Start: 2024-08-22 03:00:31 GMT [testing] Package: trinityrnaseq Source: trinityrnaseq (2.15.1+dfsg-5) Version: 2.15.1+dfsg-5+b1 Installed-Size: 7456 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libhts3t64 (>= 1.17), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4), perl:any, jaligner, libgetopt-java, libjung-free-java, bowtie, bowtie2, libwww-perl, default-jre-headless, samtools, jellyfish, r-base-core, rsem, berkeley-express, trimmomatic, parafly, ncbi-blast+, python3, liburi-perl, python3-htseq, subread, kallisto Recommends: curl, trinityrnaseq-examples, picard-tools, tabix, gmap, salmon, rna-star, hisat2, r-cran-tidyverse, r-cran-readr, r-bioc-edger, r-bioc-deseq2, r-bioc-rots, r-cran-cluster, r-cran-fastcluster, r-bioc-ctc, r-bioc-goseq, r-cran-goplot, r-cran-gplots, r-bioc-dexseq, r-cran-ape, r-bioc-biobase, r-bioc-qvalue, r-cran-argparse, r-cran-kernsmooth, python3-numpy, python3-hisat2 Suggests: collectl, transdecoder, r-bioc-tximport, r-bioc-tximportdata Description: RNA-Seq De novo Assembly Homepage: https://github.com/trinityrnaseq/trinityrnaseq Description-md5: 2ee7f38dbb99a040c33d6619f4f5668b Section: science Priority: optional Filename: pool/main/t/trinityrnaseq/trinityrnaseq_2.15.1+dfsg-5+b1_amd64.deb Size: 1720124 MD5sum: 091e1c91e745d24db55e1cc6ae5a33dc SHA256: 26095fdfb867b2e1976033be1d8a0e722cd129b4027f8f554bc381c88628464d [sid] Package: trinityrnaseq Version: 2.15.2+dfsg-1 Installed-Size: 7531 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libhts3t64 (>= 1.17), libstdc++6 (>= 14), zlib1g (>= 1:1.1.4), perl:any, jaligner, libgetopt-java, libjung-free-java, bowtie, bowtie2, libwww-perl, default-jre-headless, samtools, jellyfish, r-base-core, rsem, berkeley-express, trimmomatic, parafly, ncbi-blast+, python3, liburi-perl, python3-htseq, subread, kallisto Recommends: curl, trinityrnaseq-examples, picard-tools, tabix, gmap, salmon, rna-star, hisat2, r-cran-tidyverse, r-cran-readr, r-bioc-edger, r-bioc-deseq2, r-bioc-rots, r-cran-cluster, r-cran-fastcluster, r-bioc-ctc, r-bioc-goseq, r-cran-goplot, r-cran-gplots, r-bioc-dexseq, r-cran-ape, r-bioc-biobase, r-bioc-qvalue, r-cran-argparse, r-cran-kernsmooth, python3-numpy, python3-hisat2 Suggests: collectl, transdecoder, r-bioc-tximport, r-bioc-tximportdata Description: RNA-Seq De novo Assembly Homepage: https://github.com/trinityrnaseq/trinityrnaseq Description-md5: 2ee7f38dbb99a040c33d6619f4f5668b Section: science Priority: optional Filename: pool/main/t/trinityrnaseq/trinityrnaseq_2.15.2+dfsg-1_amd64.deb Size: 1737612 MD5sum: 174e11fbf10d59a4fb4de08221fff0f6 SHA256: 8f0ef08eaed9a05d70851021f36f64982737d1f842c38362e03084f0a0026b97 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/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt trinityrnaseq=2.15.2+dfsg-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 1.4.4~202408201642~1.4.3-11-g36a88c35 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/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt trinityrnaseq=2.15.2+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-32-amd64 #1 SMP Debian 5.10.223-1 (2024-08-10) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpoxvz5ury 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpoxvz5ury 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/proc'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/dev/pts'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpoxvz5ury/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-get', 'update'] 0m2.3s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [169 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9255 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6169 kB] Fetched 15.6 MB in 1s (12.6 MB/s) Reading package lists... 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-get', 'update'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-get', '-yf', 'dist-upgrade'] 0m3.8s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: apt libapt-pkg6.0t64 libcrypt1 libsystemd0 libudev1 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3070 kB of archives. After this operation, 3072 B of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libsystemd0 amd64 256.5-1 [381 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libudev1 amd64 256.5-1 [144 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libapt-pkg6.0t64 amd64 2.9.8 [1045 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 apt amd64 2.9.8 [1410 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libcrypt1 amd64 1:4.4.36-5 [89.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3070 kB in 0s (49.9 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 ... 5175 files and directories currently installed.) Preparing to unpack .../libsystemd0_256.5-1_amd64.deb ... Unpacking libsystemd0:amd64 (256.5-1) over (256.4-3) ... Setting up libsystemd0:amd64 (256.5-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5175 files and directories currently installed.) Preparing to unpack .../libudev1_256.5-1_amd64.deb ... Unpacking libudev1:amd64 (256.5-1) over (256.4-3) ... Setting up libudev1:amd64 (256.5-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5175 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.9.8_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.9.8) over (2.9.7) ... Setting up libapt-pkg6.0t64:amd64 (2.9.8) ... (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 ... 5175 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.8_amd64.deb ... Unpacking apt (2.9.8) over (2.9.7) ... Setting up apt (2.9.8) ... (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 ... 5175 files and directories currently installed.) Preparing to unpack .../libcrypt1_1%3a4.4.36-5_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.36-5) over (1:4.4.36-4) ... Setting up libcrypt1:amd64 (1:4.4.36-5) ... Processing triggers for libc-bin (2.39-6) ... 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-get', '-yf', 'dist-upgrade'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.7s DUMP: a3789b85ab1246376964bed0d1e3eb7f - 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.7s INFO: Running scripts post_setup 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_setup_dummy_users'] 0m5.6s 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 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_setup_dummy_users'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_setup_forbid_home'] 0m5.6s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_setup_forbid_home'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.7s 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' 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_setup_minimize'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_setup_minimize'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_setup_zz_backports'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_setup_zz_backports'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.7s DUMP: install ok installed apt apt 2.9.8 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.4 install ok installed bash bash 5.2.21-2.1+b1 install ok installed bsdutils bsdutils 1:2.40.2-1 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-1 install ok installed gpgv gpgv 2.2.43-8 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-2 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.8 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-4 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-4+b1 install ok installed libblkid1:amd64 libblkid1 2.40.2-1 install ok installed libbsd0:amd64 libbsd0 0.12.2-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.39-6 install ok installed libc6:amd64 libc6 2.39-6 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-1+b1 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.272 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3 install ok installed liblzma5:amd64 liblzma5 5.6.2-2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40.2-1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b4 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b4 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-1 install ok installed libss2:amd64 libss2 1.47.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.2.2-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-1 install ok installed libsystemd0:amd64 libsystemd0 256.5-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.5-2 install ok installed libudev1:amd64 libudev1 256.5-1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1 install ok installed login login 1:4.15.3-2 install ok installed logsave logsave 1.47.1-1 install ok installed mawk mawk 1.3.4.20240622-2 install ok installed mount mount 2.40.2-1 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2 install ok installed passwd passwd 1:4.15.3-2 install ok installed perl-base perl-base 5.38.2-5 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.10-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-4 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-1 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.7s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m5.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury'] 0m6.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury'] 0m6.0s INFO: Running scripts is_testable 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/is_testable_uninstallable'] 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/is_testable_uninstallable'] 0m6.0s INFO: Running scripts pre_test 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_test_exceptions'] 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_test_exceptions'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_test_root_password'] 0m6.0s DUMP: New password: Retype new password: passwd: password updated successfully 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_test_root_password'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-cache', 'show', '--no-all-versions', 'trinityrnaseq'] 0m6.2s DUMP: Package: trinityrnaseq Source: trinityrnaseq (2.15.1+dfsg-5) Version: 2.15.1+dfsg-5+b1 Installed-Size: 7456 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libhts3t64 (>= 1.17), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4), perl:any, jaligner, libgetopt-java, libjung-free-java, bowtie, bowtie2, libwww-perl, default-jre-headless, samtools, jellyfish, r-base-core, rsem, berkeley-express, trimmomatic, parafly, ncbi-blast+, python3, liburi-perl, python3-htseq, subread, kallisto Recommends: curl, trinityrnaseq-examples, picard-tools, tabix, gmap, salmon, rna-star, hisat2, r-cran-tidyverse, r-cran-readr, r-bioc-edger, r-bioc-deseq2, r-bioc-rots, r-cran-cluster, r-cran-fastcluster, r-bioc-ctc, r-bioc-goseq, r-cran-goplot, r-cran-gplots, r-bioc-dexseq, r-cran-ape, r-bioc-biobase, r-bioc-qvalue, r-cran-argparse, r-cran-kernsmooth, python3-numpy, python3-hisat2 Suggests: collectl, transdecoder, r-bioc-tximport, r-bioc-tximportdata Description-en: RNA-Seq De novo Assembly Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. Description-md5: 2ee7f38dbb99a040c33d6619f4f5668b Homepage: https://github.com/trinityrnaseq/trinityrnaseq Section: science Priority: optional Filename: pool/main/t/trinityrnaseq/trinityrnaseq_2.15.1+dfsg-5+b1_amd64.deb Size: 1720124 MD5sum: 091e1c91e745d24db55e1cc6ae5a33dc SHA256: 26095fdfb867b2e1976033be1d8a0e722cd129b4027f8f554bc381c88628464d 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-cache', 'show', '--no-all-versions', 'trinityrnaseq'] 0m6.2s INFO: apt-cache knows about the following packages: trinityrnaseq 0m6.2s INFO: Running scripts pre_install 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_database-server'] 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_database-server'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_exceptions'] 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_exceptions'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_extras'] 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_extras'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-cache', 'policy'] 0m6.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-cache', 'policy'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-cache', 'policy', 'trinityrnaseq'] 0m6.4s DUMP: trinityrnaseq: Installed: (none) Candidate: 2.15.1+dfsg-5+b1 Version table: 2.15.1+dfsg-5+b1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-cache', 'policy', 'trinityrnaseq'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-get', '-y', 'install', 'trinityrnaseq'] 0m39.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: adduser adwaita-icon-theme at-spi2-common berkeley-express bowtie bowtie2 ca-certificates ca-certificates-java dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service default-jre default-jre-headless fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme jaligner java-common jellyfish kallisto libapparmor1 libasound2-data libasound2t64 libatinject-jsr330-api-java libatk-bridge2.0-0t64 libatk1.0-0t64 libatomic1 libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 libbamtools2.5.2 libblas3 libboost-filesystem1.83.0 libboost-program-options1.83.0 libboost-thread1.83.0 libbrotli1 libcairo-gobject2 libcairo2 libclone-perl libcloudproviders0 libcolord2 libcups2t64 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdbus-1-3 libdconf1 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-radeon1 libdrm2 libedit2 libelf1t64 libencode-locale-perl libepoxy0 liberror-prone-java libexpat1 libfile-listing-perl libfontconfig1 libfreetype6 libfribidi0 libgdbm-compat4t64 libgdbm6t64 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgetopt-java libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libguava-java libharfbuzz0b libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts3t64 libhtscodecs2 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu72 libio-html-perl libio-socket-ssl-perl libjbig0 libjbzip2-java libjellyfish-2.0-2 libjpeg62-turbo libjsr305-java libjung-free-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 liblerc4 libllvm17t64 liblmdb0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libncurses6 libncursesw6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnspr4 libnss3 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.38t64 libpixman-1-0 libpng16-16t64 libproc2-0 libprotobuf32t64 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libsm6 libsqlite3-0 libssh2-1t64 libsystemd-shared libtcl8.6 libthai-data libthai0 libtiff6 libtimedate-perl libtirpc-common libtirpc3t64 libtk8.6 libtry-tiny-perl liburi-perl libuv1t64 libvulkan1 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwebp7 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml2 libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6t64 libxtst6 libxxf86vm1 libz3-4 media-types ncbi-blast+ ncbi-data netbase openjdk-21-jre openjdk-21-jre-headless openssl parafly perl perl-modules-5.38 perl-openssl-defaults procps python3 python3-htseq python3-minimal python3-numpy python3-pkg-resources python3-pysam python3.12 python3.12-minimal r-base-core readline-common rsem samtools sensible-utils shared-mime-info subread systemd systemd-sysv trimmomatic ucf unzip x11-common xdg-utils xkb-data zip Suggested packages: liblocale-gettext-perl cron quota bowtie-examples bowtie2-examples alsa-utils libasound2-plugins libatinject-jsr330-api-java-doc colord cups-common gdbm-l10n low-memory-monitor krb5-doc krb5-user gvfs libdata-dump-perl libjsr305-java-doc liblcms2-utils libcrypt-ssleay-perl libcryptsetup12 libtss2-rc0t64 pciutils pcscd lm-sensors libarchive13t64 libbpf1 libdw1t64 libfido2-1 libip4tc2 libpwquality1 libqrencode4 tcl8.6 tk8.6 libsub-name-perl libbusiness-isbn-perl libregexp-ipv6-perl libauthen-ntlm-perl libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl debhelper python3-doc python3-tk python3-venv gcc gfortran python-numpy-doc python3-dev python3-pytest python3-setuptools python3.12-venv python3.12-doc binutils binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html readline-doc r-bioc-ebseq hisat2 cwltool systemd-container systemd-homed systemd-userdbd systemd-boot systemd-resolved systemd-repart libtss2-tcti-device0 polkitd collectl transdecoder r-bioc-tximport r-bioc-tximportdata Recommended packages: librsvg2-common med-config alsa-ucm-conf alsa-topology-conf at-spi2-core libgdk-pixbuf2.0-bin libglib2.0-data xdg-user-dirs libgtk-3-bin libhtml-format-perl libio-compress-brotli-perl krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules libkmod2 mesa-vulkan-drivers | vulkan-icd libdata-dump-perl libhtml-form-perl libhttp-daemon-perl libmailtools-perl libatk-wrapper-java-jni fonts-dejavu-extra psmisc linux-sysctl-defaults r-recommended r-base-dev r-doc-html systemd-timesyncd | time-daemon systemd-cryptsetup libnss-systemd curl trinityrnaseq-examples picard-tools tabix gmap salmon rna-star hisat2 r-cran-tidyverse r-cran-readr r-bioc-edger r-bioc-deseq2 r-bioc-rots r-cran-cluster r-cran-fastcluster r-bioc-ctc r-bioc-goseq r-cran-goplot r-cran-gplots r-bioc-dexseq r-cran-ape r-bioc-biobase r-bioc-qvalue r-cran-argparse r-cran-kernsmooth python3-hisat2 libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: adduser adwaita-icon-theme at-spi2-common berkeley-express bowtie bowtie2 ca-certificates ca-certificates-java dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service default-jre default-jre-headless fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme jaligner java-common jellyfish kallisto libapparmor1 libasound2-data libasound2t64 libatinject-jsr330-api-java libatk-bridge2.0-0t64 libatk1.0-0t64 libatomic1 libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 libbamtools2.5.2 libblas3 libboost-filesystem1.83.0 libboost-program-options1.83.0 libboost-thread1.83.0 libbrotli1 libcairo-gobject2 libcairo2 libclone-perl libcloudproviders0 libcolord2 libcups2t64 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdbus-1-3 libdconf1 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-radeon1 libdrm2 libedit2 libelf1t64 libencode-locale-perl libepoxy0 liberror-prone-java libexpat1 libfile-listing-perl libfontconfig1 libfreetype6 libfribidi0 libgdbm-compat4t64 libgdbm6t64 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgetopt-java libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libguava-java libharfbuzz0b libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts3t64 libhtscodecs2 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu72 libio-html-perl libio-socket-ssl-perl libjbig0 libjbzip2-java libjellyfish-2.0-2 libjpeg62-turbo libjsr305-java libjung-free-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 liblerc4 libllvm17t64 liblmdb0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libncurses6 libncursesw6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnspr4 libnss3 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.38t64 libpixman-1-0 libpng16-16t64 libproc2-0 libprotobuf32t64 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libsm6 libsqlite3-0 libssh2-1t64 libsystemd-shared libtcl8.6 libthai-data libthai0 libtiff6 libtimedate-perl libtirpc-common libtirpc3t64 libtk8.6 libtry-tiny-perl liburi-perl libuv1t64 libvulkan1 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwebp7 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml2 libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6t64 libxtst6 libxxf86vm1 libz3-4 media-types ncbi-blast+ ncbi-data netbase openjdk-21-jre openjdk-21-jre-headless openssl parafly perl perl-modules-5.38 perl-openssl-defaults procps python3 python3-htseq python3-minimal python3-numpy python3-pkg-resources python3-pysam python3.12 python3.12-minimal r-base-core readline-common rsem samtools sensible-utils shared-mime-info subread systemd systemd-sysv trimmomatic trinityrnaseq ucf unzip x11-common xdg-utils xkb-data zip 0 upgraded, 253 newly installed, 0 to remove and 0 not upgraded. Need to get 262 MB of archives. After this operation, 978 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libapparmor1 amd64 3.1.7-1+b1 [42.0 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libsystemd-shared amd64 256.5-1 [2060 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 systemd amd64 256.5-1 [3489 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 systemd-sysv amd64 256.5-1 [57.7 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libdbus-1-3 amd64 1.14.10-4+b1 [203 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 dbus-bin amd64 1.14.10-4+b1 [106 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 dbus-session-bus-common all 1.14.10-4 [79.0 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 dbus-daemon amd64 1.14.10-4+b1 [185 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 adduser all 3.137 [140 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 dbus-system-bus-common all 1.14.10-4 [80.1 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 dbus amd64 1.14.10-4+b1 [98.6 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 perl-modules-5.38 all 5.38.2-5 [2905 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 libperl5.38t64 amd64 5.38.2-5 [4275 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 perl amd64 5.38.2-5 [236 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.4-3 [812 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.4-3 [2137 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.5-1 [26.7 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5-2 [135 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.0-1 [902 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.4-3 [1950 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.4-3 [664 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.5-1 [9588 B] Get:30 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.5-1 [27.6 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-5 [64.7 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-5 [878 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.2.2-1 [1364 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libpam-systemd amd64 256.5-1 [278 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-1 [9280 B] Get:40 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.81.1-3 [1496 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 shared-mime-info amd64 2.4-5 [758 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.21-1 [47.3 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-1 [139 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 gtk-update-icon-cache amd64 3.24.43-1 [46.8 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 hicolor-icon-theme all 0.18-1 [12.0 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 adwaita-icon-theme all 46.0-1 [614 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 at-spi2-common all 2.52.0-1 [166 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6 [159 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-3.1 [281 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 libboost-program-options1.83.0 amd64 1.83.0-3.1 [347 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 libboost-thread1.83.0 amd64 1.83.0-3.1 [269 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 libprotobuf32t64 amd64 3.21.12-9 [982 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 berkeley-express amd64 1.5.3+dfsg-3+b3 [233 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 bowtie amd64 1.3.1-3 [1627 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 bowtie2 amd64 2.5.4-1 [1510 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 dbus-user-session amd64 1.14.10-4+b1 [79.1 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 libdconf1 amd64 0.40.0-4+b2 [41.9 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 dconf-service amd64 0.40.0-4+b2 [32.4 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 dconf-gsettings-backend amd64 0.40.0-4+b2 [28.7 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 java-common all 0.76 [6776 B] Get:71 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.102-1 [1336 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.3.0-1 [55.4 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre-headless amd64 21.0.4+7-3 [42.0 MB] Get:76 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get:77 http://deb.debian.org/debian trixie/main amd64 libatk1.0-0t64 amd64 2.52.0-1 [50.8 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 libatspi2.0-0t64 amd64 2.52.0-1 [75.9 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 libatk-bridge2.0-0t64 amd64 2.52.0-1 [67.0 kB] Get:87 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get:93 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2 [115 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get:98 http://deb.debian.org/debian trixie/main amd64 libcairo-gobject2 amd64 1.18.0-3+b1 [129 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 libcloudproviders0 amd64 0.3.6-1 [28.9 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 libcolord2 amd64 1.4.7-1+b1 [139 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 libavahi-common-data amd64 0.8-13+b2 [112 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 libavahi-common3 amd64 0.8-13+b2 [43.3 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 libavahi-client3 amd64 0.8-13+b2 [47.0 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:105 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:106 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:107 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 libcups2t64 amd64 2.4.10-1 [249 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 libepoxy0 amd64 1.5.10-1+b2 [191 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get:112 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:116 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get:118 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.54.0+ds-1 [219 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-1 [48.0 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-1 [35.0 kB] Get:121 http://deb.debian.org/debian trixie/main amd64 libwayland-client0 amd64 1.23.0-1 [26.4 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 libwayland-cursor0 amd64 1.23.0-1 [11.3 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 libwayland-egl1 amd64 1.23.0-1 [5392 B] Get:124 http://deb.debian.org/debian trixie/main amd64 libxcomposite1 amd64 1:0.4.5-1+b1 [14.9 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b1 [20.3 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 libxcursor1 amd64 1:1.2.2-1 [37.1 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 libxdamage1 amd64 1:1.1.6-1+b1 [15.5 kB] Get:128 http://deb.debian.org/debian trixie/main amd64 libxinerama1 amd64 2:1.1.4-3+b1 [16.0 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 xkb-data all 2.42-1 [790 kB] Get:130 http://deb.debian.org/debian trixie/main amd64 libxkbcommon0 amd64 1.6.0-1+b1 [109 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 libxrandr2 amd64 2:1.5.4-1 [36.1 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 libgtk-3-common all 3.24.43-1 [4657 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 libgtk-3-0t64 amd64 3.24.43-1 [2728 kB] Get:134 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b1 [56.3 kB] Get:135 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.122-1 [7992 B] Get:136 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.122-1 [38.7 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 libglapi-mesa amd64 24.1.3-2 [36.7 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.7-1+b1 [232 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 libxcb-dri2-0 amd64 1.17.0-2 [106 kB] Get:140 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.17.0-2 [107 kB] Get:141 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.17.0-2 [122 kB] Get:142 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.17.0-2 [105 kB] Get:143 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.17.0-2 [116 kB] Get:144 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.17.0-2 [108 kB] Get:145 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.17.0-2 [109 kB] Get:146 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3-1+b1 [8852 B] Get:147 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get:148 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.3.283.0-1 [125 kB] Get:149 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.122-1 [22.2 kB] Get:150 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get:151 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.122-1 [63.6 kB] Get:152 http://deb.debian.org/debian trixie/main amd64 libdrm-radeon1 amd64 2.4.122-1 [22.3 kB] Get:153 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get:154 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20240517-1 [93.3 kB] Get:155 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get:156 http://deb.debian.org/debian trixie/main amd64 libllvm17t64 amd64 1:17.0.6-15 [23.6 MB] Get:157 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get:158 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-10 [34.7 kB] Get:159 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 24.1.3-2 [8637 kB] Get:160 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 24.1.3-2 [152 kB] Get:161 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b1 [35.0 kB] Get:162 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b1 [89.8 kB] Get:163 http://deb.debian.org/debian trixie/main amd64 libasound2-data all 1.2.12-1 [21.0 kB] Get:164 http://deb.debian.org/debian trixie/main amd64 libasound2t64 amd64 1.2.12-1 [369 kB] Get:165 http://deb.debian.org/debian trixie/main amd64 libgif7 amd64 5.2.2-1 [43.9 kB] Get:166 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:167 http://deb.debian.org/debian trixie/main amd64 libxtst6 amd64 2:1.2.3-1.1+b1 [25.9 kB] Get:168 http://deb.debian.org/debian trixie/main amd64 openjdk-21-jre amd64 21.0.4+7-3 [204 kB] Get:169 http://deb.debian.org/debian trixie/main amd64 default-jre amd64 2:1.21-76 [1068 B] Get:170 http://deb.debian.org/debian trixie/main amd64 jaligner all 1.0+dfsg-11 [133 kB] Get:171 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-7 [19.6 kB] Get:172 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-7 [57.2 kB] Get:173 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-2 [186 kB] Get:174 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.62.1-2 [74.9 kB] Get:175 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.4.0-1 [63.1 kB] Get:176 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get:177 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get:178 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:179 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:180 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB] Get:181 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.9.1-2 [470 kB] Get:182 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get:183 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB] Get:184 http://deb.debian.org/debian trixie/main amd64 libjellyfish-2.0-2 amd64 2.3.1-3+b5 [67.2 kB] Get:185 http://deb.debian.org/debian trixie/main amd64 jellyfish amd64 2.3.1-3+b5 [794 kB] Get:186 http://deb.debian.org/debian trixie/main amd64 kallisto amd64 0.48.0+dfsg-4+b1 [286 kB] Get:187 http://deb.debian.org/debian trixie/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get:188 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:189 http://deb.debian.org/debian trixie/main amd64 libclone-perl amd64 0.46-1+b2 [13.7 kB] Get:190 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.9.1-2 [463 kB] Get:191 http://deb.debian.org/debian trixie/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:192 http://deb.debian.org/debian trixie/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get:193 http://deb.debian.org/debian trixie/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get:194 http://deb.debian.org/debian trixie/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get:195 http://deb.debian.org/debian trixie/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:196 http://deb.debian.org/debian trixie/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:197 http://deb.debian.org/debian trixie/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:198 http://deb.debian.org/debian trixie/main amd64 libgetopt-java all 1.0.14+dfsg-6 [25.7 kB] Get:199 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-1 [837 kB] Get:200 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-1 [137 kB] Get:201 http://deb.debian.org/debian trixie/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get:202 http://deb.debian.org/debian trixie/main amd64 liburi-perl all 5.28-1 [98.6 kB] Get:203 http://deb.debian.org/debian trixie/main amd64 libhtml-parser-perl amd64 3.83-1 [99.4 kB] Get:204 http://deb.debian.org/debian trixie/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:205 http://deb.debian.org/debian trixie/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:206 http://deb.debian.org/debian trixie/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:207 http://deb.debian.org/debian trixie/main amd64 libhttp-message-perl all 6.46-1 [79.7 kB] Get:208 http://deb.debian.org/debian trixie/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:209 http://deb.debian.org/debian trixie/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:210 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get:211 http://deb.debian.org/debian trixie/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get:212 http://deb.debian.org/debian trixie/main amd64 libnet-ssleay-perl amd64 1.94-1+b1 [339 kB] Get:213 http://deb.debian.org/debian trixie/main amd64 libio-socket-ssl-perl all 2.088-1 [222 kB] Get:214 http://deb.debian.org/debian trixie/main amd64 libjbzip2-java all 0.9.1-8 [42.7 kB] Get:215 http://deb.debian.org/debian trixie/main amd64 libjung-free-java all 2.1.1-2 [1477 kB] Get:216 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:217 http://deb.debian.org/debian trixie/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get:218 http://deb.debian.org/debian trixie/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get:219 http://deb.debian.org/debian trixie/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get:220 http://deb.debian.org/debian trixie/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:221 http://deb.debian.org/debian trixie/main amd64 libwww-perl all 6.77-1 [183 kB] Get:222 http://deb.debian.org/debian trixie/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get:223 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get:224 http://deb.debian.org/debian trixie/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get:225 http://deb.debian.org/debian trixie/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get:226 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get:227 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB] Get:228 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B] Get:229 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get:230 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get:231 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:232 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get:233 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get:234 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB] Get:235 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get:236 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-5 [148 kB] Get:237 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get:238 http://deb.debian.org/debian trixie/main amd64 ncbi-data all 6.1.20170106+dfsg2-3 [3539 kB] Get:239 http://deb.debian.org/debian trixie/main amd64 ncbi-blast+ amd64 2.16.0+ds-6 [15.2 MB] Get:240 http://deb.debian.org/debian trixie/main amd64 parafly amd64 0.1.0-4 [17.5 kB] Get:241 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 70.3.0-2 [264 kB] Get:242 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-11 [4236 kB] Get:243 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.22.1+ds-2+b1 [3474 kB] Get:244 http://deb.debian.org/debian trixie/main amd64 python3-htseq amd64 2.0.5-2+b1 [309 kB] Get:245 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-14 [233 kB] Get:246 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get:247 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:248 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.1-1 [28.3 MB] Get:249 http://deb.debian.org/debian trixie/main amd64 rsem amd64 1.3.3+dfsg-3+b1 [36.1 MB] Get:250 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.20-3 [653 kB] Get:251 http://deb.debian.org/debian trixie/main amd64 subread amd64 2.0.6+dfsg-3 [827 kB] Get:252 http://deb.debian.org/debian trixie/main amd64 trimmomatic all 0.39+dfsg-2 [758 kB] Get:253 http://deb.debian.org/debian trixie/main amd64 trinityrnaseq amd64 2.15.1+dfsg-5+b1 [1720 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 262 MB in 2s (109 MB/s) Selecting previously unselected package libapparmor1: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 ... 5179 files and directories currently installed.) Preparing to unpack .../libapparmor1_3.1.7-1+b1_amd64.deb ... Unpacking libapparmor1:amd64 (3.1.7-1+b1) ... Selecting previously unselected package libsystemd-shared:amd64. Preparing to unpack .../libsystemd-shared_256.5-1_amd64.deb ... Unpacking libsystemd-shared:amd64 (256.5-1) ... Selecting previously unselected package systemd. Preparing to unpack .../systemd_256.5-1_amd64.deb ... Unpacking systemd (256.5-1) ... Setting up libapparmor1:amd64 (3.1.7-1+b1) ... Setting up libsystemd-shared:amd64 (256.5-1) ... Setting up systemd (256.5-1) ... Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' → '/usr/lib/systemd/system/getty@.service'. Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' → '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' → '/usr/lib/systemd/system/systemd-pstore.service'. Initializing machine ID from random generator. Creating group 'systemd-journal' with GID 999. Creating group 'systemd-network' with GID 998. Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. [ESC][0;1;39m/usr/lib/tmpfiles.d/legacy.conf:13: Duplicate line for path "/run/lock", ignoring.[ESC][0m [ESC][0;1;31m"/home" already exists and is not a directory.[ESC][0m Selecting previously unselected package systemd-sysv. (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 ... 6142 files and directories currently installed.) Preparing to unpack .../0-systemd-sysv_256.5-1_amd64.deb ... Unpacking systemd-sysv (256.5-1) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../1-libdbus-1-3_1.14.10-4+b1_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.14.10-4+b1) ... Selecting previously unselected package dbus-bin. Preparing to unpack .../2-dbus-bin_1.14.10-4+b1_amd64.deb ... Unpacking dbus-bin (1.14.10-4+b1) ... Selecting previously unselected package dbus-session-bus-common. Preparing to unpack .../3-dbus-session-bus-common_1.14.10-4_all.deb ... Unpacking dbus-session-bus-common (1.14.10-4) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../4-libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package dbus-daemon. Preparing to unpack .../5-dbus-daemon_1.14.10-4+b1_amd64.deb ... Unpacking dbus-daemon (1.14.10-4+b1) ... Selecting previously unselected package adduser. Preparing to unpack .../6-adduser_3.137_all.deb ... Unpacking adduser (3.137) ... Setting up adduser (3.137) ... Selecting previously unselected package dbus-system-bus-common. (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 ... 6288 files and directories currently installed.) Preparing to unpack .../0-dbus-system-bus-common_1.14.10-4_all.deb ... Unpacking dbus-system-bus-common (1.14.10-4) ... Selecting previously unselected package dbus. Preparing to unpack .../1-dbus_1.14.10-4+b1_amd64.deb ... Unpacking dbus (1.14.10-4+b1) ... Selecting previously unselected package perl-modules-5.38. Preparing to unpack .../2-perl-modules-5.38_5.38.2-5_all.deb ... Unpacking perl-modules-5.38 (5.38.2-5) ... Selecting previously unselected package libgdbm6t64:amd64. Preparing to unpack .../3-libgdbm6t64_1.24-2_amd64.deb ... Unpacking libgdbm6t64:amd64 (1.24-2) ... Selecting previously unselected package libgdbm-compat4t64:amd64. Preparing to unpack .../4-libgdbm-compat4t64_1.24-2_amd64.deb ... Unpacking libgdbm-compat4t64:amd64 (1.24-2) ... Selecting previously unselected package libperl5.38t64:amd64. Preparing to unpack .../5-libperl5.38t64_5.38.2-5_amd64.deb ... Unpacking libperl5.38t64:amd64 (5.38.2-5) ... Selecting previously unselected package perl. Preparing to unpack .../6-perl_5.38.2-5_amd64.deb ... Unpacking perl (5.38.2-5) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../7-libpython3.12-minimal_3.12.4-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.4-3) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../8-python3.12-minimal_3.12.4-3_amd64.deb ... Unpacking python3.12-minimal (3.12.4-3) ... Setting up libpython3.12-minimal:amd64 (3.12.4-3) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.12-minimal (3.12.4-3) ... Selecting previously unselected package python3-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 ... 8646 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.5-1_amd64.deb ... Unpacking python3-minimal (3.12.5-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../3-libncursesw6_6.5-2_amd64.deb ... Unpacking libncursesw6:amd64 (6.5-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../6-libsqlite3-0_3.46.0-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.0-1) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../7-libpython3.12-stdlib_3.12.4-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.4-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../8-python3.12_3.12.4-3_amd64.deb ... Unpacking python3.12 (3.12.4-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.12.5-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.5-1) ... Setting up python3-minimal (3.12.5-1) ... Selecting previously unselected package python3. (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 ... 9138 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.5-1_amd64.deb ... Unpacking python3 (3.12.5-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-5_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-5) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-5_amd64.deb ... Unpacking procps (2:4.0.4-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../004-openssl_3.2.2-1_amd64.deb ... Unpacking openssl (3.2.2-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../005-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libpam-systemd:amd64. Preparing to unpack .../006-libpam-systemd_256.5-1_amd64.deb ... Unpacking libpam-systemd:amd64 (256.5-1) ... Selecting previously unselected package ucf. Preparing to unpack .../007-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package libgdk-pixbuf2.0-common. Preparing to unpack .../008-libgdk-pixbuf2.0-common_2.42.12+dfsg-1_all.deb ... Unpacking libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... Selecting previously unselected package libatomic1:amd64. Preparing to unpack .../009-libatomic1_14.2.0-1_amd64.deb ... Unpacking libatomic1:amd64 (14.2.0-1) ... Selecting previously unselected package libglib2.0-0t64:amd64. Preparing to unpack .../010-libglib2.0-0t64_2.81.1-3_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.81.1-3) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../011-libicu72_72.1-5_amd64.deb ... Unpacking libicu72:amd64 (72.1-5) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../012-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../013-shared-mime-info_2.4-5_amd64.deb ... Unpacking shared-mime-info (2.4-5) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../014-libjpeg62-turbo_1%3a2.1.5-3_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-3) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../015-libpng16-16t64_1.6.43-5_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.43-5) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../016-libdeflate0_1.21-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.21-1) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../017-libjbig0_2.1-6.1+b1_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1+b1) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../203-libxft2_2.3.6-1+b1_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b1) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../204-libxss1_1%3a1.2.3-1+b1_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1+b1) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../205-libtk8.6_8.6.14-1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.14-1) ... Selecting previously unselected package libuv1t64:amd64. Preparing to unpack .../206-libuv1t64_1.48.0-5_amd64.deb ... Unpacking libuv1t64:amd64 (1.48.0-5) ... 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Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libxcb-glx0:amd64 (1.17.0-2) ... Setting up unzip (6.0-28) ... Setting up libbrotli1:amd64 (1.1.0-2+b4) ... Setting up libedit2:amd64 (3.1-20240517-1) ... Setting up libsqlite3-0:amd64 (3.46.0-1) ... Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... Setting up libuv1t64:amd64 (1.48.0-5) ... Setting up x11-common (1:7.7+23.1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libsensors-config (1:3.6.0-10) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.62.1-2) ... Setting up libdeflate0:amd64 (1.21-1) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up libboost-thread1.83.0:amd64 (1.83.0-3.1) ... Setting up xkb-data (2.42-1) ... Setting up libxcb-shm0:amd64 (1.17.0-2) ... Setting up libboost-filesystem1.83.0:amd64 (1.83.0-3.1) ... Setting up libgomp1:amd64 (14.2.0-1) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-7) ... Setting up libxcb-present0:amd64 (1.17.0-2) ... Setting up libjellyfish-2.0-2:amd64 (2.3.1-3+b5) ... Setting up libasound2-data (1.2.12-1) ... Setting up zip (3.0-14) ... Setting up libz3-4:amd64 (4.8.12-3.1+b2) ... Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libasound2t64:amd64 (1.2.12-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libepoxy0:amd64 (1.5.10-1+b2) ... Setting up libnspr4:amd64 (2:4.35-1.1+b1) ... Setting up libxcb-sync1:amd64 (1.17.0-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libavahi-common-data:amd64 (0.8-13+b2) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libdbus-1-3:amd64 (1.14.10-4+b1) ... Setting up libfribidi0:amd64 (1.0.15-1) ... Setting up perl-modules-5.38 (5.38.2-5) ... Setting up libproc2-0:amd64 (2:4.0.4-5) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up libatomic1:amd64 (14.2.0-1) ... Setting up libtcl8.6:amd64 (8.6.14+dfsg-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libjbzip2-java (0.9.1-8) ... Setting up libpcsclite1:amd64 (2.3.0-1) ... Setting up libsensors5:amd64 (1:3.6.0-10) ... Setting up libncursesw6:amd64 (6.5-2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libbamtools2.5.2:amd64 (2.5.2+dfsg-6) ... Setting up libglapi-mesa:amd64 (24.1.3-2) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-7) ... Setting up libgfortran5:amd64 (14.2.0-1) ... Setting up berkeley-express (1.5.3+dfsg-3+b3) ... Setting up libvulkan1:amd64 (1.3.283.0-1) ... Setting up libnghttp3-9:amd64 (1.4.0-1) ... Setting up libwebp7:amd64 (1.4.0-0.1) ... Setting up libxcb-dri2-0:amd64 (1.17.0-2) ... Setting up libgif7:amd64 (5.2.2-1) ... Setting up sensible-utils (0.0.24) ... Setting up libxshmfence1:amd64 (1.3-1+b1) ... Setting up subread (2.0.6+dfsg-3) ... Setting up at-spi2-common (2.52.0-1) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up libxcb-randr0:amd64 (1.17.0-2) ... Setting up dbus-session-bus-common (1.14.10-4) ... Setting up procps (2:4.0.4-5) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:amd64 (1.6.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libwayland-egl1:amd64 (1.23.0-1) ... Setting up libperl5.38t64:amd64 (5.38.2-5) ... Setting up libssh2-1t64:amd64 (1.11.0-7) ... Setting up dbus-system-bus-common (1.14.10-4) ... Setting up openssl (3.2.2-1) ... Setting up libdrm-common (2.4.122-1) ... Setting up libxcomposite1:amd64 (1:0.4.5-1+b1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up dbus-bin (1.14.10-4+b1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up libxkbcommon0:amd64 (1.6.0-1+b1) ... Setting up libwayland-client0:amd64 (1.23.0-1) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2) ... Setting up libx11-xcb1:amd64 (2:1.8.7-1+b1) ... Setting up libice6:amd64 (2:1.0.10-1+b1) ... Setting up parafly (0.1.0-4) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libmbedx509-1t64:amd64 (2.28.8-1) ... Setting up libxdamage1:amd64 (1:1.1.6-1+b1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libavahi-common3:amd64 (0.8-13+b2) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libnss3:amd64 (2:3.102-1) ... Setting up dbus-daemon (1.14.10-4+b1) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-2) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up perl (5.38.2-5) ... Setting up libglib2.0-0t64:amd64 (2.81.1-3) ... Setting up libllvm17t64:amd64 (1:17.0.6-15) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b1) ... Setting up dbus (1.14.10-4+b1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5) ... Warning: program compiled against libxml 212 using older 209 Setting up libxinerama1:amd64 (2:1.1.4-3+b1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libio-html-perl (1.004-3) ... Setting up libxrandr2:amd64 (2:1.5.4-1) ... Setting up ucf (3.0043+nmu1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up libdrm2:amd64 (2.4.122-1) ... Setting up libmbedtls14t64:amd64 (2.28.8-1) ... Setting up libwayland-cursor0:amd64 (1.23.0-1) ... Setting up libpam-systemd:amd64 (256.5-1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libsm6:amd64 (2:1.2.3-1+b1) ... Setting up libavahi-client3:amd64 (0.8-13+b2) ... Setting up liburi-perl (5.28-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.122-1) ... Setting up libnet-ssleay-perl:amd64 (1.94-1+b1) ... Setting up libpaper1:amd64 (1.1.29+b1) ... Creating config file /etc/papersize with new version Setting up gtk-update-icon-cache (3.24.43-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libatk1.0-0t64:amd64 (2.52.0-1) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.4-3) ... Setting up openjdk-21-jre-headless:amd64 (21.0.4+7-3) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:amd64 (2:1.8.1-1) ... Setting up libcurl4t64:amd64 (8.9.1-2) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up libclone-perl:amd64 (0.46-1+b2) ... Setting up libdrm-radeon1:amd64 (2.4.122-1) ... Setting up libxtst6:amd64 (2:1.2.3-1.1+b1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libtk8.6:amd64 (8.6.14-1) ... Setting up python3.12 (3.12.4-3) ... Setting up libxcursor1:amd64 (1:1.2.2-1) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.122-1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libgl1-mesa-dri:amd64 (24.1.3-2) ... Setting up libtry-tiny-perl (0.32-1) ... Setting up libcurl3t64-gnutls:amd64 (8.9.1-2) ... Setting up libcloudproviders0:amd64 (0.3.6-1) ... Setting up libnet-http-perl (6.23-1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up libcolord2:amd64 (1.4.7-1+b1) ... Setting up libdconf1:amd64 (0.40.0-4+b2) ... Setting up dbus-user-session (1.14.10-4+b1) ... Setting up adwaita-icon-theme (46.0-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libatspi2.0-0t64:amd64 (2.52.0-1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libhtml-parser-perl:amd64 (3.83-1) ... Setting up libhts3t64:amd64 (1.20+ds-1) ... Setting up libcairo-gobject2:amd64 (1.18.0-3+b1) ... Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-1) ... Setting up kallisto (0.48.0+dfsg-4+b1) ... Setting up libcups2t64:amd64 (2.4.10-1) ... Setting up libio-socket-ssl-perl (2.088-1) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-1) ... Setting up libpython3-stdlib:amd64 (3.12.5-1) ... Setting up libhttp-message-perl (6.46-1) ... Setting up libatk-bridge2.0-0t64:amd64 (2.52.0-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libglx-mesa0:amd64 (24.1.3-2) ... Setting up libglx0:amd64 (1.7.0-1+b1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up dconf-service (0.40.0-4+b2) ... Setting up python3 (3.12.5-1) ... Setting up samtools (1.20-3) ... Setting up bowtie2 (2.5.4-1) ... Setting up ncbi-blast+ (2.16.0+ds-6) ... Setting up libgl1:amd64 (1.7.0-1+b1) ... Setting up jellyfish (2.3.1-3+b5) ... Setting up r-base-core (4.4.1-1) ... Creating config file /etc/R/Renviron with new version Setting up rsem (1.3.3+dfsg-3+b1) ... Setting up python3-pkg-resources (70.3.0-2) ... Setting up python3-pysam (0.22.1+ds-2+b1) ... Setting up dconf-gsettings-backend:amd64 (0.40.0-4+b2) ... Setting up bowtie (1.3.1-3) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up python3-htseq (2.0.5-2+b1) ... /usr/lib/python3/dist-packages/HTSeq/__init__.py:583: SyntaxWarning: invalid escape sequence '\=' _re_vcf_meta_comment = re.compile("^##([a-zA-Z]+)\=(.*)$") /usr/lib/python3/dist-packages/HTSeq/features.py:14: SyntaxWarning: invalid escape sequence '\s' _re_attr_main = re.compile("\s*([^\s\=]+)[\s=]+(.*)") /usr/lib/python3/dist-packages/HTSeq/features.py:15: SyntaxWarning: invalid escape sequence '\s' _re_attr_empty = re.compile("^\s*$") /usr/lib/python3/dist-packages/HTSeq/features.py:16: SyntaxWarning: invalid escape sequence '\s' _re_gff_meta_comment = re.compile("##\s*(\S+)\s+(\S*)") Setting up libgtk-3-common (3.24.43-1) ... Setting up libgtk-3-0t64:amd64 (3.24.43-1) ... Setting up libwww-perl (6.77-1) ... Setting up libguava-java (32.0.1-1) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libjung-free-java (2.1.1-2) ... Processing triggers for libc-bin (2.39-6) ... Processing triggers for systemd (256.5-1) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up openjdk-21-jre:amd64 (21.0.4+7-3) ... Setting up default-jre-headless (2:1.21-76) ... Setting up jaligner (1.0+dfsg-11) ... Setting up default-jre (2:1.21-76) ... Setting up trimmomatic (0.39+dfsg-2) ... Setting up trinityrnaseq (2.15.1+dfsg-5+b1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. 0m39.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-get', '-y', 'install', 'trinityrnaseq'] 0m39.6s INFO: Running scripts post_install 0m39.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_install_exceptions'] 0m39.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_install_exceptions'] 0m39.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury'] 0m40.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury'] 0m40.6s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpoxvz5ury to sid 0m40.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m40.6s INFO: Running scripts pre_distupgrade 0m40.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m40.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m40.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_distupgrade_exceptions'] 0m40.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_distupgrade_exceptions'] 0m40.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m40.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m40.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m40.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m40.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m40.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m40.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-get', 'update'] 0m43.7s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9950 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7302 kB] Fetched 17.5 MB in 2s (7597 kB/s) Reading package lists... 0m43.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-get', 'update'] 0m43.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-get', '-yf', 'dist-upgrade'] 0m54.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libnsl2 login.defs openssl-provider-legacy python3-autocommand python3-inflect python3-jaraco.context python3-jaraco.functools python3-more-itertools python3-typeguard python3-typing-extensions The following packages will be upgraded: at-spi2-common bash bsdutils gcc-14-base gtk-update-icon-cache libatk-bridge2.0-0t64 libatk1.0-0t64 libatomic1 libatspi2.0-0t64 libaudit-common libaudit1 libblkid1 libbz2-1.0 libc-bin libc6 libcap-ng0 libgcc-s1 libgfortran5 libgl1-mesa-dri libglapi-mesa libglib2.0-0t64 libglx-mesa0 libgomp1 libgtk-3-0t64 libgtk-3-common libharfbuzz0b libmount1 libnss3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpython3.12-minimal libpython3.12-stdlib libreadline8t64 libselinux1 libsmartcols1 libsqlite3-0 libssl3t64 libstdc++6 libuuid1 libxml2 login mawk mount openssl passwd python3-pkg-resources python3.12 python3.12-minimal readline-common trinityrnaseq util-linux 52 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. Need to get 44.5 MB of archives. After this operation, 817 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.32-1 [1499 kB] Get:2 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.40.2-7 [105 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-3 [9288 B] Get:4 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-3 [137 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-3 [837 kB] Get:6 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.2.0-3 [46.2 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14.2.0-3 [72.8 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14.2.0-3 [713 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.39-7 [2791 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40.2-7 [35.3 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.40.2-7 [167 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.40.2-7 [199 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.40.2-7 [139 kB] Get:14 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.40.2-7 [1217 kB] Get:15 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40.2-7 [154 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.7-1+b1 [76.6 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.39-7 [610 kB] Get:18 http://deb.debian.org/debian sid/main amd64 login.defs all 1:4.16.0-4 [185 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:4.0.1-1 [12.3 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.5-2 [17.2 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:4.0.1-1 [54.5 kB] Get:22 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.40.2-7 [57.7 kB] Get:23 http://deb.debian.org/debian sid/main amd64 openssl-provider-legacy amd64 3.3.1-7 [298 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.3.1-7 [2269 kB] Get:25 http://deb.debian.org/debian sid/main amd64 python3.12 amd64 3.12.5-1 [666 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libpython3.12-stdlib amd64 3.12.5-1 [1982 kB] Get:27 http://deb.debian.org/debian sid/main amd64 python3.12-minimal amd64 3.12.5-1 [2166 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libpython3.12-minimal amd64 3.12.5-1 [813 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-6 [37.9 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get:31 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-5 [69.3 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:34 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.16.0-4 [1232 kB] Get:35 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20240819-2 [138 kB] Get:36 http://deb.debian.org/debian sid/main amd64 at-spi2-common all 2.53.1-1 [170 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.81.2-1 [1497 kB] Get:38 http://deb.debian.org/debian sid/main amd64 gtk-update-icon-cache amd64 3.24.43-2 [46.9 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libatk1.0-0t64 amd64 2.53.1-1 [51.1 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libatspi2.0-0t64 amd64 2.53.1-1 [76.3 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libatk-bridge2.0-0t64 amd64 2.53.1-1 [67.8 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libglx-mesa0 amd64 24.1.6-1 [154 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libgl1-mesa-dri amd64 24.1.6-1 [8718 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libglapi-mesa amd64 24.1.6-1 [37.0 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 9.0.0-1 [474 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-2 [35.2 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-2 [54.4 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.54.0+ds-2 [223 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libgtk-3-common all 3.24.43-2 [4655 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libgtk-3-0t64 amd64 3.24.43-2 [2755 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libnss3 amd64 2:3.103-1 [1352 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.12.7+dfsg-3+b1 [671 kB] Get:53 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.3.1-7 [1381 kB] Get:54 http://deb.debian.org/debian sid/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:55 http://deb.debian.org/debian sid/main amd64 python3-more-itertools all 10.3.0-1 [62.0 kB] Get:56 http://deb.debian.org/debian sid/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:57 http://deb.debian.org/debian sid/main amd64 python3-typeguard all 4.3.0-1 [36.5 kB] Get:58 http://deb.debian.org/debian sid/main amd64 python3-inflect all 7.3.1-1 [42.2 kB] Get:59 http://deb.debian.org/debian sid/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:60 http://deb.debian.org/debian sid/main amd64 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get:61 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 73.0.0-1 [212 kB] Get:62 http://deb.debian.org/debian sid/main amd64 trinityrnaseq amd64 2.15.2+dfsg-1 [1738 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 44.5 MB in 1s (60.4 MB/s) (Reading database ... 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Unpacking openssl-provider-legacy (3.3.1-7) ... Setting up libssl3t64:amd64 (3.3.1-7) ... Setting up openssl-provider-legacy (3.3.1-7) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19687 files and directories currently installed.) Preparing to unpack .../python3.12_3.12.5-1_amd64.deb ... Unpacking python3.12 (3.12.5-1) over (3.12.4-3) ... Preparing to unpack .../libpython3.12-stdlib_3.12.5-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.5-1) over (3.12.4-3) ... 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Leaving 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Leaving 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Leaving 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Leaving 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) over (8.2-4) ... Preparing to unpack .../libsqlite3-0_3.46.1-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.1-1) over (3.46.0-1) ... Preparing to unpack .../passwd_1%3a4.16.0-4_amd64.deb ... Unpacking passwd (1:4.16.0-4) over (1:4.15.3-2) ... Setting up passwd (1:4.16.0-4) ... (Reading database ... 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Setting up python3-autocommand (2.2.2-3) ... Setting up libatomic1:amd64 (14.2.0-3) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up libglapi-mesa:amd64 (24.1.6-1) ... Setting up libgfortran5:amd64 (14.2.0-3) ... Setting up mount (2.40.2-7) ... Setting up at-spi2-common (2.53.1-1) ... Setting up libnsl2:amd64 (1.3.0-3+b2) ... Setting up mawk (1.3.4.20240819-2) ... Setting up openssl (3.3.1-7) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up trinityrnaseq (2.15.2+dfsg-1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... Setting up libgtk-3-common (3.24.43-2) ... Setting up login (1:4.16.0-2+really2.40.2-7) ... Setting up python3.12-minimal (3.12.5-1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up libgl1-mesa-dri:amd64 (24.1.6-1) ... Setting up python3-inflect (7.3.1-1) ... Setting up libglib2.0-0t64:amd64 (2.81.2-1) ... Setting up libatspi2.0-0t64:amd64 (2.53.1-1) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up libharfbuzz0b:amd64 (9.0.0-1) ... Setting up python3-pkg-resources (73.0.0-1) ... Setting up gtk-update-icon-cache (3.24.43-2) ... Setting up libglx-mesa0:amd64 (24.1.6-1) ... Setting up libatk1.0-0t64:amd64 (2.53.1-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.5-1) ... Setting up python3.12 (3.12.5-1) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-2) ... Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-2) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-2) ... Setting up libatk-bridge2.0-0t64:amd64 (2.53.1-1) ... Setting up libgtk-3-0t64:amd64 (3.24.43-2) ... Processing triggers for libc-bin (2.39-7) ... Processing triggers for systemd (256.5-1) ... Processing triggers for debianutils (5.20) ... 0m54.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-get', '-yf', 'dist-upgrade'] 0m54.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m55.0s DUMP: a6de81260fb5a1a2f6e251006dd96d42 - 0m55.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m55.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-cache', 'show', '--no-all-versions', 'trinityrnaseq'] 0m55.2s DUMP: Package: trinityrnaseq Version: 2.15.2+dfsg-1 Installed-Size: 7531 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libhts3t64 (>= 1.17), libstdc++6 (>= 14), zlib1g (>= 1:1.1.4), perl:any, jaligner, libgetopt-java, libjung-free-java, bowtie, bowtie2, libwww-perl, default-jre-headless, samtools, jellyfish, r-base-core, rsem, berkeley-express, trimmomatic, parafly, ncbi-blast+, python3, liburi-perl, python3-htseq, subread, kallisto Recommends: curl, trinityrnaseq-examples, picard-tools, tabix, gmap, salmon, rna-star, hisat2, r-cran-tidyverse, r-cran-readr, r-bioc-edger, r-bioc-deseq2, r-bioc-rots, r-cran-cluster, r-cran-fastcluster, r-bioc-ctc, r-bioc-goseq, r-cran-goplot, r-cran-gplots, r-bioc-dexseq, r-cran-ape, r-bioc-biobase, r-bioc-qvalue, r-cran-argparse, r-cran-kernsmooth, python3-numpy, python3-hisat2 Suggests: collectl, transdecoder, r-bioc-tximport, r-bioc-tximportdata Description-en: RNA-Seq De novo Assembly Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. Description-md5: 2ee7f38dbb99a040c33d6619f4f5668b Homepage: https://github.com/trinityrnaseq/trinityrnaseq Section: science Priority: optional Filename: pool/main/t/trinityrnaseq/trinityrnaseq_2.15.2+dfsg-1_amd64.deb Size: 1737612 MD5sum: 174e11fbf10d59a4fb4de08221fff0f6 SHA256: 8f0ef08eaed9a05d70851021f36f64982737d1f842c38362e03084f0a0026b97 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-cache', 'show', '--no-all-versions', 'trinityrnaseq'] 0m55.2s INFO: apt-cache knows about the following packages: trinityrnaseq 0m55.2s INFO: Running scripts pre_install 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_database-server'] 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_database-server'] 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_exceptions'] 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_exceptions'] 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_extras'] 0m55.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_extras'] 0m55.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_foreign_architecture'] 0m55.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_foreign_architecture'] 0m55.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m55.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m55.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-cache', 'policy'] 0m55.4s 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: 0m55.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-cache', 'policy'] 0m55.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-cache', 'policy', 'trinityrnaseq'] 0m55.4s DUMP: trinityrnaseq: Installed: 2.15.2+dfsg-1 Candidate: 2.15.2+dfsg-1 Version table: *** 2.15.2+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m55.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-cache', 'policy', 'trinityrnaseq'] 0m55.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-get', '-y', 'install', 'trinityrnaseq'] 0m55.9s DUMP: Reading package lists... Building dependency tree... Reading state information... trinityrnaseq is already the newest version (2.15.2+dfsg-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m55.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-get', '-y', 'install', 'trinityrnaseq'] 0m55.9s INFO: Running scripts post_install 0m55.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_install_exceptions'] 0m55.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_install_exceptions'] 0m55.9s INFO: Running scripts post_distupgrade 0m55.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m55.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m55.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_distupgrade_exceptions'] 0m55.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_distupgrade_exceptions'] 0m55.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m55.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m55.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m55.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m55.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_distupgrade_zz_backports'] 0m55.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_distupgrade_zz_backports'] 0m55.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury'] 0m57.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury'] 0m57.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury'] 0m58.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury'] 0m58.1s INFO: Running scripts pre_install 0m58.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_database-server'] 0m58.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_database-server'] 0m58.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_exceptions'] 0m58.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_exceptions'] 0m58.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_extras'] 0m58.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_extras'] 0m58.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_foreign_architecture'] 0m58.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_foreign_architecture'] 0m58.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m58.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m58.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-cache', 'policy'] 0m58.2s 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: 0m58.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-cache', 'policy'] 0m58.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-cache', 'policy', 'trinityrnaseq'] 0m58.3s DUMP: trinityrnaseq: Installed: 2.15.2+dfsg-1 Candidate: 2.15.2+dfsg-1 Version table: *** 2.15.2+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m58.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-cache', 'policy', 'trinityrnaseq'] 0m58.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-get', '-y', 'install', 'trinityrnaseq=2.15.2+dfsg-1'] 0m58.7s DUMP: Reading package lists... Building dependency tree... Reading state information... trinityrnaseq is already the newest version (2.15.2+dfsg-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m58.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-get', '-y', 'install', 'trinityrnaseq=2.15.2+dfsg-1'] 0m58.7s INFO: Running scripts post_install 0m58.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_install_exceptions'] 0m58.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_install_exceptions'] 0m58.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury'] 0m59.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury'] 1m1.1s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', '-ac', '--ignore-obsolete'] 1m5.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', '-ac', '--ignore-obsolete'] 1m5.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m5.8s DUMP: 0.15.6 1m5.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m5.8s INFO: Running adequate version 0.15.6 now. 1m5.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'trinityrnaseq'] 1m6.1s DUMP: trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/TGLOBALS.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/__init__.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/misc/alt_GG_read_partitioning_JCornish/genwig2.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/support_scripts/tests/sample_data_tests.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/support_scripts/tests/test_prep.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/support_scripts/tests/tests.py 1m6.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'trinityrnaseq'] 1m6.1s ERROR: WARN: Inadequate results from running adequate! trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/TGLOBALS.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/__init__.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/misc/alt_GG_read_partitioning_JCornish/genwig2.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/support_scripts/tests/sample_data_tests.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/support_scripts/tests/test_prep.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/support_scripts/tests/tests.py 1m6.1s ERROR: WARN: Running adequate resulted in inadequate tags found: py-file-not-bytecompiled 1m6.1s INFO: Running scripts pre_remove 1m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m11.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_remove_exceptions'] 1m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/pre_remove_exceptions'] 1m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m11.4s DUMP: install ok installed adduser adduser 3.137 install ok installed adwaita-icon-theme adwaita-icon-theme 46.0-1 install ok installed apt apt 2.9.8 install ok installed at-spi2-common at-spi2-common 2.53.1-1 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.4 install ok installed bash bash 5.2.32-1 install ok installed berkeley-express berkeley-express 1.5.3+dfsg-3+b3 install ok installed bowtie bowtie 1.3.1-3 install ok installed bowtie2 bowtie2 2.5.4-1 install ok installed bsdutils bsdutils 1:2.40.2-7 install ok installed ca-certificates ca-certificates 20240203 install ok installed ca-certificates-java ca-certificates-java 20240118 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-9 install ok installed dbus dbus 1.14.10-4+b1 install ok installed dbus-bin dbus-bin 1.14.10-4+b1 install ok installed dbus-daemon dbus-daemon 1.14.10-4+b1 install ok installed dbus-session-bus-common dbus-session-bus-common 1.14.10-4 install ok installed dbus-system-bus-common dbus-system-bus-common 1.14.10-4 install ok installed dbus-user-session dbus-user-session 1.14.10-4+b1 install ok installed dconf-gsettings-backend:amd64 dconf-gsettings-backend 0.40.0-4+b2 install ok installed dconf-service dconf-service 0.40.0-4+b2 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed default-jre default-jre 2:1.21-76 install ok installed default-jre-headless default-jre-headless 2:1.21-76 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1 install ok installed findutils findutils 4.10.0-3 install ok installed fontconfig fontconfig 2.15.0-1.1 install ok installed fontconfig-config fontconfig-config 2.15.0-1.1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-3 install ok installed gpgv gpgv 2.2.43-8 install ok installed grep grep 3.11-4 install ok installed gtk-update-icon-cache gtk-update-icon-cache 3.24.43-2 install ok installed gzip gzip 1.12-1.1 install ok installed hicolor-icon-theme hicolor-icon-theme 0.18-1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed jaligner jaligner 1.0+dfsg-11 install ok installed java-common java-common 0.76 install ok installed jellyfish jellyfish 2.3.1-3+b5 install ok installed kallisto kallisto 0.48.0+dfsg-4+b1 install ok installed libacl1:amd64 libacl1 2.3.2-2 install ok installed libapparmor1:amd64 libapparmor1 3.1.7-1+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.8 install ok installed libasound2-data libasound2-data 1.2.12-1 install ok installed libasound2t64:amd64 libasound2t64 1.2.12-1 install ok installed libatinject-jsr330-api-java libatinject-jsr330-api-java 1.0+ds1-5 install ok installed libatk-bridge2.0-0t64:amd64 libatk-bridge2.0-0t64 2.53.1-1 install ok installed libatk1.0-0t64:amd64 libatk1.0-0t64 2.53.1-1 install ok installed libatomic1:amd64 libatomic1 14.2.0-3 install ok installed libatspi2.0-0t64:amd64 libatspi2.0-0t64 2.53.1-1 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:4.0.1-1 install ok installed libaudit1:amd64 libaudit1 1:4.0.1-1 install ok installed libavahi-client3:amd64 libavahi-client3 0.8-13+b2 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.8-13+b2 install ok installed libavahi-common3:amd64 libavahi-common3 0.8-13+b2 install ok installed libbamtools2.5.2:amd64 libbamtools2.5.2 2.5.2+dfsg-6 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblkid1:amd64 libblkid1 2.40.2-7 install ok installed libboost-filesystem1.83.0:amd64 libboost-filesystem1.83.0 1.83.0-3.1 install ok installed libboost-program-options1.83.0:amd64 libboost-program-options1.83.0 1.83.0-3.1 install ok installed libboost-thread1.83.0:amd64 libboost-thread1.83.0 1.83.0-3.1 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b4 install ok installed libbsd0:amd64 libbsd0 0.12.2-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.39-7 install ok installed libc6:amd64 libc6 2.39-7 install ok installed libcairo-gobject2:amd64 libcairo-gobject2 1.18.0-3+b1 install ok installed libcairo2:amd64 libcairo2 1.18.0-3+b1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libclone-perl:amd64 libclone-perl 0.46-1+b2 install ok installed libcloudproviders0:amd64 libcloudproviders0 0.3.6-1 install ok installed libcolord2:amd64 libcolord2 1.4.7-1+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libcups2t64:amd64 libcups2t64 2.4.10-1 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.9.1-2 install ok installed libcurl4t64:amd64 libcurl4t64 8.9.1-2 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdbus-1-3:amd64 libdbus-1-3 1.14.10-4+b1 install ok installed libdconf1:amd64 libdconf1 0.40.0-4+b2 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.272 install ok installed libdeflate0:amd64 libdeflate0 1.21-1 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.122-1 install ok installed libdrm-common libdrm-common 2.4.122-1 install ok installed libdrm-intel1:amd64 libdrm-intel1 2.4.122-1 install ok installed libdrm-radeon1:amd64 libdrm-radeon1 2.4.122-1 install ok installed libdrm2:amd64 libdrm2 2.4.122-1 install ok installed libedit2:amd64 libedit2 3.1-20240517-1 install ok installed libelf1t64:amd64 libelf1t64 0.191-2 install ok installed libencode-locale-perl libencode-locale-perl 1.05-3 install ok installed libepoxy0:amd64 libepoxy0 1.5.10-1+b2 install ok installed liberror-prone-java liberror-prone-java 2.18.0-1 install ok installed libexpat1:amd64 libexpat1 2.6.2-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfile-listing-perl libfile-listing-perl 6.16-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1.1 install ok installed libfreetype6:amd64 libfreetype6 2.13.2+dfsg-1+b4 install ok installed libfribidi0:amd64 libfribidi0 1.0.15-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-3 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2 install ok installed libgdk-pixbuf-2.0-0:amd64 libgdk-pixbuf-2.0-0 2.42.12+dfsg-1 install ok installed libgdk-pixbuf2.0-common libgdk-pixbuf2.0-common 2.42.12+dfsg-1 install ok installed libgetopt-java libgetopt-java 1.0.14+dfsg-6 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-3 install ok installed libgif7:amd64 libgif7 5.2.2-1 install ok installed libgl1:amd64 libgl1 1.7.0-1+b1 install ok installed libgl1-mesa-dri:amd64 libgl1-mesa-dri 24.1.6-1 install ok installed libglapi-mesa:amd64 libglapi-mesa 24.1.6-1 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.81.2-1 install ok installed libglvnd0:amd64 libglvnd0 1.7.0-1+b1 install ok installed libglx-mesa0:amd64 libglx-mesa0 24.1.6-1 install ok installed libglx0:amd64 libglx0 1.7.0-1+b1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2 install ok installed libgomp1:amd64 libgomp1 14.2.0-3 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-3 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libgtk-3-0t64:amd64 libgtk-3-0t64 3.24.43-2 install ok installed libgtk-3-common libgtk-3-common 3.24.43-2 install ok installed libguava-java libguava-java 32.0.1-1 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 9.0.0-1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1 install ok installed libhtml-parser-perl:amd64 libhtml-parser-perl 3.83-1 install ok installed libhtml-tagset-perl libhtml-tagset-perl 3.24-1 install ok installed libhtml-tree-perl libhtml-tree-perl 5.07-3 install ok installed libhts3t64:amd64 libhts3t64 1.20+ds-1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.0-1+b1 install ok installed libhttp-cookies-perl libhttp-cookies-perl 6.11-1 install ok installed libhttp-date-perl libhttp-date-perl 6.06-1 install ok installed libhttp-message-perl libhttp-message-perl 6.46-1 install ok installed libhttp-negotiate-perl libhttp-negotiate-perl 6.01-2 install ok installed libice6:amd64 libice6 2:1.0.10-1+b1 install ok installed libicu72:amd64 libicu72 72.1-5 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libio-html-perl libio-html-perl 1.004-3 install ok installed libio-socket-ssl-perl libio-socket-ssl-perl 2.088-1 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b1 install ok installed libjbzip2-java libjbzip2-java 0.9.1-8 install ok installed libjellyfish-2.0-2:amd64 libjellyfish-2.0-2 2.3.1-3+b5 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3 install ok installed libjsr305-java libjsr305-java 0.1~+svn49-11 install ok installed libjung-free-java libjung-free-java 2.1.1-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2+b1 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.18+dfsg-2 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-4+b1 install ok installed libllvm17t64:amd64 libllvm17t64 1:17.0.6-15 install ok installed liblmdb0:amd64 liblmdb0 0.9.31-1+b1 install ok installed liblwp-mediatypes-perl liblwp-mediatypes-perl 6.04-2 install ok installed liblwp-protocol-https-perl liblwp-protocol-https-perl 6.14-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3 install ok installed liblzma5:amd64 liblzma5 5.6.2-2 install ok installed libmbedcrypto7t64:amd64 libmbedcrypto7t64 2.28.8-1 install ok installed libmbedtls14t64:amd64 libmbedtls14t64 2.28.8-1 install ok installed libmbedx509-1t64:amd64 libmbedx509-1t64 2.28.8-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40.2-7 install ok installed libncurses6:amd64 libncurses6 6.5-2 install ok installed libncursesw6:amd64 libncursesw6 6.5-2 install ok installed libnet-http-perl libnet-http-perl 6.23-1 install ok installed libnet-ssleay-perl:amd64 libnet-ssleay-perl 1.94-1+b1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.62.1-2 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.4.0-1 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.6.0-1 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.6.0-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b2 install ok installed libnspr4:amd64 libnspr4 2:4.35-1.1+b1 install ok installed libnss3:amd64 libnss3 2:3.103-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam-systemd:amd64 libpam-systemd 256.5-1 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.54.0+ds-2 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.54.0+ds-2 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.54.0+ds-2 install ok installed libpaper-utils libpaper-utils 1.1.29+b1 install ok installed libpaper1:amd64 libpaper1 1.1.29+b1 install ok installed libpciaccess0:amd64 libpciaccess0 0.17-3+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libpcsclite1:amd64 libpcsclite1 2.3.0-1 install ok installed libperl5.38t64:amd64 libperl5.38t64 5.38.2-5 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1+b1 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.43-5 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-5 install ok installed libprotobuf32t64:amd64 libprotobuf32t64 3.21.12-9 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.12.5-1 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.5-1 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.5-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-5 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b4 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-7 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-7 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b1 install ok installed libselinux1:amd64 libselinux1 3.7-1+b1 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b4 install ok installed libsensors-config libsensors-config 1:3.6.0-10 install ok installed libsensors5:amd64 libsensors5 1:3.6.0-10 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.4.0-0.1 install ok installed libsm6:amd64 libsm6 2:1.2.3-1+b1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-7 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.1-1 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.0-7 install ok installed libssl3t64:amd64 libssl3t64 3.3.1-7 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-3 install ok installed libsystemd-shared:amd64 libsystemd-shared 256.5-1 install ok installed libsystemd0:amd64 libsystemd0 256.5-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.14+dfsg-1 install ok installed libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-5 install ok installed libtimedate-perl libtimedate-perl 2.3300-2 install ok installed libtinfo6:amd64 libtinfo6 6.5-2 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3 install ok installed libtk8.6:amd64 libtk8.6 8.6.14-1 install ok installed libtry-tiny-perl libtry-tiny-perl 0.32-1 install ok installed libudev1:amd64 libudev1 256.5-1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed liburi-perl liburi-perl 5.28-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-7 install ok installed libuv1t64:amd64 libuv1t64 1.48.0-5 install ok installed libvulkan1:amd64 libvulkan1 1.3.283.0-1 install ok installed libwayland-client0:amd64 libwayland-client0 1.23.0-1 install ok installed libwayland-cursor0:amd64 libwayland-cursor0 1.23.0-1 install ok installed libwayland-egl1:amd64 libwayland-egl1 1.23.0-1 install ok installed libwebp7:amd64 libwebp7 1.4.0-0.1 install ok installed libwww-perl libwww-perl 6.77-1 install ok installed libwww-robotrules-perl libwww-robotrules-perl 6.02-1 install ok installed libx11-6:amd64 libx11-6 2:1.8.7-1+b1 install ok installed libx11-data libx11-data 2:1.8.7-1 install ok installed libx11-xcb1:amd64 libx11-xcb1 2:1.8.7-1+b1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1+b1 install ok installed libxcb-dri2-0:amd64 libxcb-dri2-0 1.17.0-2 install ok installed libxcb-dri3-0:amd64 libxcb-dri3-0 1.17.0-2 install ok installed libxcb-glx0:amd64 libxcb-glx0 1.17.0-2 install ok installed libxcb-present0:amd64 libxcb-present0 1.17.0-2 install ok installed libxcb-randr0:amd64 libxcb-randr0 1.17.0-2 install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-2 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2 install ok installed libxcb-sync1:amd64 libxcb-sync1 1.17.0-2 install ok installed libxcb-xfixes0:amd64 libxcb-xfixes0 1.17.0-2 install ok installed libxcb1:amd64 libxcb1 1.17.0-2 install ok installed libxcomposite1:amd64 libxcomposite1 1:0.4.5-1+b1 install ok installed libxcursor1:amd64 libxcursor1 1:1.2.2-1 install ok installed libxdamage1:amd64 libxdamage1 1:1.1.6-1+b1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3+b1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxfixes3:amd64 libxfixes3 1:6.0.0-2+b1 install ok installed libxft2:amd64 libxft2 2.3.6-1+b1 install ok installed libxi6:amd64 libxi6 2:1.8.1-1 install ok installed libxinerama1:amd64 libxinerama1 2:1.1.4-3+b1 install ok installed libxkbcommon0:amd64 libxkbcommon0 1.6.0-1+b1 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg-3+b1 install ok installed libxrandr2:amd64 libxrandr2 2:1.5.4-1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1+b1 install ok installed libxshmfence1:amd64 libxshmfence1 1.3-1+b1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1+b1 install ok installed libxt6t64:amd64 libxt6t64 1:1.2.1-1.2 install ok installed libxtst6:amd64 libxtst6 2:1.2.3-1.1+b1 install ok installed libxxf86vm1:amd64 libxxf86vm1 1:1.1.4-1+b2 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libz3-4:amd64 libz3-4 4.8.12-3.1+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1 install ok installed login login 1:4.16.0-2+really2.40.2-7 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1 install ok installed mawk mawk 1.3.4.20240819-2 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.40.2-7 install ok installed ncbi-blast+ ncbi-blast+ 2.16.0+ds-6 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg2-3 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2 install ok installed netbase netbase 6.4 install ok installed openjdk-21-jre:amd64 openjdk-21-jre 21.0.4+7-3 install ok installed openjdk-21-jre-headless:amd64 openjdk-21-jre-headless 21.0.4+7-3 install ok installed openssl openssl 3.3.1-7 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.1-7 install ok installed parafly parafly 0.1.0-4 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl perl 5.38.2-5 install ok installed perl-base perl-base 5.38.2-5 install ok installed perl-modules-5.38 perl-modules-5.38 5.38.2-5 install ok installed perl-openssl-defaults:amd64 perl-openssl-defaults 7+b2 install ok installed procps procps 2:4.0.4-5 install ok installed python3 python3 3.12.5-1 install ok installed python3-autocommand python3-autocommand 2.2.2-3 install ok installed python3-htseq python3-htseq 2.0.5-2+b1 install ok installed python3-inflect python3-inflect 7.3.1-1 install ok installed python3-jaraco.context python3-jaraco.context 6.0.0-1 install ok installed python3-jaraco.functools python3-jaraco.functools 4.0.2-1 install ok installed python3-minimal python3-minimal 3.12.5-1 install ok installed python3-more-itertools python3-more-itertools 10.3.0-1 install ok installed python3-numpy python3-numpy 1:1.26.4+ds-11 install ok installed python3-pkg-resources python3-pkg-resources 73.0.0-1 install ok installed python3-pysam python3-pysam 0.22.1+ds-2+b1 install ok installed python3-typeguard python3-typeguard 4.3.0-1 install ok installed python3-typing-extensions python3-typing-extensions 4.12.2-2 install ok installed python3.12 python3.12 3.12.5-1 install ok installed python3.12-minimal python3.12-minimal 3.12.5-1 install ok installed r-base-core r-base-core 4.4.1-1 install ok installed readline-common readline-common 8.2-5 install ok installed rsem rsem 1.3.3+dfsg-3+b1 install ok installed samtools samtools 1.20-3 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.24 install ok installed shared-mime-info shared-mime-info 2.4-5 install ok installed subread subread 2.0.6+dfsg-3 install ok installed systemd systemd 256.5-1 install ok installed systemd-sysv systemd-sysv 256.5-1 install ok installed sysvinit-utils sysvinit-utils 3.10-1 install ok installed tar tar 1.35+dfsg-3 install ok installed trimmomatic trimmomatic 0.39+dfsg-2 install ok installed trinityrnaseq trinityrnaseq 2.15.2+dfsg-1 install ok installed tzdata tzdata 2024a-4 install ok installed ucf ucf 3.0043+nmu1 install ok installed unzip unzip 6.0-28 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-7 install ok installed x11-common x11-common 1:7.7+23.1 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed xkb-data xkb-data 2.42-1 install ok installed zip zip 3.0-14 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1 1m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-get', 'remove', 'adduser', 'adwaita-icon-theme', 'at-spi2-common', 'berkeley-express', 'bowtie', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'default-jre', 'default-jre-headless', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'jaligner', 'java-common', 'jellyfish', 'kallisto', 'libapparmor1:amd64', 'libasound2-data', 'libasound2t64:amd64', 'libatinject-jsr330-api-java', 'libatk-bridge2.0-0t64:amd64', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libatspi2.0-0t64:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbamtools2.5.2:amd64', 'libblas3:amd64', 'libboost-filesystem1.83.0:amd64', 'libboost-program-options1.83.0:amd64', 'libboost-thread1.83.0:amd64', 'libbrotli1:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libclone-perl:amd64', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libencode-locale-perl', 'libepoxy0:amd64', 'liberror-prone-java', 'libexpat1:amd64', 'libfile-listing-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgetopt-java', 'libgfortran5:amd64', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libguava-java', 'libharfbuzz0b:amd64', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu72:amd64', 'libio-html-perl', 'libio-socket-ssl-perl', 'libjbig0:amd64', 'libjbzip2-java', 'libjellyfish-2.0-2:amd64', 'libjpeg62-turbo:amd64', 'libjsr305-java', 'libjung-free-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm17t64:amd64', 'liblmdb0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto7t64:amd64', 'libmbedtls14t64:amd64', 'libmbedx509-1t64:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.38t64:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libprotobuf32t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libsystemd-shared:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtimedate-perl', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libuv1t64:amd64', 'libvulkan1:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwebp7:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml2:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'openjdk-21-jre:amd64', 'openjdk-21-jre-headless:amd64', 'openssl', 'parafly', 'perl', 'perl-modules-5.38', 'perl-openssl-defaults:amd64', 'procps', 'python3', 'python3-autocommand', 'python3-htseq', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-numpy', 'python3-pkg-resources', 'python3-pysam', 'python3-typeguard', 'python3-typing-extensions', 'python3.12', 'python3.12-minimal', 'r-base-core', 'readline-common', 'rsem', 'samtools', 'sensible-utils', 'shared-mime-info', 'subread', 'systemd', 'systemd-sysv', 'trimmomatic', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'xkb-data', 'zip', 'trinityrnaseq'] 1m15.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: adduser adwaita-icon-theme at-spi2-common berkeley-express bowtie bowtie2 ca-certificates ca-certificates-java dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service default-jre default-jre-headless fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono gtk-update-icon-cache hicolor-icon-theme jaligner java-common jellyfish kallisto libapparmor1 libasound2-data libasound2t64 libatinject-jsr330-api-java libatk-bridge2.0-0t64 libatk1.0-0t64 libatomic1 libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 libbamtools2.5.2 libblas3 libboost-filesystem1.83.0 libboost-program-options1.83.0 libboost-thread1.83.0 libbrotli1 libcairo-gobject2 libcairo2 libclone-perl libcloudproviders0 libcolord2 libcups2t64 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdbus-1-3 libdconf1 libdeflate0 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-radeon1 libdrm2 libedit2 libelf1t64 libencode-locale-perl libepoxy0 liberror-prone-java libexpat1 libfile-listing-perl libfontconfig1 libfreetype6 libfribidi0 libgdbm-compat4t64 libgdbm6t64 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgetopt-java libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0t64 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libguava-java libharfbuzz0b libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts3t64 libhtscodecs2 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu72 libio-html-perl libio-socket-ssl-perl libjbig0 libjbzip2-java libjellyfish-2.0-2 libjpeg62-turbo libjsr305-java libjung-free-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.5-0 liblerc4 libllvm17t64 liblmdb0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libncurses6 libncursesw6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libnspr4 libnss3 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.38t64 libpixman-1-0 libpng16-16t64 libproc2-0 libprotobuf32t64 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libsm6 libsqlite3-0 libssh2-1t64 libsystemd-shared libtcl8.6 libthai-data libthai0 libtiff6 libtimedate-perl libtirpc-common libtirpc3t64 libtk8.6 libtry-tiny-perl liburi-perl libuv1t64 libvulkan1 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwebp7 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml2 libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6t64 libxtst6 libxxf86vm1 libz3-4 media-types ncbi-blast+ ncbi-data netbase openjdk-21-jre openjdk-21-jre-headless openssl parafly perl perl-modules-5.38 perl-openssl-defaults procps python3 python3-autocommand python3-htseq python3-inflect python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-numpy python3-pkg-resources python3-pysam python3-typeguard python3-typing-extensions python3.12 python3.12-minimal r-base-core readline-common rsem samtools sensible-utils shared-mime-info subread systemd systemd-sysv trimmomatic trinityrnaseq ucf unzip x11-common xdg-utils xkb-data zip 0 upgraded, 0 newly installed, 261 to remove and 0 not upgraded. After this operation, 979 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 ... 19864 files and directories currently installed.) Removing trinityrnaseq (2.15.2+dfsg-1) ... Removing trimmomatic (0.39+dfsg-2) ... Removing default-jre (2:1.21-76) ... Removing openjdk-21-jre:amd64 (21.0.4+7-3) ... Removing libgtk-3-0t64:amd64 (3.24.43-2) ... Removing libgtk-3-common (3.24.43-2) ... Removing dconf-gsettings-backend:amd64 (0.40.0-4+b2) ... Removing dconf-service (0.40.0-4+b2) ... Removing dbus-user-session (1.14.10-4+b1) ... Removing libpam-systemd:amd64 (256.5-1) ... Removing dbus (1.14.10-4+b1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of stop. Removing dbus-system-bus-common (1.14.10-4) ... Removing adduser (3.137) ... Removing adwaita-icon-theme (46.0-1) ... Removing libatk-bridge2.0-0t64:amd64 (2.53.1-1) ... Removing libatk1.0-0t64:amd64 (2.53.1-1) ... Removing at-spi2-common (2.53.1-1) ... Removing berkeley-express (1.5.3+dfsg-3+b3) ... Removing rsem (1.3.3+dfsg-3+b1) ... Removing bowtie (1.3.1-3) ... Removing bowtie2 (2.5.4-1) ... Removing r-base-core (4.4.1-1) ... Removing jaligner (1.0+dfsg-11) ... Removing default-jre-headless (2:1.21-76) ... Removing openjdk-21-jre-headless:amd64 (21.0.4+7-3) ... Removing ca-certificates-java (20240118) ... Removing dbus-daemon (1.14.10-4+b1) ... Removing dbus-bin (1.14.10-4+b1) ... Removing dbus-session-bus-common (1.14.10-4) ... Removing libpangocairo-1.0-0:amd64 (1.54.0+ds-2) ... Removing libpangoft2-1.0-0:amd64 (1.54.0+ds-2) ... Removing libpango-1.0-0:amd64 (1.54.0+ds-2) ... Removing fontconfig (2.15.0-1.1) ... Removing libtk8.6:amd64 (8.6.14-1) ... Removing libxft2:amd64 (2.3.6-1+b1) ... Removing libcairo-gobject2:amd64 (1.18.0-3+b1) ... Removing libcairo2:amd64 (1.18.0-3+b1) ... Removing libfontconfig1:amd64 (2.15.0-1.1) ... Removing fontconfig-config (2.15.0-1.1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing gtk-update-icon-cache (3.24.43-2) ... Removing hicolor-icon-theme (0.18-1) ... Removing java-common (0.76) ... Removing jellyfish (2.3.1-3+b5) ... Removing kallisto (0.48.0+dfsg-4+b1) ... Removing systemd-sysv (256.5-1) ... Removing systemd (256.5-1) ... Removing libsystemd-shared:amd64 (256.5-1) ... Removing libapparmor1:amd64 (3.1.7-1+b1) ... Removing libasound2t64:amd64 (1.2.12-1) ... Removing libasound2-data (1.2.12-1) ... Removing libjung-free-java (2.1.1-2) ... Removing libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1) ... Removing shared-mime-info (2.4-5) ... Removing libcloudproviders0:amd64 (0.3.6-1) ... Removing libatspi2.0-0t64:amd64 (2.53.1-1) ... Removing libcups2t64:amd64 (2.4.10-1) ... Removing libavahi-client3:amd64 (0.8-13+b2) ... Removing libavahi-common3:amd64 (0.8-13+b2) ... Removing libavahi-common-data:amd64 (0.8-13+b2) ... Removing libbamtools2.5.2:amd64 (2.5.2+dfsg-6) ... Removing python3-htseq (2.0.5-2+b1) ... Removing python3-numpy (1:1.26.4+ds-11) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing libboost-filesystem1.83.0:amd64 (1.83.0-3.1) ... Removing libboost-program-options1.83.0:amd64 (1.83.0-3.1) ... Removing libboost-thread1.83.0:amd64 (1.83.0-3.1) ... Removing libharfbuzz0b:amd64 (9.0.0-1) ... Removing libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Removing libcurl4t64:amd64 (8.9.1-2) ... Removing libcolord2:amd64 (1.4.7-1+b1) ... Removing samtools (1.20-3) ... Removing python3-pysam (0.22.1+ds-2+b1) ... Removing libhts3t64:amd64 (1.20+ds-1) ... Removing libcurl3t64-gnutls:amd64 (8.9.1-2) ... Removing libthai0:amd64 (0.1.29-2) ... Removing libdatrie1:amd64 (0.2.13-3) ... Removing libdbus-1-3:amd64 (1.14.10-4+b1) ... Removing libdconf1:amd64 (0.40.0-4+b2) ... Removing libtiff6:amd64 (4.5.1+git230720-5) ... Removing libdeflate0:amd64 (1.21-1) ... Removing libgl1:amd64 (1.7.0-1+b1) ... Removing libglx0:amd64 (1.7.0-1+b1) ... Removing libglx-mesa0:amd64 (24.1.6-1) ... Removing libgl1-mesa-dri:amd64 (24.1.6-1) ... Removing libdrm-amdgpu1:amd64 (2.4.122-1) ... Removing libdrm-radeon1:amd64 (2.4.122-1) ... Removing libdrm-intel1:amd64 (2.4.122-1) ... Removing libdrm2:amd64 (2.4.122-1) ... Removing libdrm-common (2.4.122-1) ... Removing libllvm17t64:amd64 (1:17.0.6-15) ... Removing libedit2:amd64 (3.1-20240517-1) ... Removing libelf1t64:amd64 (0.191-2) ... Removing libepoxy0:amd64 (1.5.10-1+b2) ... Removing python3-pkg-resources (73.0.0-1) ... Removing python3-inflect (7.3.1-1) ... Removing python3-typeguard (4.3.0-1) ... Removing ncbi-blast+ (2.16.0+ds-6) ... Removing python3-typing-extensions (4.12.2-2) ... Removing libfribidi0:amd64 (1.0.15-1) ... Removing libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... Removing libgetopt-java (1.0.14+dfsg-6) ... Removing libgfortran5:amd64 (14.2.0-3) ... Removing libgif7:amd64 (5.2.2-1) ... Removing libglapi-mesa:amd64 (24.1.6-1) ... Removing libglvnd0:amd64 (1.7.0-1+b1) ... Removing parafly (0.1.0-4) ... Removing libgomp1:amd64 (14.2.0-3) ... Removing libgraphite2-3:amd64 (1.3.14-2) ... Removing libhtscodecs2:amd64 (1.6.0-1+b1) ... Removing libxt6t64:amd64 (1:1.2.1-1.2) ... Removing libsm6:amd64 (2:1.2.3-1+b1) ... Removing libice6:amd64 (2:1.0.10-1+b1) ... Removing libxml2:amd64 (2.12.7+dfsg-3+b1) ... Removing libicu72:amd64 (72.1-5) ... Removing libjbig0:amd64 (2.1-6.1+b1) ... Removing libjbzip2-java (0.9.1-8) ... Removing libjellyfish-2.0-2:amd64 (2.3.1-3+b5) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3) ... Removing liblcms2-2:amd64 (2.14-2+b1) ... Removing libldap-2.5-0:amd64 (2.5.18+dfsg-2) ... Removing liblerc4:amd64 (4.0.0+ds-4+b1) ... Removing liblmdb0:amd64 (0.9.31-1+b1) ... Removing libmbedtls14t64:amd64 (2.28.8-1) ... Removing libmbedx509-1t64:amd64 (2.28.8-1) ... Removing libmbedcrypto7t64:amd64 (2.28.8-1) ... Removing libncurses6:amd64 (6.5-2) ... Removing procps (2:4.0.4-5) ... Removing libnghttp2-14:amd64 (1.62.1-2) ... Removing libnghttp3-9:amd64 (1.4.0-1) ... Removing libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Removing libngtcp2-16:amd64 (1.6.0-1) ... Removing libnss3:amd64 (2:3.103-1) ... Removing libnspr4:amd64 (2:4.35-1.1+b1) ... Removing libpaper-utils (1.1.29+b1) ... Removing libpaper1:amd64 (1.1.29+b1) ... Removing libpciaccess0:amd64 (0.17-3+b1) ... Removing libpcsclite1:amd64 (2.3.0-1) ... Removing libpixman-1-0:amd64 (0.42.2-1+b1) ... Removing libpng16-16t64:amd64 (1.6.43-5) ... Removing libproc2-0:amd64 (2:4.0.4-5) ... Removing libprotobuf32t64:amd64 (3.21.12-9) ... Removing libpsl5t64:amd64 (0.21.2-1.1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-7) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-7) ... Removing libsensors5:amd64 (1:3.6.0-10) ... Removing libsensors-config (1:3.6.0-10) ... Removing libwebp7:amd64 (1.4.0-0.1) ... Removing libsharpyuv0:amd64 (1.4.0-0.1) ... Removing libssh2-1t64:amd64 (1.11.0-7) ... Removing libtcl8.6:amd64 (8.6.14+dfsg-1) ... Removing libthai-data (0.1.29-2) ... Removing libuv1t64:amd64 (1.48.0-5) ... Removing libvulkan1:amd64 (1.3.283.0-1) ... Removing libwayland-cursor0:amd64 (1.23.0-1) ... Removing libwayland-client0:amd64 (1.23.0-1) ... Removing libwayland-egl1:amd64 (1.23.0-1) ... Removing libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Removing libxtst6:amd64 (2:1.2.3-1.1+b1) ... Removing libx11-xcb1:amd64 (2:1.8.7-1+b1) ... Removing libxcb-xfixes0:amd64 (1.17.0-2) ... Removing libxcb-sync1:amd64 (1.17.0-2) ... Removing libxcb-dri2-0:amd64 (1.17.0-2) ... Removing libxcb-dri3-0:amd64 (1.17.0-2) ... Removing libxcb-glx0:amd64 (1.17.0-2) ... Removing libxcb-present0:amd64 (1.17.0-2) ... Removing libxcb-randr0:amd64 (1.17.0-2) ... Removing libxcb-render0:amd64 (1.17.0-2) ... Removing libxcb-shm0:amd64 (1.17.0-2) ... Removing libxcomposite1:amd64 (1:0.4.5-1+b1) ... Removing libxcursor1:amd64 (1:1.2.2-1) ... Removing libxdamage1:amd64 (1:1.1.6-1+b1) ... Removing libxss1:amd64 (1:1.2.3-1+b1) ... Removing libxfixes3:amd64 (1:6.0.0-2+b1) ... Removing libxi6:amd64 (2:1.8.1-1) ... Removing libxinerama1:amd64 (2:1.1.4-3+b1) ... Removing libxkbcommon0:amd64 (1.6.0-1+b1) ... Removing libxrandr2:amd64 (2:1.5.4-1) ... Removing libxrender1:amd64 (1:0.9.10-1.1+b1) ... Removing libxshmfence1:amd64 (1.3-1+b1) ... Removing libz3-4:amd64 (4.8.12-3.1+b2) ... Removing ncbi-data (6.1.20170106+dfsg2-3) ... Removing python3-autocommand (2.2.2-3) ... Removing python3-jaraco.context (6.0.0-1) ... Removing python3-jaraco.functools (4.0.2-1) ... Removing python3-more-itertools (10.3.0-1) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.24) ... Removing subread (2.0.6+dfsg-3) ... Removing unzip (6.0-28) ... Removing x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-utils (1.1.3-4.1) ... Removing xkb-data (2.42-1) ... Removing zip (3.0-14) ... Removing libglib2.0-0t64:amd64 (2.81.2-1) ... Removing libatomic1:amd64 (14.2.0-3) ... Removing libbrotli1:amd64 (1.1.0-2+b4) ... Removing python3 (3.12.5-1) ... Removing python3-minimal (3.12.5-1) ... Removing python3.12 (3.12.5-1) ... Removing python3.12-minimal (3.12.5-1) ... Removing libexpat1:amd64 (2.6.2-1) ... Removing libpython3-stdlib:amd64 (3.12.5-1) ... Removing libpython3.12-stdlib:amd64 (3.12.5-1) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-3+b2) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libgssapi-krb5-2:amd64 (1.21.3-3) ... Removing libkrb5-3:amd64 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-3) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing libncursesw6:amd64 (6.5-2) ... Removing libpython3.12-minimal:amd64 (3.12.5-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-5) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsqlite3-0:amd64 (3.46.1-1) ... Removing libtirpc-common (1.3.4+ds-1.3) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing media-types (10.1.0) ... Removing readline-common (8.2-5) ... Removing libx11-6:amd64 (2:1.8.7-1+b1) ... Removing libx11-data (2:1.8.7-1) ... Removing libxcb1:amd64 (1.17.0-2) ... Removing libxau6:amd64 (1:1.0.9-1+b1) ... Removing libxdmcp6:amd64 (1:1.1.2-3+b1) ... Removing liberror-prone-java (2.18.0-1) ... Removing libguava-java (32.0.1-1) ... Removing libatinject-jsr330-api-java (1.0+ds1-5) ... Removing libwww-perl (6.77-1) ... Removing liblwp-protocol-https-perl (6.14-1) ... Removing libhttp-negotiate-perl (6.01-2) ... Removing libfile-listing-perl (6.16-1) ... Removing libwww-robotrules-perl (6.02-1) ... Removing libhttp-cookies-perl (6.11-1) ... Removing libnet-http-perl (6.23-1) ... Removing libhtml-tree-perl (5.07-3) ... Removing libhtml-parser-perl:amd64 (3.83-1) ... Removing libio-socket-ssl-perl (2.088-1) ... Removing libnet-ssleay-perl:amd64 (1.94-1+b1) ... Removing libtry-tiny-perl (0.32-1) ... Removing libhtml-tagset-perl (3.24-1) ... Removing libjsr305-java (0.1~+svn49-11) ... Removing netbase (6.4) ... Removing perl-openssl-defaults:amd64 (7+b2) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libhttp-message-perl (6.46-1) ... Removing libclone-perl:amd64 (0.46-1+b2) ... Removing libencode-locale-perl (1.05-3) ... Removing libhttp-date-perl (6.06-1) ... Removing liburi-perl (5.28-1) ... Removing libio-html-perl (1.004-3) ... Removing liblwp-mediatypes-perl (6.04-2) ... Removing libtimedate-perl (2.3300-2) ... Removing openssl (3.3.1-7) ... Removing perl (5.38.2-5) ... Removing libperl5.38t64:amd64 (5.38.2-5) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing perl-modules-5.38 (5.38.2-5) ... Processing triggers for libc-bin (2.39-7) ... 1m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-get', 'remove', 'adduser', 'adwaita-icon-theme', 'at-spi2-common', 'berkeley-express', 'bowtie', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'default-jre', 'default-jre-headless', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'jaligner', 'java-common', 'jellyfish', 'kallisto', 'libapparmor1:amd64', 'libasound2-data', 'libasound2t64:amd64', 'libatinject-jsr330-api-java', 'libatk-bridge2.0-0t64:amd64', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libatspi2.0-0t64:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbamtools2.5.2:amd64', 'libblas3:amd64', 'libboost-filesystem1.83.0:amd64', 'libboost-program-options1.83.0:amd64', 'libboost-thread1.83.0:amd64', 'libbrotli1:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libclone-perl:amd64', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libencode-locale-perl', 'libepoxy0:amd64', 'liberror-prone-java', 'libexpat1:amd64', 'libfile-listing-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgetopt-java', 'libgfortran5:amd64', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libguava-java', 'libharfbuzz0b:amd64', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu72:amd64', 'libio-html-perl', 'libio-socket-ssl-perl', 'libjbig0:amd64', 'libjbzip2-java', 'libjellyfish-2.0-2:amd64', 'libjpeg62-turbo:amd64', 'libjsr305-java', 'libjung-free-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm17t64:amd64', 'liblmdb0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto7t64:amd64', 'libmbedtls14t64:amd64', 'libmbedx509-1t64:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.38t64:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libprotobuf32t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libsystemd-shared:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtimedate-perl', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libuv1t64:amd64', 'libvulkan1:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwebp7:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml2:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'openjdk-21-jre:amd64', 'openjdk-21-jre-headless:amd64', 'openssl', 'parafly', 'perl', 'perl-modules-5.38', 'perl-openssl-defaults:amd64', 'procps', 'python3', 'python3-autocommand', 'python3-htseq', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-numpy', 'python3-pkg-resources', 'python3-pysam', 'python3-typeguard', 'python3-typing-extensions', 'python3.12', 'python3.12-minimal', 'r-base-core', 'readline-common', 'rsem', 'samtools', 'sensible-utils', 'shared-mime-info', 'subread', 'systemd', 'systemd-sysv', 'trimmomatic', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'xkb-data', 'zip', 'trinityrnaseq'] 1m15.9s INFO: Running scripts post_remove 1m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_remove_exceptions'] 1m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_remove_exceptions'] 1m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'dpkg', '--purge', 'adduser', 'adwaita-icon-theme', 'at-spi2-common', 'berkeley-express', 'bowtie', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'default-jre', 'default-jre-headless', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'jaligner', 'java-common', 'jellyfish', 'kallisto', 'libapparmor1:amd64', 'libasound2-data', 'libasound2t64:amd64', 'libatinject-jsr330-api-java', 'libatk-bridge2.0-0t64:amd64', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libatspi2.0-0t64:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbamtools2.5.2:amd64', 'libblas3:amd64', 'libboost-filesystem1.83.0:amd64', 'libboost-program-options1.83.0:amd64', 'libboost-thread1.83.0:amd64', 'libbrotli1:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libclone-perl:amd64', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libencode-locale-perl', 'libepoxy0:amd64', 'liberror-prone-java', 'libexpat1:amd64', 'libfile-listing-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgetopt-java', 'libgfortran5:amd64', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libguava-java', 'libharfbuzz0b:amd64', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu72:amd64', 'libio-html-perl', 'libio-socket-ssl-perl', 'libjbig0:amd64', 'libjbzip2-java', 'libjellyfish-2.0-2:amd64', 'libjpeg62-turbo:amd64', 'libjsr305-java', 'libjung-free-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm17t64:amd64', 'liblmdb0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto7t64:amd64', 'libmbedtls14t64:amd64', 'libmbedx509-1t64:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.38t64:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libprotobuf32t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libsystemd-shared:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtimedate-perl', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libuv1t64:amd64', 'libvulkan1:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwebp7:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml2:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openjdk-21-jre:amd64', 'openjdk-21-jre-headless:amd64', 'openssl', 'parafly', 'perl', 'perl-modules-5.38', 'perl-openssl-defaults:amd64', 'procps', 'python3', 'python3-autocommand', 'python3-htseq', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-numpy', 'python3-pkg-resources', 'python3-pysam', 'python3-typeguard', 'python3-typing-extensions', 'python3.12', 'python3.12-minimal', 'r-base-core', 'readline-common', 'rsem', 'samtools', 'sensible-utils', 'shared-mime-info', 'subread', 'systemd', 'systemd-sysv', 'trimmomatic', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'xkb-data', 'zip'] 1m16.8s DUMP: (Reading database ... 5267 files and directories currently installed.) Purging configuration files for adduser (3.137) ... Purging configuration files for adwaita-icon-theme (46.0-1) ... dpkg: warning: ignoring request to remove at-spi2-common which isn't installed dpkg: warning: ignoring request to remove berkeley-express which isn't installed dpkg: warning: ignoring request to remove bowtie which isn't installed dpkg: warning: ignoring request to remove bowtie2 which isn't installed Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for ca-certificates-java (20240118) ... Purging configuration files for dbus (1.14.10-4+b1) ... rmdir: failed to remove '/var/run/dbus': Directory not empty rmdir: failed to remove '/var/lib/dbus': Directory not empty dpkg: warning: while removing dbus, directory '/var/lib/dbus' not empty so not removed dpkg: warning: ignoring request to remove dbus-bin which isn't installed Purging configuration files for dbus-daemon (1.14.10-4+b1) ... dpkg: warning: ignoring request to remove dbus-session-bus-common which isn't installed dpkg: warning: ignoring request to remove dbus-system-bus-common which isn't installed Purging configuration files for dbus-user-session (1.14.10-4+b1) ... dpkg: warning: ignoring request to remove dconf-gsettings-backend which isn't installed dpkg: warning: ignoring request to remove dconf-service which isn't installed dpkg: warning: ignoring request to remove default-jre which isn't installed dpkg: warning: ignoring request to remove default-jre-headless which isn't installed Purging configuration files for fontconfig (2.15.0-1.1) ... Purging configuration files for fontconfig-config (2.15.0-1.1) ... dpkg: warning: while removing fontconfig-config, directory '/etc/fonts/conf.d' not empty so not removed Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: while removing fonts-dejavu-mono, directory '/etc/fonts' not empty so not removed dpkg: warning: ignoring request to remove gtk-update-icon-cache which isn't installed dpkg: warning: ignoring request to remove hicolor-icon-theme which isn't installed dpkg: warning: ignoring request to remove jaligner which isn't installed Purging configuration files for java-common (0.76) ... dpkg: warning: ignoring request to remove jellyfish which isn't installed dpkg: warning: ignoring request to remove kallisto which isn't installed dpkg: warning: ignoring request to remove libapparmor1 which isn't installed dpkg: warning: ignoring request to remove libasound2-data which isn't installed dpkg: warning: ignoring request to remove libasound2t64 which isn't installed dpkg: warning: ignoring request to remove libatinject-jsr330-api-java which isn't installed dpkg: warning: ignoring request to remove libatk-bridge2.0-0t64 which isn't installed dpkg: warning: ignoring request to remove libatk1.0-0t64 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libatspi2.0-0t64 which isn't installed dpkg: warning: ignoring request to remove libavahi-client3 which isn't installed dpkg: warning: ignoring request to remove libavahi-common-data which isn't installed dpkg: warning: ignoring request to remove libavahi-common3 which isn't installed dpkg: warning: ignoring request to remove libbamtools2.5.2 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libboost-filesystem1.83.0 which isn't installed dpkg: warning: ignoring request to remove libboost-program-options1.83.0 which isn't installed dpkg: warning: ignoring request to remove libboost-thread1.83.0 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcairo-gobject2 which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libclone-perl which isn't installed dpkg: warning: ignoring request to remove libcloudproviders0 which isn't installed dpkg: warning: ignoring request to remove libcolord2 which isn't installed dpkg: warning: ignoring request to remove libcups2t64 which isn't installed dpkg: warning: ignoring request to remove libcurl3t64-gnutls which isn't installed dpkg: warning: ignoring request to remove libcurl4t64 which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdbus-1-3 which isn't installed dpkg: warning: ignoring request to remove libdconf1 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libdrm-amdgpu1 which isn't installed dpkg: warning: ignoring request to remove libdrm-common which isn't installed dpkg: warning: ignoring request to remove libdrm-intel1 which isn't installed dpkg: warning: ignoring request to remove libdrm-radeon1 which isn't installed dpkg: warning: ignoring request to remove libdrm2 which isn't installed dpkg: warning: ignoring request to remove libedit2 which isn't installed dpkg: warning: ignoring request to remove libelf1t64 which isn't installed dpkg: warning: ignoring request to remove libencode-locale-perl which isn't installed dpkg: warning: ignoring request to remove libepoxy0 which isn't installed dpkg: warning: ignoring request to remove liberror-prone-java which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfile-listing-perl which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4t64 which isn't installed dpkg: warning: ignoring request to remove libgdbm6t64 which isn't installed Purging configuration files for libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1) ... dpkg: warning: ignoring request to remove libgdk-pixbuf2.0-common which isn't installed dpkg: warning: ignoring request to remove libgetopt-java which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libgif7 which isn't installed dpkg: warning: ignoring request to remove libgl1 which isn't installed Purging configuration files for libgl1-mesa-dri:amd64 (24.1.6-1) ... dpkg: warning: ignoring request to remove libglapi-mesa which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.81.2-1) ... dpkg: warning: ignoring request to remove libglvnd0 which isn't installed dpkg: warning: ignoring request to remove libglx-mesa0 which isn't installed dpkg: warning: ignoring request to remove libglx0 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-3) ... Purging configuration files for libgtk-3-0t64:amd64 (3.24.43-2) ... Purging configuration files for libgtk-3-common (3.24.43-2) ... dpkg: warning: ignoring request to remove libguava-java which isn't installed dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhtml-parser-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tagset-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tree-perl which isn't installed dpkg: warning: ignoring request to remove libhts3t64 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libhttp-cookies-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-date-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-message-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-negotiate-perl which isn't installed dpkg: warning: ignoring request to remove libice6 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libio-html-perl which isn't installed dpkg: warning: ignoring request to remove libio-socket-ssl-perl which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjbzip2-java which isn't installed dpkg: warning: ignoring request to remove libjellyfish-2.0-2 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libjsr305-java which isn't installed dpkg: warning: ignoring request to remove libjung-free-java which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove libllvm17t64 which isn't installed dpkg: warning: ignoring request to remove liblmdb0 which isn't installed dpkg: warning: ignoring request to remove liblwp-mediatypes-perl which isn't installed dpkg: warning: ignoring request to remove liblwp-protocol-https-perl which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto7t64 which isn't installed dpkg: warning: ignoring request to remove libmbedtls14t64 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-1t64 which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnet-http-perl which isn't installed dpkg: warning: ignoring request to remove libnet-ssleay-perl which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnghttp3-9 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-16 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-crypto-gnutls8 which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libnspr4 which isn't installed dpkg: warning: ignoring request to remove libnss3 which isn't installed dpkg: warning: ignoring request to remove libpam-systemd which isn't installed dpkg: warning: ignoring request to remove libpango-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangoft2-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpaper-utils which isn't installed Purging configuration files for libpaper1:amd64 (1.1.29+b1) ... dpkg: warning: ignoring request to remove libpciaccess0 which isn't installed dpkg: warning: ignoring request to remove libpcsclite1 which isn't installed dpkg: warning: ignoring request to remove libperl5.38t64 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libproc2-0 which isn't installed dpkg: warning: ignoring request to remove libprotobuf32t64 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.12-minimal:amd64 (3.12.5-1) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-5) ... 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 Purging configuration files for libsensors-config (1:3.6.0-10) ... dpkg: warning: ignoring request to remove libsensors5 which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsm6 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libsystemd-shared which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed dpkg: warning: ignoring request to remove libtimedate-perl which isn't installed Purging configuration files for libtirpc-common (1.3.4+ds-1.3) ... Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.3) ... dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libtry-tiny-perl which isn't installed dpkg: warning: ignoring request to remove liburi-perl which isn't installed dpkg: warning: ignoring request to remove libuv1t64 which isn't installed dpkg: warning: ignoring request to remove libvulkan1 which isn't installed dpkg: warning: ignoring request to remove libwayland-client0 which isn't installed dpkg: warning: ignoring request to remove libwayland-cursor0 which isn't installed dpkg: warning: ignoring request to remove libwayland-egl1 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwww-perl which isn't installed dpkg: warning: ignoring request to remove libwww-robotrules-perl which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libx11-xcb1 which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-dri2-0 which isn't installed dpkg: warning: ignoring request to remove libxcb-dri3-0 which isn't installed dpkg: warning: ignoring request to remove libxcb-glx0 which isn't installed dpkg: warning: ignoring request to remove libxcb-present0 which isn't installed dpkg: warning: ignoring request to remove libxcb-randr0 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb-sync1 which isn't installed dpkg: warning: ignoring request to remove libxcb-xfixes0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxcomposite1 which isn't installed dpkg: warning: ignoring request to remove libxcursor1 which isn't installed dpkg: warning: ignoring request to remove libxdamage1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxfixes3 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxi6 which isn't installed dpkg: warning: ignoring request to remove libxinerama1 which isn't installed dpkg: warning: ignoring request to remove libxkbcommon0 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxrandr2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxshmfence1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove libxt6t64 which isn't installed dpkg: warning: ignoring request to remove libxtst6 which isn't installed dpkg: warning: ignoring request to remove libxxf86vm1 which isn't installed dpkg: warning: ignoring request to remove libz3-4 which isn't installed Purging configuration files for media-types (10.1.0) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg2-3) ... Purging configuration files for netbase (6.4) ... dpkg: warning: ignoring request to remove openjdk-21-jre which isn't installed Purging configuration files for openjdk-21-jre-headless:amd64 (21.0.4+7-3) ... Purging configuration files for openssl (3.3.1-7) ... dpkg: warning: ignoring request to remove parafly which isn't installed Purging configuration files for perl (5.38.2-5) ... dpkg: warning: ignoring request to remove perl-modules-5.38 which isn't installed dpkg: warning: ignoring request to remove perl-openssl-defaults which isn't installed Purging configuration files for procps (2:4.0.4-5) ... Purging configuration files for python3 (3.12.5-1) ... dpkg: warning: ignoring request to remove python3-autocommand which isn't installed dpkg: warning: ignoring request to remove python3-htseq which isn't installed dpkg: warning: ignoring request to remove python3-inflect which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.context which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.functools which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-more-itertools which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3-typeguard which isn't installed dpkg: warning: ignoring request to remove python3-typing-extensions which isn't installed dpkg: warning: ignoring request to remove python3.12 which isn't installed Purging configuration files for python3.12-minimal (3.12.5-1) ... Purging configuration files for r-base-core (4.4.1-1) ... Purging configuration files for readline-common (8.2-5) ... dpkg: warning: ignoring request to remove rsem which isn't installed dpkg: warning: ignoring request to remove samtools which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed Purging configuration files for shared-mime-info (2.4-5) ... dpkg: warning: ignoring request to remove subread which isn't installed Purging configuration files for systemd (256.5-1) ... dpkg: warning: ignoring request to remove systemd-sysv which isn't installed dpkg: warning: ignoring request to remove trimmomatic which isn't installed Purging configuration files for ucf (3.0043+nmu1) ... Purging configuration files for unzip (6.0-28) ... Purging configuration files for x11-common (1:7.7+23.1) ... dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove xkb-data which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed 1m16.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'dpkg', '--purge', 'adduser', 'adwaita-icon-theme', 'at-spi2-common', 'berkeley-express', 'bowtie', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'default-jre', 'default-jre-headless', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'jaligner', 'java-common', 'jellyfish', 'kallisto', 'libapparmor1:amd64', 'libasound2-data', 'libasound2t64:amd64', 'libatinject-jsr330-api-java', 'libatk-bridge2.0-0t64:amd64', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libatspi2.0-0t64:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbamtools2.5.2:amd64', 'libblas3:amd64', 'libboost-filesystem1.83.0:amd64', 'libboost-program-options1.83.0:amd64', 'libboost-thread1.83.0:amd64', 'libbrotli1:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libclone-perl:amd64', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'libencode-locale-perl', 'libepoxy0:amd64', 'liberror-prone-java', 'libexpat1:amd64', 'libfile-listing-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgetopt-java', 'libgfortran5:amd64', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0t64:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libguava-java', 'libharfbuzz0b:amd64', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu72:amd64', 'libio-html-perl', 'libio-socket-ssl-perl', 'libjbig0:amd64', 'libjbzip2-java', 'libjellyfish-2.0-2:amd64', 'libjpeg62-turbo:amd64', 'libjsr305-java', 'libjung-free-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm17t64:amd64', 'liblmdb0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto7t64:amd64', 'libmbedtls14t64:amd64', 'libmbedx509-1t64:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.38t64:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libprotobuf32t64:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libsystemd-shared:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtimedate-perl', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libuv1t64:amd64', 'libvulkan1:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwebp7:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml2:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openjdk-21-jre:amd64', 'openjdk-21-jre-headless:amd64', 'openssl', 'parafly', 'perl', 'perl-modules-5.38', 'perl-openssl-defaults:amd64', 'procps', 'python3', 'python3-autocommand', 'python3-htseq', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-numpy', 'python3-pkg-resources', 'python3-pysam', 'python3-typeguard', 'python3-typing-extensions', 'python3.12', 'python3.12-minimal', 'r-base-core', 'readline-common', 'rsem', 'samtools', 'sensible-utils', 'shared-mime-info', 'subread', 'systemd', 'systemd-sysv', 'trimmomatic', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'xkb-data', 'zip'] 1m16.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'dpkg', '--purge', 'trinityrnaseq'] 1m16.8s DUMP: dpkg: warning: ignoring request to remove trinityrnaseq which isn't installed 1m16.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'dpkg', '--purge', 'trinityrnaseq'] 1m16.8s INFO: Running scripts post_purge 1m16.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_purge_exceptions'] 1m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_purge_exceptions'] 1m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'dpkg', '--purge', '--pending'] 1m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'dpkg', '--purge', '--pending'] 1m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'dpkg', '--remove', '--pending'] 1m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'dpkg', '--remove', '--pending'] 1m16.9s INFO: Running scripts post_test 1m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_test_exceptions'] 1m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'tmp/scripts/post_test_exceptions'] 1m16.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury'] 1m17.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury'] 1m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'dpkg-divert', '--list'] 1m17.4s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 1m17.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'dpkg-divert', '--list'] 1m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-get', 'clean'] 1m17.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury', 'apt-get', 'clean'] 1m17.5s DEBUG: Recording chroot state 1m18.2s INFO: Warning: Package purging left files on system: /etc/default/locale -> ../locale.conf not owned /etc/fonts/ owned by: fontconfig-config, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/ owned by: fontconfig-config, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf not owned /etc/vconsole.conf -> default/keyboard not owned /root/.ssh/ not owned /var/cache/private/ not owned /var/lib/private/ not owned /var/lib/systemd/coredump/ not owned /var/lib/systemd/ephemeral-trees/ not owned /var/lib/systemd/network/ not owned /var/lib/systemd/pstore/ not owned /var/log/private/ not owned 1m18.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/dev/shm'] 1m18.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/dev/shm'] 1m18.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/dev/console'] 1m18.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/dev/console'] 1m18.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/dev/ptmx'] 1m18.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/dev/ptmx'] 1m18.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/dev/pts'] 1m18.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/dev/pts'] 1m18.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/proc'] 1m18.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury/proc'] 1m18.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury'] 1m18.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpoxvz5ury'] 1m18.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpoxvz5ury 1m18.9s INFO: PASS: Upgrading between Debian distributions. 1m18.9s INFO: PASS: All tests. 1m18.9s INFO: piuparts run ends. ret=0 End: 2024-08-22 03:01:50 GMT