1.46.5-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-3+b1 install ok installed mount mount 2.37.3-1+b1 install ok installed ncurses-base ncurses-base 6.3-2 install ok installed ncurses-bin ncurses-bin 6.3-2 install ok installed passwd passwd 1:4.11.1+dfsg1-2 install ok installed perl-base perl-base 5.34.0-3 install ok installed sed sed 4.8-1 install ok installed sysvinit-utils sysvinit-utils 3.01-1 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2022a-1 install ok installed util-linux util-linux 2.37.3-1+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.8s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m4.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6stzco1'] 0m5.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6stzco1'] 0m5.1s INFO: Running scripts is_testable 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/is_testable_uninstallable'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/is_testable_uninstallable'] 0m5.1s INFO: Running scripts pre_test 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_test_exceptions'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_test_exceptions'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_test_root_password'] 0m5.1s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_test_root_password'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-cache', 'show', '--no-all-versions', 'parallel-fastq-dump'] 0m5.3s DUMP: Package: parallel-fastq-dump Version: 0.6.7-2 Installed-Size: 24 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, sra-toolkit Description-en: parallel fastq-dump wrapper NCBI fastq-dump can be very slow sometimes, even if you have the resources (network, IO, CPU) to go faster, even if you already downloaded the sra file. This tool speeds up the process by dividing the work into multiple threads. . This is possible because fastq-dump have options (-N and -X) to query specific ranges of the sra file, this tool works by dividing the work into the requested number of threads, running multiple fastq-dump in parallel and concatenating the results back together, as if you had just executed a plain fastq-dump call. Description-md5: 12a1cac080addde82a2286cafbd92156 Homepage: https://github.com/rvalieris/parallel-fastq-dump Section: science Priority: optional Filename: pool/main/p/parallel-fastq-dump/parallel-fastq-dump_0.6.7-2_amd64.deb Size: 5552 MD5sum: 877d044b1e41cd6445336ebb9c0da419 SHA256: e68596d40c1c184161d38eef62789937134ca5a162b6d96011bfc51ff8963b4c 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-cache', 'show', '--no-all-versions', 'parallel-fastq-dump'] 0m5.3s INFO: apt-cache knows about the following packages: parallel-fastq-dump 0m5.3s INFO: Running scripts pre_install 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_database-server'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_database-server'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_exceptions'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_exceptions'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_extras'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_extras'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-cache', 'policy'] 0m5.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release o=Debian,a=testing,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-cache', 'policy'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-cache', 'policy', 'parallel-fastq-dump'] 0m5.4s DUMP: parallel-fastq-dump: Installed: (none) Candidate: 0.6.7-2 Version table: 0.6.7-2 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-cache', 'policy', 'parallel-fastq-dump'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-get', '-y', 'install', 'parallel-fastq-dump'] 0m10.2s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: libaec0 libbrotli1 libcurl4 libexpat1 libfuse2 libhdf5-103-1 libicu67 libkdf5-2 libldap-2.5-0 libmagic-mgc libmagic1 libmbedcrypto7 libmbedtls-dev libmbedtls14 libmbedx509-1 libmpdec3 libncbi-vdb2 libncbi-wvdb2 libncursesw6 libnghttp2-14 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libsz2 libxml2 media-types python3 python3-minimal python3.9 python3.9-minimal readline-common sra-toolkit Suggested packages: fuse file libmbedtls-doc python3-doc python3-tk python3-venv python3.9-venv python3.9-doc binutils binfmt-support readline-doc Recommended packages: ca-certificates libldap-common libgpm2 publicsuffix libsasl2-modules med-config The following NEW packages will be installed: libaec0 libbrotli1 libcurl4 libexpat1 libfuse2 libhdf5-103-1 libicu67 libkdf5-2 libldap-2.5-0 libmagic-mgc libmagic1 libmbedcrypto7 libmbedtls-dev libmbedtls14 libmbedx509-1 libmpdec3 libncbi-vdb2 libncbi-wvdb2 libncursesw6 libnghttp2-14 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libsz2 libxml2 media-types parallel-fastq-dump python3 python3-minimal python3.9 python3.9-minimal readline-common sra-toolkit 0 upgraded, 40 newly installed, 0 to remove and 0 not upgraded. Need to get 27.9 MB of archives. After this operation, 101 MB of additional disk space will be used. 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Preparing to unpack .../26-parallel-fastq-dump_0.6.7-2_amd64.deb ... Unpacking parallel-fastq-dump (0.6.7-2) ... Setting up media-types (7.0.0) ... Setting up libpsl5:amd64 (0.21.0-1.2) ... Setting up libicu67:amd64 (67.1-7) ... Setting up libmagic-mgc (1:5.41-2) ... Setting up libbrotli1:amd64 (1.0.9-2+b3) ... Setting up libsqlite3-0:amd64 (3.38.1-1) ... Setting up libnghttp2-14:amd64 (1.43.0-1) ... Setting up libmagic1:amd64 (1:5.41-2) ... Setting up libfuse2:amd64 (2.9.9-5) ... Setting up libaec0:amd64 (1.0.6-1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-2+b1) ... Setting up libmbedcrypto7:amd64 (2.28.0-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncursesw6:amd64 (6.3-2) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-2+b1) ... Setting up libmpdec3:amd64 (2.5.1-2) ... Setting up libssh2-1:amd64 (1.10.0-3) ... Setting up readline-common (8.1.2-1) ... Setting up libxml2:amd64 (2.9.13+dfsg-1) ... Setting up libsz2:amd64 (1.0.6-1) ... Setting up libmbedx509-1:amd64 (2.28.0-1) ... Setting up libmbedtls14:amd64 (2.28.0-1) ... Setting up libreadline8:amd64 (8.1.2-1) ... Setting up libmbedtls-dev:amd64 (2.28.0-1) ... Setting up libncbi-vdb2 (2.11.2+dfsg-4+b1) ... Setting up libldap-2.5-0:amd64 (2.5.11+dfsg-1) ... Setting up libncbi-wvdb2 (2.11.2+dfsg-4+b1) ... Setting up libcurl4:amd64 (7.82.0-2) ... Setting up libpython3.9-stdlib:amd64 (3.9.12-1) ... Setting up libpython3-stdlib:amd64 (3.9.8-1) ... Setting up libhdf5-103-1:amd64 (1.10.7+repack-4) ... Setting up python3.9 (3.9.12-1) ... Setting up python3 (3.9.8-1) ... Setting up libkdf5-2 (2.11.2+dfsg-4+b1) ... Setting up sra-toolkit (2.11.3+dfsg-1) ... Setting up parallel-fastq-dump (0.6.7-2) ... Processing triggers for libc-bin (2.33-7) ... 0m10.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-get', '-y', 'install', 'parallel-fastq-dump'] 0m10.2s INFO: Running scripts post_install 0m10.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_install_exceptions'] 0m10.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_install_exceptions'] 0m10.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6stzco1'] 0m10.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6stzco1'] 0m10.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpl6stzco1 to sid 0m10.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m10.5s INFO: Running scripts pre_distupgrade 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_distupgrade_exceptions'] 0m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_distupgrade_exceptions'] 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-get', 'update'] 0m14.6s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [165 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9127 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6769 kB] Fetched 16.1 MB in 3s (5216 kB/s) Reading package lists... 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-get', 'update'] 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-get', '-yf', 'dist-upgrade'] 0m17.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libpython3.9-minimal libpython3.9-stdlib python3.9 python3.9-minimal Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libpython3.10-minimal libpython3.10-stdlib python3.10 python3.10-minimal The following packages will be upgraded: dpkg libcap-ng0 libexpat1 libmagic-mgc libmagic1 libpython3-stdlib libsqlite3-0 parallel-fastq-dump python3 python3-minimal zlib1g 11 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 9174 kB of archives. After this operation, 19.7 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.21.6 [2555 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libpython3.10-minimal amd64 3.10.4-1 [823 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.4.8-1 [109 kB] Get:4 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.2.11.dfsg-4 [91.6 kB] Get:5 http://deb.debian.org/debian sid/main amd64 python3.10-minimal amd64 3.10.4-1 [1984 kB] Get:6 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.10.4-1 [38.6 kB] Get:7 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.10.4-1 [38.1 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.38.2-1 [829 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libpython3.10-stdlib amd64 3.10.4-1 [1704 kB] Get:10 http://deb.debian.org/debian sid/main amd64 python3.10 amd64 3.10.4-1 [536 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.10.4-1 [21.7 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.7.9-2.2+b2 [14.7 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libmagic-mgc amd64 1:5.41-3 [295 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libmagic1 amd64 1:5.41-3 [130 kB] Get:15 http://deb.debian.org/debian sid/main amd64 parallel-fastq-dump amd64 0.6.7-3 [5616 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 9174 kB in 0s (95.3 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 7875 files and directories currently installed.) Preparing to unpack .../archives/dpkg_1.21.6_amd64.deb ... Unpacking dpkg (1.21.6) over (1.21.2) ... Setting up dpkg (1.21.6) ... Selecting previously unselected package libpython3.10-minimal: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 ... 7875 files and directories currently installed.) Preparing to unpack .../libpython3.10-minimal_3.10.4-1_amd64.deb ... Unpacking libpython3.10-minimal:amd64 (3.10.4-1) ... Preparing to unpack .../libexpat1_2.4.8-1_amd64.deb ... Unpacking libexpat1:amd64 (2.4.8-1) over (2.4.7-1) ... Preparing to unpack .../zlib1g_1%3a1.2.11.dfsg-4_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.11.dfsg-4) over (1:1.2.11.dfsg-2) ... Setting up zlib1g:amd64 (1:1.2.11.dfsg-4) ... Selecting previously unselected package python3.10-minimal. (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 ... 8160 files and directories currently installed.) Preparing to unpack .../python3.10-minimal_3.10.4-1_amd64.deb ... Unpacking python3.10-minimal (3.10.4-1) ... Setting up libpython3.10-minimal:amd64 (3.10.4-1) ... Setting up libexpat1:amd64 (2.4.8-1) ... Setting up python3.10-minimal (3.10.4-1) ... (Reading database ... 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Unpacking libpython3.10-stdlib:amd64 (3.10.4-1) ... Selecting previously unselected package python3.10. Preparing to unpack .../3-python3.10_3.10.4-1_amd64.deb ... Unpacking python3.10 (3.10.4-1) ... Preparing to unpack .../4-libpython3-stdlib_3.10.4-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.10.4-1) over (3.9.8-1) ... Preparing to unpack .../5-libcap-ng0_0.7.9-2.2+b2_amd64.deb ... Unpacking libcap-ng0:amd64 (0.7.9-2.2+b2) over (0.7.9-2.2+b1) ... Setting up libcap-ng0:amd64 (0.7.9-2.2+b2) ... (Reading database ... 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Setting up libsqlite3-0:amd64 (3.38.2-1) ... Setting up libmagic1:amd64 (1:5.41-3) ... Setting up libpython3.10-stdlib:amd64 (3.10.4-1) ... Setting up libpython3-stdlib:amd64 (3.10.4-1) ... Setting up python3.10 (3.10.4-1) ... Setting up python3 (3.10.4-1) ... Setting up parallel-fastq-dump (0.6.7-3) ... Processing triggers for libc-bin (2.33-7) ... 0m17.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-get', '-yf', 'dist-upgrade'] 0m17.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.3s DUMP: 199af2724e1a0f153f1ad5230aba62e8 - 0m18.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-cache', 'show', '--no-all-versions', 'parallel-fastq-dump'] 0m18.6s DUMP: Package: parallel-fastq-dump Version: 0.6.7-3 Installed-Size: 24 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3:any, sra-toolkit Description-en: parallel fastq-dump wrapper NCBI fastq-dump can be very slow sometimes, even if you have the resources (network, IO, CPU) to go faster, even if you already downloaded the sra file. This tool speeds up the process by dividing the work into multiple threads. . This is possible because fastq-dump have options (-N and -X) to query specific ranges of the sra file, this tool works by dividing the work into the requested number of threads, running multiple fastq-dump in parallel and concatenating the results back together, as if you had just executed a plain fastq-dump call. Description-md5: 12a1cac080addde82a2286cafbd92156 Homepage: https://github.com/rvalieris/parallel-fastq-dump Section: science Priority: optional Filename: pool/main/p/parallel-fastq-dump/parallel-fastq-dump_0.6.7-3_amd64.deb Size: 5616 MD5sum: da2dc8c27b50e6a20548a7bbd6851948 SHA256: 6ba8b32a21be2485b7f02d4ac2ec25291f10256c19b1e2f48d8d6da6cdcdf04f 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-cache', 'show', '--no-all-versions', 'parallel-fastq-dump'] 0m18.6s INFO: apt-cache knows about the following packages: parallel-fastq-dump 0m18.6s INFO: Running scripts pre_install 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_database-server'] 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_database-server'] 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_exceptions'] 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_exceptions'] 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_extras'] 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_extras'] 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-cache', 'policy'] 0m18.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-cache', 'policy'] 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-cache', 'policy', 'parallel-fastq-dump'] 0m18.7s DUMP: parallel-fastq-dump: Installed: 0.6.7-3 Candidate: 0.6.7-3 Version table: *** 0.6.7-3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-cache', 'policy', 'parallel-fastq-dump'] 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-get', '-y', 'install', 'parallel-fastq-dump'] 0m19.2s DUMP: Reading package lists... Building dependency tree... Reading state information... parallel-fastq-dump is already the newest version (0.6.7-3). The following packages were automatically installed and are no longer required: libpython3.9-minimal libpython3.9-stdlib python3.9 python3.9-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-get', '-y', 'install', 'parallel-fastq-dump'] 0m19.2s INFO: Running scripts post_install 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_install_exceptions'] 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_install_exceptions'] 0m19.2s INFO: Running scripts post_distupgrade 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_distupgrade_exceptions'] 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_distupgrade_exceptions'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_distupgrade_zz_backports'] 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_distupgrade_zz_backports'] 0m19.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6stzco1'] 0m19.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6stzco1'] 0m19.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6stzco1'] 0m20.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6stzco1'] 0m20.5s INFO: Running scripts pre_install 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_database-server'] 0m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_database-server'] 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_exceptions'] 0m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_exceptions'] 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_extras'] 0m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_extras'] 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-cache', 'policy'] 0m20.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-cache', 'policy'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-cache', 'policy', 'parallel-fastq-dump'] 0m20.6s DUMP: parallel-fastq-dump: Installed: 0.6.7-3 Candidate: 0.6.7-3 Version table: *** 0.6.7-3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-cache', 'policy', 'parallel-fastq-dump'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-get', '-y', 'install', 'parallel-fastq-dump=0.6.7-3'] 0m21.1s DUMP: Reading package lists... Building dependency tree... Reading state information... parallel-fastq-dump is already the newest version (0.6.7-3). The following packages were automatically installed and are no longer required: libpython3.9-minimal libpython3.9-stdlib python3.9 python3.9-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-get', '-y', 'install', 'parallel-fastq-dump=0.6.7-3'] 0m21.1s INFO: Running scripts post_install 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_install_exceptions'] 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_install_exceptions'] 0m21.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6stzco1'] 0m21.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6stzco1'] 0m22.0s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', '-ac', '--ignore-obsolete'] 0m22.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', '-ac', '--ignore-obsolete'] 0m22.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m22.9s DUMP: 0.15.2 0m22.9s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m22.9s INFO: Running adequate version 0.15.2 now. 0m22.9s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'parallel-fastq-dump'] 0m22.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'parallel-fastq-dump'] 0m22.9s INFO: Running scripts pre_remove 0m22.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m22.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m22.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m22.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m22.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_remove_exceptions'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/pre_remove_exceptions'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m23.7s DUMP: install ok installed adduser adduser 3.121 install ok installed apt apt 2.4.3 install ok installed base-files base-files 12.2 install ok installed base-passwd base-passwd 3.5.52 install ok installed bash bash 5.1-6 install ok installed bsdutils bsdutils 1:2.37.3-1+b1 install ok installed coreutils coreutils 8.32-4.1 install ok installed dash dash 0.5.11+git20210903+057cd650a4ed-8 install ok installed debconf debconf 1.5.79 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 5.7-0.1 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.21.6 install ok installed e2fsprogs e2fsprogs 1.46.5-2 install ok installed findutils findutils 4.9.0-2 install ok installed gcc-12-base:amd64 gcc-12-base 12-20220319-1 install ok installed gpgv gpgv 2.2.27-3+b1 install ok installed grep grep 3.7-1 install ok installed gzip gzip 1.10-4 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.62 install ok installed libacl1:amd64 libacl1 2.3.1-1 install ok installed libaec0:amd64 libaec0 1.0.6-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.4.3 install ok installed libattr1:amd64 libattr1 1:2.5.1-1 install ok installed libaudit-common libaudit-common 1:3.0.7-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.7-1+b1 install ok installed libblkid1:amd64 libblkid1 2.37.3-1+b1 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5 install ok installed libc-bin libc-bin 2.33-7 install ok installed libc6:amd64 libc6 2.33-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b2 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.5-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.27-1.1 install ok installed libcurl4:amd64 libcurl4 7.82.0-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.261 install ok installed libexpat1:amd64 libexpat1 2.4.8-1 install ok installed libext2fs2:amd64 libext2fs2 1.46.5-2 install ok installed libffi8:amd64 libffi8 3.4.2-4 install ok installed libfuse2:amd64 libfuse2 2.9.9-5 install ok installed libgcc-s1:amd64 libgcc-s1 12-20220319-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.9.4-5 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-3 install ok installed libgnutls30:amd64 libgnutls30 3.7.3-4+b1 install ok installed libgpg-error0:amd64 libgpg-error0 1.43-3 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.19.2-2+b1 install ok installed libhdf5-103-1:amd64 libhdf5-103-1 1.10.7+repack-4 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libicu67:amd64 libicu67 67.1-7 install ok installed libidn2-0:amd64 libidn2-0 2.3.2-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.19.2-2+b1 install ok installed libkdf5-2 libkdf5-2 2.11.2+dfsg-4+b1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.19.2-2+b1 install ok installed libkrb5support0:amd64 libkrb5support0 1.19.2-2+b1 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.11+dfsg-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2 install ok installed libmagic-mgc libmagic-mgc 1:5.41-3 install ok installed libmagic1:amd64 libmagic1 1:5.41-3 install ok installed libmbedcrypto7:amd64 libmbedcrypto7 2.28.0-1 install ok installed libmbedtls-dev:amd64 libmbedtls-dev 2.28.0-1 install ok installed libmbedtls14:amd64 libmbedtls14 2.28.0-1 install ok installed libmbedx509-1:amd64 libmbedx509-1 2.28.0-1 install ok installed libmount1:amd64 libmount1 2.37.3-1+b1 install ok installed libmpdec3:amd64 libmpdec3 2.5.1-2 install ok installed libncbi-vdb2 libncbi-vdb2 2.11.2+dfsg-4+b1 install ok installed libncbi-wvdb2 libncbi-wvdb2 2.11.2+dfsg-4+b1 install ok installed libncursesw6:amd64 libncursesw6 6.3-2 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.43.0-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.0-6 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-11 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-11 install ok installed libpam-runtime libpam-runtime 1.4.0-11 install ok installed libpam0g:amd64 libpam0g 1.4.0-11 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.39-3 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libpsl5:amd64 libpsl5 0.21.0-1.2 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.10.4-1 install ok installed libpython3.10-minimal:amd64 libpython3.10-minimal 3.10.4-1 install ok installed libpython3.10-stdlib:amd64 libpython3.10-stdlib 3.10.4-1 install ok installed libpython3.9-minimal:amd64 libpython3.9-minimal 3.9.12-1 install ok installed libpython3.9-stdlib:amd64 libpython3.9-stdlib 3.9.12-1 install ok installed libreadline8:amd64 libreadline8 8.1.2-1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg-2+b1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg-2+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.3-2 install ok installed libselinux1:amd64 libselinux1 3.3-1+b2 install ok installed libsemanage-common libsemanage-common 3.3-1 install ok installed libsemanage2:amd64 libsemanage2 3.3-1+b2 install ok installed libsepol2:amd64 libsepol2 3.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.37.3-1+b1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.38.2-1 install ok installed libss2:amd64 libss2 1.46.5-2 install ok installed libssh2-1:amd64 libssh2-1 1.10.0-3 install ok installed libssl1.1:amd64 libssl1.1 1.1.1n-1 install ok installed libstdc++6:amd64 libstdc++6 12-20220319-1 install ok installed libsystemd0:amd64 libsystemd0 250.4-1 install ok installed libsz2:amd64 libsz2 1.0.6-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.18.0-4 install ok installed libtinfo6:amd64 libtinfo6 6.3-2 install ok installed libtirpc-common libtirpc-common 1.3.2-2 install ok installed libtirpc3:amd64 libtirpc3 1.3.2-2 install ok installed libudev1:amd64 libudev1 250.4-1 install ok installed libunistring2:amd64 libunistring2 1.0-1 install ok installed libuuid1:amd64 libuuid1 2.37.3-1+b1 install ok installed libxml2:amd64 libxml2 2.9.13+dfsg-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.4.9+dfsg-1 install ok installed login login 1:4.11.1+dfsg1-2 install ok installed logsave logsave 1.46.5-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-3+b1 install ok installed media-types media-types 7.0.0 install ok installed mount mount 2.37.3-1+b1 install ok installed ncurses-base ncurses-base 6.3-2 install ok installed ncurses-bin ncurses-bin 6.3-2 install ok installed parallel-fastq-dump parallel-fastq-dump 0.6.7-3 install ok installed passwd passwd 1:4.11.1+dfsg1-2 install ok installed perl-base perl-base 5.34.0-3 install ok installed python3 python3 3.10.4-1 install ok installed python3-minimal python3-minimal 3.10.4-1 install ok installed python3.10 python3.10 3.10.4-1 install ok installed python3.10-minimal python3.10-minimal 3.10.4-1 install ok installed python3.9 python3.9 3.9.12-1 install ok installed python3.9-minimal python3.9-minimal 3.9.12-1 install ok installed readline-common readline-common 8.1.2-1 install ok installed sed sed 4.8-1 install ok installed sra-toolkit sra-toolkit 2.11.3+dfsg-1 install ok installed sysvinit-utils sysvinit-utils 3.01-1 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2022a-1 install ok installed util-linux util-linux 2.37.3-1+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-4 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-get', 'remove', 'libaec0:amd64', 'libbrotli1:amd64', 'libcurl4:amd64', 'libexpat1:amd64', 'libfuse2:amd64', 'libhdf5-103-1:amd64', 'libicu67:amd64', 'libkdf5-2', 'libldap-2.5-0:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto7:amd64', 'libmbedtls-dev:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmpdec3:amd64', 'libncbi-vdb2', 'libncbi-wvdb2', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.10-minimal:amd64', 'libpython3.10-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libsz2:amd64', 'libxml2:amd64', 'media-types', 'python3', 'python3-minimal', 'python3.10', 'python3.10-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'sra-toolkit', 'parallel-fastq-dump'] 0m24.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libaec0 libbrotli1 libcurl4 libexpat1 libfuse2 libhdf5-103-1 libicu67 libkdf5-2 libldap-2.5-0 libmagic-mgc libmagic1 libmbedcrypto7 libmbedtls-dev libmbedtls14 libmbedx509-1 libmpdec3 libncbi-vdb2 libncbi-wvdb2 libncursesw6 libnghttp2-14 libpsl5 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libsz2 libxml2 media-types parallel-fastq-dump python3 python3-minimal python3.10 python3.10-minimal python3.9 python3.9-minimal readline-common sra-toolkit 0 upgraded, 0 newly installed, 44 to remove and 0 not upgraded. After this operation, 120 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 ... 8528 files and directories currently installed.) Removing parallel-fastq-dump (0.6.7-3) ... Removing sra-toolkit (2.11.3+dfsg-1) ... Removing libkdf5-2 (2.11.2+dfsg-4+b1) ... Removing libhdf5-103-1:amd64 (1.10.7+repack-4) ... Removing libsz2:amd64 (1.0.6-1) ... Removing libaec0:amd64 (1.0.6-1) ... Removing libcurl4:amd64 (7.82.0-2) ... Removing libbrotli1:amd64 (1.0.9-2+b3) ... Removing python3.9 (3.9.12-1) ... Removing python3.9-minimal (3.9.12-1) ... Removing python3 (3.10.4-1) ... Removing python3-minimal (3.10.4-1) ... Removing libfuse2:amd64 (2.9.9-5) ... Removing libncbi-wvdb2 (2.11.2+dfsg-4+b1) ... Removing libncbi-vdb2 (2.11.2+dfsg-4+b1) ... Removing libxml2:amd64 (2.9.13+dfsg-1) ... Removing libicu67:amd64 (67.1-7) ... Removing libldap-2.5-0:amd64 (2.5.11+dfsg-1) ... Removing libmagic1:amd64 (1:5.41-3) ... Removing libmagic-mgc (1:5.41-3) ... Removing libmbedtls-dev:amd64 (2.28.0-1) ... Removing libmbedtls14:amd64 (2.28.0-1) ... Removing libmbedx509-1:amd64 (2.28.0-1) ... Removing libmbedcrypto7:amd64 (2.28.0-1) ... Removing libpython3.9-stdlib:amd64 (3.9.12-1) ... Removing python3.10 (3.10.4-1) ... Removing libnghttp2-14:amd64 (1.43.0-1) ... Removing libpsl5:amd64 (0.21.0-1.2) ... Removing libpython3-stdlib:amd64 (3.10.4-1) ... Removing libpython3.9-minimal:amd64 (3.9.12-1) ... find: '/usr/lib/python3': No such file or directory Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg-2+b1) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg-2+b1) ... Removing libssh2-1:amd64 (1.10.0-3) ... Removing python3.10-minimal (3.10.4-1) ... Removing libexpat1:amd64 (2.4.8-1) ... Removing libpython3.10-stdlib:amd64 (3.10.4-1) ... find: '/usr/lib/python3': No such file or directory Removing libmpdec3:amd64 (2.5.1-2) ... Removing libncursesw6:amd64 (6.3-2) ... Removing libpython3.10-minimal:amd64 (3.10.4-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.1.2-1) ... Removing libsqlite3-0:amd64 (3.38.2-1) ... Removing media-types (7.0.0) ... Removing readline-common (8.1.2-1) ... Processing triggers for libc-bin (2.33-7) ... 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-get', 'remove', 'libaec0:amd64', 'libbrotli1:amd64', 'libcurl4:amd64', 'libexpat1:amd64', 'libfuse2:amd64', 'libhdf5-103-1:amd64', 'libicu67:amd64', 'libkdf5-2', 'libldap-2.5-0:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto7:amd64', 'libmbedtls-dev:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmpdec3:amd64', 'libncbi-vdb2', 'libncbi-wvdb2', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.10-minimal:amd64', 'libpython3.10-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libsz2:amd64', 'libxml2:amd64', 'media-types', 'python3', 'python3-minimal', 'python3.10', 'python3.10-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'sra-toolkit', 'parallel-fastq-dump'] 0m24.7s INFO: Running scripts post_remove 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_remove_exceptions'] 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_remove_exceptions'] 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'dpkg', '--purge', 'libaec0:amd64', 'libbrotli1:amd64', 'libcurl4:amd64', 'libexpat1:amd64', 'libfuse2:amd64', 'libhdf5-103-1:amd64', 'libicu67:amd64', 'libkdf5-2', 'libldap-2.5-0:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto7:amd64', 'libmbedtls-dev:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmpdec3:amd64', 'libncbi-vdb2', 'libncbi-wvdb2', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.10-minimal:amd64', 'libpython3.10-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libsz2:amd64', 'libxml2:amd64', 'media-types', 'python3', 'python3-minimal', 'python3.10', 'python3.10-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'sra-toolkit'] 0m24.7s DUMP: dpkg: warning: ignoring request to remove libaec0 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcurl4 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfuse2 which isn't installed dpkg: warning: ignoring request to remove libhdf5-103-1 which isn't installed dpkg: warning: ignoring request to remove libicu67 which isn't installed dpkg: warning: ignoring request to remove libkdf5-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove libmagic-mgc which isn't installed (Reading database ... 6701 files and directories currently installed.) Purging configuration files for libmagic1:amd64 (1:5.41-3) ... dpkg: warning: ignoring request to remove libmbedcrypto7 which isn't installed dpkg: warning: ignoring request to remove libmbedtls-dev which isn't installed dpkg: warning: ignoring request to remove libmbedtls14 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-1 which isn't installed dpkg: warning: ignoring request to remove libmpdec3 which isn't installed dpkg: warning: ignoring request to remove libncbi-vdb2 which isn't installed dpkg: warning: ignoring request to remove libncbi-wvdb2 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 libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.10-minimal:amd64 (3.10.4-1) ... dpkg: warning: ignoring request to remove libpython3.10-stdlib which isn't installed Purging configuration files for libpython3.9-minimal:amd64 (3.9.12-1) ... dpkg: warning: ignoring request to remove libpython3.9-stdlib which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed dpkg: warning: ignoring request to remove libsz2 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed Purging configuration files for media-types (7.0.0) ... Purging configuration files for python3 (3.10.4-1) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3.10 which isn't installed Purging configuration files for python3.10-minimal (3.10.4-1) ... dpkg: warning: ignoring request to remove python3.9 which isn't installed Purging configuration files for python3.9-minimal (3.9.12-1) ... Purging configuration files for readline-common (8.1.2-1) ... Purging configuration files for sra-toolkit (2.11.3+dfsg-1) ... 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'dpkg', '--purge', 'libaec0:amd64', 'libbrotli1:amd64', 'libcurl4:amd64', 'libexpat1:amd64', 'libfuse2:amd64', 'libhdf5-103-1:amd64', 'libicu67:amd64', 'libkdf5-2', 'libldap-2.5-0:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto7:amd64', 'libmbedtls-dev:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmpdec3:amd64', 'libncbi-vdb2', 'libncbi-wvdb2', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.10-minimal:amd64', 'libpython3.10-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libsz2:amd64', 'libxml2:amd64', 'media-types', 'python3', 'python3-minimal', 'python3.10', 'python3.10-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'sra-toolkit'] 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'dpkg', '--purge', 'parallel-fastq-dump'] 0m24.7s DUMP: dpkg: warning: ignoring request to remove parallel-fastq-dump which isn't installed 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'dpkg', '--purge', 'parallel-fastq-dump'] 0m24.7s INFO: Running scripts post_purge 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_purge_exceptions'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_purge_exceptions'] 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'dpkg', '--purge', '--pending'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'dpkg', '--purge', '--pending'] 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'dpkg', '--remove', '--pending'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'dpkg', '--remove', '--pending'] 0m24.8s INFO: Running scripts post_test 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_test_exceptions'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'tmp/scripts/post_test_exceptions'] 0m24.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6stzco1'] 0m25.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl6stzco1'] 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'dpkg-divert', '--list'] 0m25.1s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m25.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'dpkg-divert', '--list'] 0m25.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-get', 'clean'] 0m25.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl6stzco1', 'apt-get', 'clean'] 0m25.1s DEBUG: Recording chroot state 0m25.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/dev/shm'] 0m25.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/dev/shm'] 0m25.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/dev/console'] 0m25.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/dev/console'] 0m25.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/dev/ptmx'] 0m25.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/dev/ptmx'] 0m25.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/dev/pts'] 0m25.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/dev/pts'] 0m25.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/proc'] 0m25.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl6stzco1/proc'] 0m25.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpl6stzco1'] 0m26.0s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpl6stzco1'] 0m26.0s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpl6stzco1 0m26.0s INFO: PASS: Upgrading between Debian distributions. 0m26.0s INFO: PASS: All tests. 0m26.0s INFO: piuparts run ends. ret=0 End: 2022-03-30 06:26:48 GMT