Start: 2023-12-14 21:44:32 GMT [testing] Package: python3-ete3 Source: python-ete3 Version: 3.1.2+dfsg-3 Installed-Size: 2828 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3:any, python3-numpy, python3-six Recommends: python3-lxml, python3-pyqt5.qtopengl, python3-pyqt5.qtsvg, python3-scipy, python3-skbio Description: Python Environment for (phylogenetic) Tree Exploration - Python 3.X Homepage: http://etetoolkit.org Description-md5: 62fa80cd1d7a708098c4e11beda86263 Section: python Priority: optional Filename: pool/main/p/python-ete3/python3-ete3_3.1.2+dfsg-3_all.deb Size: 373928 MD5sum: 85baa42d6d6a30d09cbcfb61f12a078f SHA256: 4b38e43ad9bee76a126130d2b2fc552e3e3b02c4c2fa4fdc8b9ffb8be49719b8 [sid] Package: python3-ete3 Source: python-ete3 Version: 3.1.3+dfsg-2 Installed-Size: 2832 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-six, python3:any, python3-numpy Recommends: python3-lxml, python3-pyqt5.qtopengl, python3-pyqt5.qtsvg, python3-scipy, python3-skbio Description: Python Environment for (phylogenetic) Tree Exploration - Python 3.X Homepage: http://etetoolkit.org Description-md5: 62fa80cd1d7a708098c4e11beda86263 Section: python Priority: optional Filename: pool/main/p/python-ete3/python3-ete3_3.1.3+dfsg-2_all.deb Size: 374596 MD5sum: c3ab132e1a695c8fabfb1c6ef35524df SHA256: 397f8fad8dd82dd135bda8e57a74c54f8c2ea4c934919129baaca7549e92889a Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt python3-ete3=3.1.3+dfsg-2 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 1.2 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt python3-ete3=3.1.3+dfsg-2 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-26-amd64 #1 SMP Debian 5.10.197-1 (2023-09-29) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp_xkerg84 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp_xkerg84 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m2.1s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/proc'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/proc'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/dev/pts'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/dev/pts'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/dev/ptmx'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/dev/ptmx'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/dev/console'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/dev/console'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/dev/shm'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/dev/shm'] 0m2.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m2.1s DEBUG: Created policy-rc.d and chmodded it. 0m2.1s DEBUG: Created resolv.conf. 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp_xkerg84/tmp/scripts/ 0m2.2s INFO: Running scripts post_chroot_unpack 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-get', 'update'] 0m4.9s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [151 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8787 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [6109 kB] Fetched 15.0 MB in 2s (7794 kB/s) Reading package lists... 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-get', 'update'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-get', '-yf', 'dist-upgrade'] 0m8.1s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: base-files libc-bin libc6 libgnutls30 libsystemd0 libudev1 perl-base tzdata 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 7179 kB of archives. After this operation, 5120 B of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 base-files amd64 12.4+deb12u4 [70.8 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 perl-base amd64 5.36.0-7+deb12u1 [1608 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libc6 amd64 2.36-9+deb12u3 [2755 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libc-bin amd64 2.36-9+deb12u3 [606 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 libgnutls30 amd64 3.7.9-2+deb12u1 [1404 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libsystemd0 amd64 252.19-1~deb12u1 [331 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libudev1 amd64 252.19-1~deb12u1 [108 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 tzdata all 2023c-5+deb12u1 [296 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7179 kB in 0s (78.4 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 ... 6098 files and directories currently installed.) Preparing to unpack .../base-files_12.4+deb12u4_amd64.deb ... Unpacking base-files (12.4+deb12u4) over (12.4+deb12u2) ... Setting up base-files (12.4+deb12u4) ... Installing new version of config file /etc/debian_version ... (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 ... 6098 files and directories currently installed.) Preparing to unpack .../perl-base_5.36.0-7+deb12u1_amd64.deb ... Unpacking perl-base (5.36.0-7+deb12u1) over (5.36.0-7) ... Setting up perl-base (5.36.0-7+deb12u1) ... (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 ... 6098 files and directories currently installed.) Preparing to unpack .../libc6_2.36-9+deb12u3_amd64.deb ... Unpacking libc6:amd64 (2.36-9+deb12u3) over (2.36-9+deb12u2) ... Setting up libc6:amd64 (2.36-9+deb12u3) ... (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 ... 6098 files and directories currently installed.) Preparing to unpack .../libc-bin_2.36-9+deb12u3_amd64.deb ... Unpacking libc-bin (2.36-9+deb12u3) over (2.36-9+deb12u2) ... Setting up libc-bin (2.36-9+deb12u3) ... (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 ... 6098 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.9-2+deb12u1_amd64.deb ... Unpacking libgnutls30:amd64 (3.7.9-2+deb12u1) over (3.7.9-2) ... Setting up libgnutls30:amd64 (3.7.9-2+deb12u1) ... (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 ... 6098 files and directories currently installed.) Preparing to unpack .../libsystemd0_252.19-1~deb12u1_amd64.deb ... Unpacking libsystemd0:amd64 (252.19-1~deb12u1) over (252.17-1~deb12u1) ... Setting up libsystemd0:amd64 (252.19-1~deb12u1) ... (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 ... 6098 files and directories currently installed.) Preparing to unpack .../libudev1_252.19-1~deb12u1_amd64.deb ... Unpacking libudev1:amd64 (252.19-1~deb12u1) over (252.17-1~deb12u1) ... Setting up libudev1:amd64 (252.19-1~deb12u1) ... (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 ... 6098 files and directories currently installed.) Preparing to unpack .../tzdata_2023c-5+deb12u1_all.deb ... Unpacking tzdata (2023c-5+deb12u1) over (2023c-5) ... Setting up tzdata (2023c-5+deb12u1) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Dec 14 21:44:40 UTC 2023. Universal Time is now: Thu Dec 14 21:44:40 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Processing triggers for libc-bin (2.36-9+deb12u3) ... 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-get', '-yf', 'dist-upgrade'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m8.5s DUMP: c39ed9ca72afa1f69a1eea88b0965329 - 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m8.5s INFO: Running scripts post_setup 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_setup_dummy_users'] 0m9.4s 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 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_setup_dummy_users'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_setup_forbid_home'] 0m9.4s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_setup_forbid_home'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_setup_force-unsafe-io'] 0m9.4s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_setup_force-unsafe-io'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_setup_minimize'] 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_setup_minimize'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_setup_squeeze-backports'] 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_setup_squeeze-backports'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_setup_zz_backports'] 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_setup_zz_backports'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.5s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u4 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b2 install ok installed bsdutils bsdutils 1:2.38.1-5+b1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u3 install ok installed libc6:amd64 libc6 2.36-9+deb12u3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u1 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+b1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+b1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.19-1~deb12u1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.19-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+b1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2 install ok installed tzdata tzdata 2023c-5+deb12u1 install ok installed usr-is-merged usr-is-merged 35 install ok installed util-linux util-linux 2.38.1-5+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m9.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_xkerg84'] 0m10.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_xkerg84'] 0m10.0s INFO: Running scripts is_testable 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/is_testable_uninstallable'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/is_testable_uninstallable'] 0m10.0s INFO: Running scripts pre_test 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_test_exceptions'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_test_exceptions'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_test_root_password'] 0m10.0s DUMP: New password: Retype new password: passwd: password updated successfully 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_test_root_password'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-cache', 'show', '--no-all-versions', 'python3-ete3'] 0m10.3s DUMP: Package: python3-ete3 Source: python-ete3 Version: 3.1.2+dfsg-3 Installed-Size: 2828 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3:any, python3-numpy, python3-six Recommends: python3-lxml, python3-pyqt5.qtopengl, python3-pyqt5.qtsvg, python3-scipy, python3-skbio Description-en: Python Environment for (phylogenetic) Tree Exploration - Python 3.X The Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees (although clustering trees or any other tree-like data structure are also supported). . ETE is currently developed as a tool for researchers working in phylogenetics and genomics. If you use ETE for a published work, please cite: . Visit http://etetoolkit.org for more info. Description-md5: 62fa80cd1d7a708098c4e11beda86263 Homepage: http://etetoolkit.org Section: python Priority: optional Filename: pool/main/p/python-ete3/python3-ete3_3.1.2+dfsg-3_all.deb Size: 373928 MD5sum: 85baa42d6d6a30d09cbcfb61f12a078f SHA256: 4b38e43ad9bee76a126130d2b2fc552e3e3b02c4c2fa4fdc8b9ffb8be49719b8 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-cache', 'show', '--no-all-versions', 'python3-ete3'] 0m10.3s INFO: apt-cache knows about the following packages: python3-ete3 0m10.3s INFO: Running scripts pre_install 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_database-server'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_database-server'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_exceptions'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_exceptions'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_extras'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_extras'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-cache', 'policy'] 0m10.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.4,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-cache', 'policy'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-cache', 'policy', 'python3-ete3'] 0m10.4s DUMP: python3-ete3: Installed: (none) Candidate: 3.1.2+dfsg-3 Version table: 3.1.2+dfsg-3 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-cache', 'policy', 'python3-ete3'] 0m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-get', '-y', 'install', 'python3-ete3'] 0m20.1s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libblas3 libexpat1 libgfortran5 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libncursesw6 libnsl2 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 libsqlite3-0 libssl3 libtirpc-common libtirpc3 media-types python3 python3-minimal python3-numpy python3-pkg-resources python3-six python3.11 python3.11-minimal readline-common Suggested packages: krb5-doc krb5-user python3-doc python3-tk python3-venv gcc gfortran python3-dev python3-pytest python3-setuptools python3.11-venv python3.11-doc binutils binfmt-support readline-doc Recommended packages: krb5-locales libgpm2 python3-lxml python3-pyqt5.qtopengl python3-pyqt5.qtsvg python3-scipy python3-skbio ca-certificates The following NEW packages will be installed: libblas3 libexpat1 libgfortran5 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libncursesw6 libnsl2 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 libsqlite3-0 libssl3 libtirpc-common libtirpc3 media-types python3 python3-ete3 python3-minimal python3-numpy python3-pkg-resources python3-six python3.11 python3.11-minimal readline-common 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 18.7 MB of archives. After this operation, 77.0 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.11-1~deb12u2 [2019 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.4-4 [134 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:11 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get:22 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 python3-ete3 all 3.1.2+dfsg-3 [374 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 18.7 MB in 0s (84.6 MB/s) Selecting previously unselected package libssl3: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 ... 6100 files and directories currently installed.) Preparing to unpack .../libssl3_3.0.11-1~deb12u2_amd64.deb ... Unpacking libssl3:amd64 (3.0.11-1~deb12u2) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. 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Unpacking python3-ete3 (3.1.2+dfsg-3) ... Setting up media-types (10.0.0) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up libtirpc-common (1.3.3+ds-1) ... Setting up libsqlite3-0:amd64 (3.40.1-2) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Setting up libblas3:amd64 (3.11.0-2) ... 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 libquadmath0:amd64 (12.2.0-14) ... Setting up libncursesw6:amd64 (6.4-4) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up readline-common (8.2-1.3) ... Setting up liblapack3:amd64 (3.11.0-2) ... 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 libreadline8:amd64 (8.2-1.3) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up python3 (3.11.2-1+b1) ... Setting up python3-six (1.16.0-4) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-ete3 (3.1.2+dfsg-3) ... /usr/lib/python3/dist-packages/ete3/evol/parser/codemlparser.py:221: SyntaxWarning: "is" with a literal. Did you mean "=="? if line is '\n': Processing triggers for libc-bin (2.36-9+deb12u3) ... 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-get', '-y', 'install', 'python3-ete3'] 0m20.1s INFO: Running scripts post_install 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_install_exceptions'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_install_exceptions'] 0m20.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_xkerg84'] 0m20.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_xkerg84'] 0m20.8s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp_xkerg84 to sid 0m20.8s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m20.8s INFO: Running scripts pre_distupgrade 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_distupgrade_exceptions'] 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_distupgrade_exceptions'] 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-get', 'update'] 0m25.9s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9596 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7068 kB] Fetched 16.9 MB in 4s (4296 kB/s) Reading package lists... 0m25.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-get', 'update'] 0m25.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-get', '-yf', 'dist-upgrade'] 0m52.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libquadmath0 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: gcc-13-base libpython3.12-minimal libpython3.12-stdlib libunistring5 netbase python3.12 python3.12-minimal The following packages will be upgraded: adduser apt base-files base-passwd bash bsdutils coreutils dash debian-archive-keyring debianutils diffutils dpkg e2fsprogs findutils gcc-12-base grep init-system-helpers libapt-pkg6.0 libaudit-common libaudit1 libblkid1 libc-bin libc6 libcap-ng0 libcom-err2 libcrypt1 libdb5.3 libdebconfclient0 libexpat1 libext2fs2 libffi8 libgcc-s1 libgcrypt20 libgfortran5 libgmp10 libgnutls30 libgpg-error0 libgssapi-krb5-2 libhogweed6 libidn2-0 libk5crypto3 libkrb5-3 libkrb5support0 liblzma5 libmd0 libmount1 libncursesw6 libnettle8 libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssl3 libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtirpc-common libtirpc3 libudev1 libuuid1 libxxhash0 libzstd1 login logsave mawk media-types mount ncurses-base ncurses-bin passwd perl-base python3 python3-ete3 python3-minimal python3-numpy python3-pkg-resources python3.11 python3.11-minimal readline-common sysvinit-utils tar tzdata usr-is-merged util-linux util-linux-extra zlib1g 103 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. Need to get 53.7 MB of archives. After this operation, 40.4 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 base-files amd64 13 [70.6 kB] Get:2 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.14 [88.3 kB] Get:3 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.21-2 [1492 kB] Get:4 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.39.3-2 [96.7 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-13 [2753 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-13 [602 kB] Get:7 http://deb.debian.org/debian sid/main amd64 gcc-13-base amd64 13.2.0-8 [41.1 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 13.2.0-8 [57.7 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2 [557 kB] Get:10 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.4-2+b1 [2948 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [295 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 13.2.0-8 [695 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.47-3 [77.8 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.3-2 [708 kB] Get:15 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.4.5-0.1 [239 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 255-1 [360 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 255-1 [122 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.2-2 [26.4 kB] Get:19 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg-3 [87.5 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0 amd64 2.7.7 [946 kB] Get:21 http://deb.debian.org/debian sid/main amd64 tar amd64 1.34+dfsg-1.3 [837 kB] Get:22 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.1 [1561 kB] Get:23 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:24 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:25 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:26 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-3 [431 kB] Get:27 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.13+dfsg1-3 [616 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20231209-1 [135 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20231209-1 [341 kB] Get:30 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20231209-1 [430 kB] Get:31 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.36.0-10 [1602 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.39.3-2 [159 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4 [261 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-1+b1 [74.5 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.39.3-2 [190 kB] Get:36 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amd64 libidn2-0 amd64 2.3.4-1+b1 [125 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.19.0-3 [48.3 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libgnutls30 amd64 3.8.2-1 [1424 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.271 [9940 B] Get:51 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.3 [50.8 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-2 [89.7 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.5.2-9.1 [65.5 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:55 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.5-2 [277 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1+b1 [90.3 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.2-9.1 [49.9 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 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libkrb5support0 amd64 1.20.1-5 [32.9 kB] Get:82 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.0-2+b1 [20.1 kB] Get:83 http://deb.debian.org/debian sid/main amd64 libssl3 amd64 3.1.4-2 [2058 kB] Get:84 http://deb.debian.org/debian sid/main amd64 libtirpc3 amd64 1.3.4+ds-1 [82.1 kB] Get:85 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3 [40.0 kB] Get:86 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-3 [69.1 kB] Get:87 http://deb.debian.org/debian sid/main amd64 libreadline8 amd64 8.2-3 [167 kB] Get:88 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.44.2-1 [882 kB] Get:89 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.39.3-2 [29.6 kB] Get:90 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.7-2 [1822 kB] Get:91 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.7-2 [2035 kB] Get:92 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal 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[803 kB] Get:104 http://deb.debian.org/debian sid/main amd64 gcc-12-base amd64 12.3.0-12 [41.0 kB] Get:105 http://deb.debian.org/debian sid/main amd64 libpython3.12-stdlib amd64 3.12.1-2 [1919 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libss2 amd64 1.47.0-2+b1 [24.8 kB] Get:107 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get:108 http://deb.debian.org/debian sid/main amd64 python3.12 amd64 3.12.1-2 [646 kB] Get:109 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.24.2-2 [6299 kB] Get:110 http://deb.debian.org/debian sid/main amd64 python3-ete3 all 3.1.3+dfsg-2 [375 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 53.7 MB in 0s (126 MB/s) (Reading database ... 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(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 ... 8223 files and directories currently installed.) Preparing to unpack .../libselinux1_3.5-1+b1_amd64.deb ... Unpacking libselinux1:amd64 (3.5-1+b1) over (3.4-1+b6) ... Setting up libselinux1:amd64 (3.5-1+b1) ... (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 ... 8223 files and directories currently installed.) Preparing to unpack .../libmount1_2.39.3-2_amd64.deb ... Unpacking libmount1:amd64 (2.39.3-2) over (2.38.1-5+b1) ... Setting up libmount1:amd64 (2.39.3-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8222 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a3.1.2-1_all.deb ... Unpacking libaudit-common (1:3.1.2-1) over (1:3.0.9-1) ... Setting up libaudit-common (1:3.1.2-1) ... (Reading database ... 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(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 ... 8221 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.1.2-1_amd64.deb ... Unpacking libaudit1:amd64 (1:3.1.2-1) over (1:3.0.9-1) ... Setting up libaudit1:amd64 (1:3.1.2-1) ... (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 ... 8221 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.39.3-2_amd64.deb ... Unpacking libsmartcols1:amd64 (2.39.3-2) over (2.38.1-5+b1) ... Setting up libsmartcols1:amd64 (2.39.3-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8220 files and directories currently installed.) Preparing to unpack .../util-linux-extra_2.39.3-2_amd64.deb ... Unpacking util-linux-extra (2.39.3-2) over (2.38.1-5+b1) ... dpkg: warning: unable to delete old directory '/usr/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/usr/lib/udev': Directory not empty dpkg: warning: unable to delete old directory '/etc/init.d': Directory not empty Setting up util-linux-extra (2.39.3-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8224 files and directories currently installed.) 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Setting up python3-ete3 (3.1.3+dfsg-2) ... /usr/lib/python3/dist-packages/ete3/coretype/tree.py:365: SyntaxWarning: invalid escape sequence '\-' """ /usr/lib/python3/dist-packages/ete3/coretype/tree.py:436: SyntaxWarning: invalid escape sequence '\-' """Prunes the topology of a node to conserve only the selected list of leaf /usr/lib/python3/dist-packages/ete3/coretype/tree.py:1508: SyntaxWarning: invalid escape sequence '\-' """ /usr/lib/python3/dist-packages/ete3/evol/evoltree.py:468: SyntaxWarning: invalid escape sequence '\[' nwk += sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1', /usr/lib/python3/dist-packages/ete3/evol/evoltree.py:471: SyntaxWarning: invalid escape sequence '\[' nwk = sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1', /usr/lib/python3/dist-packages/ete3/evol/model.py:367: SyntaxWarning: invalid escape sequence '\.' if sub('\..*', '', model) in AVAIL: /usr/lib/python3/dist-packages/ete3/evol/model.py:368: SyntaxWarning: invalid escape sequence '\.' return model, AVAIL [sub('\..*', '', model)] /usr/lib/python3/dist-packages/ete3/evol/parser/codemlparser.py:74: SyntaxWarning: invalid escape sequence '\(' k = int(re.sub ('.* \(K=([0-9]+)\)\n', '\\1', line)) /usr/lib/python3/dist-packages/ete3/evol/parser/codemlparser.py:78: SyntaxWarning: invalid escape sequence '\d' re.match ('^[a-z]+.*(\d+\.\d{5} *){'+ str(k) +'}', line): /usr/lib/python3/dist-packages/ete3/evol/parser/codemlparser.py:82: SyntaxWarning: invalid escape sequence '\d' classes[var] = [float(v) for v in re.findall('\d+\.\d{5}', line)] /usr/lib/python3/dist-packages/ete3/evol/parser/codemlparser.py:86: SyntaxWarning: invalid escape sequence '\d' k = int(re.sub('.*for (\d+) classes.*\n', '\\1', line)) /usr/lib/python3/dist-packages/ete3/evol/parser/codemlparser.py:92: SyntaxWarning: invalid escape sequence '\d' k = int(re.sub('.*for (\d+) classes.*\n', '\\1', line)) /usr/lib/python3/dist-packages/ete3/evol/parser/codemlparser.py:217: SyntaxWarning: invalid escape sequence '\(' model._tree = EvolTree (re.findall ('\(.*\);', ''.join(all_lines))[2]) /usr/lib/python3/dist-packages/ete3/evol/parser/codemlparser.py:227: SyntaxWarning: invalid escape sequence '\d' line = list(map (float, re.findall ('\d\.\d+', all_lines [i+j+1]))) /usr/lib/python3/dist-packages/ete3/evol/parser/codemlparser.py:240: SyntaxWarning: invalid escape sequence '\d' line = re.sub ('.* np: *(\d+)\): +(-\d+\.\d+).*', /usr/lib/python3/dist-packages/ete3/evol/parser/codemlparser.py:245: SyntaxWarning: invalid escape sequence '\d' line = re.sub ('.* np: *(\d+)\): +(nan).*', /usr/lib/python3/dist-packages/ete3/evol/parser/codemlparser.py:252: SyntaxWarning: invalid escape sequence '\d' labels = re.findall ('\d+\.\.\d+', line + ' ') /usr/lib/python3/dist-packages/ete3/evol/parser/codemlparser.py:258: SyntaxWarning: invalid escape sequence '\d' model.stats ['kappa'] = float (re.sub ('.*(\d+\.\d+).*', /usr/lib/python3/dist-packages/ete3/evol/parser/codemlparser.py:264: SyntaxWarning: invalid escape sequence '\d' if not re.match (' +\d+\.\.\d+ +\d+\.\d+ ', line): /usr/lib/python3/dist-packages/ete3/evol/parser/codemlparser.py:265: SyntaxWarning: invalid escape sequence '\d' if re.match (' +( +\d+\.\d+){8}', all_lines [i+1]): /usr/lib/python3/dist-packages/ete3/parser/newick.py:51: SyntaxWarning: invalid escape sequence '\[' _ILEGAL_NEWICK_CHARS = ":;(),\[\]\t\n\r=" /usr/lib/python3/dist-packages/ete3/parser/newick.py:54: SyntaxWarning: invalid escape sequence '\[' _NHX_RE = "\[&&NHX:[^\]]*\]" /usr/lib/python3/dist-packages/ete3/parser/newick.py:55: SyntaxWarning: invalid escape sequence '\s' _FLOAT_RE = "\s*[+-]?\d+\.?\d*(?:[eE][-+]?\d+)?\s*" /usr/lib/python3/dist-packages/ete3/parser/newick.py:402: SyntaxWarning: invalid escape sequence '\s' matcher_str= '^\s*%s\s*%s\s*(%s)?\s*$' % (FIRST_MATCH, SECOND_MATCH, _NHX_RE) /usr/lib/python3/dist-packages/ete3/parser/phylip.py:76: SyntaxWarning: invalid escape sequence '\s' m = re.match("^\s*(\d+)\s+(\d+)",line) /usr/lib/python3/dist-packages/ete3/parser/phylip.py:108: SyntaxWarning: invalid escape sequence '\s' SG.id2seq[id_counter] += re.sub("\s","", line) /usr/lib/python3/dist-packages/ete3/parser/phylip.py:123: SyntaxWarning: invalid escape sequence '\s' seq = re.sub("\s","",m.groups()[1]) /usr/lib/python3/dist-packages/ete3/parser/phylip.py:138: SyntaxWarning: invalid escape sequence '\s' seq = re.sub("\s", "", line) /usr/lib/python3/dist-packages/ete3/phylo/phylotree.py:132: SyntaxWarning: invalid escape sequence '\d' id_match = re.compile("([^0-9])?(\d+)([^0-9])?") /usr/lib/python3/dist-packages/ete3/phylo/phylotree.py:188: SyntaxWarning: invalid escape sequence '\d' id_match = re.compile("([^0-9])(\d+)([^0-9])") /usr/lib/python3/dist-packages/ete3/phylomedb/phylomeDB.py:255: SyntaxWarning: invalid escape sequence '\w' QUERYID_GENERAL_REGEXP_FILTER = "^[\w\d\-_,;:.|#@\/\\\()'<>!]+$" /usr/lib/python3/dist-packages/ete3/phylomedb/phylomeDB.py:256: SyntaxWarning: invalid escape sequence '\w' QUERYID_INTERNAL_ID_REGEXP_FILTER = "^\w{3}\d{7}$" /usr/lib/python3/dist-packages/ete3/phylomedb/phylomeDB3.py:75: SyntaxWarning: invalid escape sequence '\w' ID_PATTERN = re.compile("^[Pp][Hh][Yy]\w{7}(_\w{2,7})?$") /usr/lib/python3/dist-packages/ete3/phylomedb/phylomeDB3.py:153: SyntaxWarning: invalid escape sequence '\w' m = re.search("Phy(\w{7})_[\w\d]+", name) /usr/lib/python3/dist-packages/ete3/phylomedb/phylomeDB3.py:500: SyntaxWarning: invalid escape sequence '\w' QUERY_OLD_REGEXP_FILTER = "^\w{3}\d{1,}$" /usr/lib/python3/dist-packages/ete3/phylomedb/phylomeDB3.py:756: SyntaxWarning: invalid escape sequence '\w' QUERY_GEN_REGEXP_FILTER = "^[\w\d\-_,;:.|#@\/\\\()'<>!]+$" /usr/lib/python3/dist-packages/ete3/phylomedb/phylomeDB3.py:757: SyntaxWarning: invalid escape sequence '\w' QUERY_OLD_REGEXP_FILTER = "^\w{3}\d{1,}$" /usr/lib/python3/dist-packages/ete3/phylomedb/phylomeDB3.py:758: SyntaxWarning: invalid escape sequence '\w' QUERY_INT_REGEXP_FILTER = "^[Pp][Hh][Yy]\w{7}(_\w{2,7})?$" /usr/lib/python3/dist-packages/ete3/tools/common.py:158: SyntaxWarning: invalid escape sequence '\w' func_match = re.search("(\w+)\(([^)]*)\)", fvalue) /usr/lib/python3/dist-packages/ete3/tools/ete_build.py:818: SyntaxWarning: invalid escape sequence '\s' default='^([^\s]+)') /usr/lib/python3/dist-packages/ete3/tools/ete_build_lib/interface.py:114: SyntaxWarning: invalid escape sequence '\d' TAG = re.compile("@@((\d+),)?(\d+):", re.MULTILINE) /usr/lib/python3/dist-packages/ete3/tools/ete_build_lib/sge.py:56: SyntaxWarning: invalid escape sequence '\d' OK_PATTERN = 'Your job-array ([\d]+).\d+\-\d+:\d+ \("[^"]*"\) has been submitted' /usr/lib/python3/dist-packages/ete3/tools/ete_build_lib/task/iqtree.py:77: SyntaxWarning: invalid escape sequence '\s' m = re.search('Log-likelihood of the tree:\s+(-?\d+\.\d+)', /usr/lib/python3/dist-packages/ete3/tools/ete_build_lib/task/phyml.py:170: SyntaxWarning: invalid escape sequence '\s' m = re.search('Log-likelihood:\s+(-?\d+\.\d+)', /usr/lib/python3/dist-packages/ete3/tools/ete_build_lib/task/prottest.py:135: SyntaxWarning: invalid escape sequence '\s' m = re.search('Log-likelihood:\s+(-?\d+\.\d+)', /usr/lib/python3/dist-packages/ete3/tools/ete_build_lib/task/prottest2.py:139: SyntaxWarning: invalid escape sequence '\s' m = re.search('Log-likelihood:\s+(-?\d+\.\d+)', /usr/lib/python3/dist-packages/ete3/tools/ete_build_lib/task/raxml.py:271: SyntaxWarning: invalid escape sequence '\d' nw, nsubs = re.subn(":(\d+\.\d+)\[(\d+)\]", parse_alrt, raw_nw, flags=re.MULTILINE) /usr/lib/python3/dist-packages/ete3/tools/ete_build_lib/task/raxml.py:274: SyntaxWarning: invalid escape sequence '\d' nw, nsubs = re.subn(":(\d+\.\d+)\[(\d+)\]", parse_alrt, raw_nw) /usr/lib/python3/dist-packages/ete3/tools/ete_build_lib/utils.py:375: SyntaxWarning: invalid escape sequence '\[' return len(re.sub('\\033\[\d+m', '', _str(i))) /usr/lib/python3/dist-packages/ete3/tools/ete_build_lib/utils.py:519: SyntaxWarning: invalid escape sequence '\.' m = re.search("npr\.([\d\.]+)\.db", fname) /usr/lib/python3/dist-packages/ete3/tools/ete_build_lib/utils.py:538: SyntaxWarning: invalid escape sequence '\.' m = re.search("npr\.([\d\.]+)\.db", member.name) /usr/lib/python3/dist-packages/ete3/tools/ete_build_lib/utils.py:629: SyntaxWarning: invalid escape sequence '\[' return re.sub("\\033\[[^m]+m", "", string) /usr/lib/python3/dist-packages/ete3/tools/ete_build_lib/visualize.py:201: SyntaxWarning: invalid escape sequence '\{' lf.add_features(genename=re.sub('\{[^}]+\}', '', lf.name).strip()) /usr/lib/python3/dist-packages/ete3/tools/ete_build_lib/visualize.py:205: SyntaxWarning: invalid escape sequence '\{' m = re.search('\{([^}]+)\}', name) /usr/lib/python3/dist-packages/ete3/tools/ete_build_lib/workflow/genetree.py:163: SyntaxWarning: invalid escape sequence '\s' m = re.search("#MaxIdentity\s+(\d+\.\d+)", line) /usr/lib/python3/dist-packages/ete3/tools/ete_view.py:209: SyntaxWarning: invalid escape sequence '\d' nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read()) /usr/lib/python3/dist-packages/ete3/tools/ete_view.py:275: SyntaxWarning: invalid escape sequence '\d' nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read()) /usr/lib/python3/dist-packages/ete3/tools/ete_view.py:372: SyntaxWarning: invalid escape sequence '\(' auto_m = re.search("auto\(([^)]*)\)", fcolor) /usr/lib/python3/dist-packages/ete3/tools/ete_view.py:392: SyntaxWarning: invalid escape sequence '\(' auto_m = re.search("auto\(([^)]*)\)", fbgcolor) /usr/lib/python3/dist-packages/ete3/tools/utils.py:28: SyntaxWarning: invalid escape sequence '\[' return re.sub("\\033\[[^m]+m", "", string) /usr/lib/python3/dist-packages/ete3/treeview/faces.py:159: SyntaxWarning: invalid escape sequence '\_' """Base Face object. All Face types (i.e. TextFace, SeqMotifFace, /usr/lib/python3/dist-packages/ete3/treeview/main.py:64: SyntaxWarning: invalid escape sequence '\d' _COLOR_MATCH = re.compile("^#[A-Fa-f\d]{6}$") /usr/lib/python3/dist-packages/ete3/treeview/main.py:712: SyntaxWarning: invalid escape sequence '\d' compatible_code = re.sub('font-size="(\d+)"', 'font-size="\\1pt"', compatible_code) /usr/lib/python3/dist-packages/ete3/treeview/main.py:714: SyntaxWarning: invalid escape sequence '\s' compatible_code = re.sub(']+>\s*', '', compatible_code) /usr/lib/python3/dist-packages/ete3/utils.py:82: SyntaxWarning: invalid escape sequence '\[' return re.sub("\\033\[[^m]+m", "", string) Processing triggers for debianutils (5.14) ... Processing triggers for libc-bin (2.37-13) ... 0m52.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-get', '-yf', 'dist-upgrade'] 0m52.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m54.1s DUMP: c685a72bffc3f0235393e38cc047a210 - 0m54.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m54.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-cache', 'show', '--no-all-versions', 'python3-ete3'] 0m54.4s DUMP: Package: python3-ete3 Source: python-ete3 Version: 3.1.3+dfsg-2 Installed-Size: 2832 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-six, python3:any, python3-numpy Recommends: python3-lxml, python3-pyqt5.qtopengl, python3-pyqt5.qtsvg, python3-scipy, python3-skbio Description-en: Python Environment for (phylogenetic) Tree Exploration - Python 3.X The Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees (although clustering trees or any other tree-like data structure are also supported). . ETE is currently developed as a tool for researchers working in phylogenetics and genomics. If you use ETE for a published work, please cite: . Visit http://etetoolkit.org for more info. Description-md5: 62fa80cd1d7a708098c4e11beda86263 Homepage: http://etetoolkit.org Section: python Priority: optional Filename: pool/main/p/python-ete3/python3-ete3_3.1.3+dfsg-2_all.deb Size: 374596 MD5sum: c3ab132e1a695c8fabfb1c6ef35524df SHA256: 397f8fad8dd82dd135bda8e57a74c54f8c2ea4c934919129baaca7549e92889a 0m54.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-cache', 'show', '--no-all-versions', 'python3-ete3'] 0m54.4s INFO: apt-cache knows about the following packages: python3-ete3 0m54.4s INFO: Running scripts pre_install 0m54.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_database-server'] 0m54.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_database-server'] 0m54.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_exceptions'] 0m54.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_exceptions'] 0m54.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_extras'] 0m54.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_extras'] 0m54.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_foreign_architecture'] 0m54.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_foreign_architecture'] 0m54.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m54.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m54.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-cache', 'policy'] 0m54.5s 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: 0m54.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-cache', 'policy'] 0m54.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-cache', 'policy', 'python3-ete3'] 0m54.6s DUMP: python3-ete3: Installed: 3.1.3+dfsg-2 Candidate: 3.1.3+dfsg-2 Version table: *** 3.1.3+dfsg-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m54.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-cache', 'policy', 'python3-ete3'] 0m54.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-get', '-y', 'install', 'python3-ete3'] 0m55.2s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-ete3 is already the newest version (3.1.3+dfsg-2). The following package was automatically installed and is no longer required: libquadmath0 Use 'sudo apt autoremove' to remove it. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-get', '-y', 'install', 'python3-ete3'] 0m55.2s INFO: Running scripts post_install 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_install_exceptions'] 0m55.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_install_exceptions'] 0m55.3s INFO: Running scripts post_distupgrade 0m55.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m55.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m55.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_distupgrade_exceptions'] 0m55.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_distupgrade_exceptions'] 0m55.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m55.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m55.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m55.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m55.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_distupgrade_zz_backports'] 0m55.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_distupgrade_zz_backports'] 0m55.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_xkerg84'] 0m55.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_xkerg84'] 0m55.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_xkerg84'] 0m56.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_xkerg84'] 0m56.6s INFO: Running scripts pre_install 0m56.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_database-server'] 0m56.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_database-server'] 0m56.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_exceptions'] 0m56.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_exceptions'] 0m56.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_extras'] 0m56.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_extras'] 0m56.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_foreign_architecture'] 0m56.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_foreign_architecture'] 0m56.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m56.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m56.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-cache', 'policy'] 0m56.7s 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: 0m56.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-cache', 'policy'] 0m56.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-cache', 'policy', 'python3-ete3'] 0m56.8s DUMP: python3-ete3: Installed: 3.1.3+dfsg-2 Candidate: 3.1.3+dfsg-2 Version table: *** 3.1.3+dfsg-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m56.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-cache', 'policy', 'python3-ete3'] 0m56.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-get', '-y', 'install', 'python3-ete3=3.1.3+dfsg-2'] 0m57.4s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-ete3 is already the newest version (3.1.3+dfsg-2). The following package was automatically installed and is no longer required: libquadmath0 Use 'sudo apt autoremove' to remove it. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m57.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-get', '-y', 'install', 'python3-ete3=3.1.3+dfsg-2'] 0m57.4s INFO: Running scripts post_install 0m57.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_install_exceptions'] 0m57.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_install_exceptions'] 0m57.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_xkerg84'] 0m58.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_xkerg84'] 0m58.1s INFO: /bin converted to /usr/bin by /usr merge 0m58.1s INFO: /lib converted to /usr/lib by /usr merge 0m58.1s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m58.1s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m58.1s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m58.1s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m58.1s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m58.1s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m58.1s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m58.1s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m58.1s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m58.1s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m58.1s INFO: /sbin converted to /usr/sbin by /usr merge 0m58.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', '-ac', '--ignore-obsolete'] 1m0.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', '-ac', '--ignore-obsolete'] 1m0.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m0.3s DUMP: 0.15.6 1m0.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m0.3s INFO: Running adequate version 0.15.6 now. 1m0.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'python3-ete3'] 1m0.4s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'python3-ete3'] 1m0.4s INFO: Running scripts pre_remove 1m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_remove_exceptions'] 1m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/pre_remove_exceptions'] 1m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m1.9s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.7.7 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.39.3-2 install ok installed coreutils coreutils 9.4-2+b1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.14 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.1 install ok installed e2fsprogs e2fsprogs 1.47.0-2+b1 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-12-base:amd64 gcc-12-base 12.3.0-12 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-8 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.11-3 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.7.7 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.1.2-1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-1 install ok installed libblas3:amd64 libblas3 3.11.0-2 install ok installed libblkid1:amd64 libblkid1 2.39.3-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.37-13 install ok installed libc6:amd64 libc6 2.37-13 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-4 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271 install ok installed libexpat1:amd64 libexpat1 2.5.0-2 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2+b1 install ok installed libffi8:amd64 libffi8 3.4.4-2 install ok installed libgcc-s1:amd64 libgcc-s1 13.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgfortran5:amd64 libgfortran5 13.2.0-8 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2 install ok installed libgnutls30:amd64 libgnutls30 3.8.2-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-5 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.4-1+b1 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-5 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-5 install ok installed liblapack3:amd64 liblapack3 3.11.0-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.5-0.1 install ok installed libmd0:amd64 libmd0 1.1.0-1 install ok installed libmount1:amd64 libmount1 2.39.3-2 install ok installed libncursesw6:amd64 libncursesw6 6.4+20231209-1 install ok installed libnettle8:amd64 libnettle8 3.9.1-2 install ok installed libnsl2:amd64 libnsl2 1.3.0-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-9.1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-9.1 install ok installed libpam-runtime libpam-runtime 1.5.2-9.1 install ok installed libpam0g:amd64 libpam0g 1.5.2-9.1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.6-1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.7-2 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.7-2 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.1-2 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.1-2 install ok installed libquadmath0:amd64 libquadmath0 13.2.0-8 install ok installed libreadline8:amd64 libreadline8 8.2-3 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-2+b1 install ok installed libselinux1:amd64 libselinux1 3.5-1+b1 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b1 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-2 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.44.2-1 install ok installed libss2:amd64 libss2 1.47.0-2+b1 install ok installed libssl3:amd64 libssl3 3.1.4-2 install ok installed libstdc++6:amd64 libstdc++6 13.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 255-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3 install ok installed libtinfo6:amd64 libtinfo6 6.4+20231209-1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.4+ds-1 install ok installed libudev1:amd64 libudev1 255-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed libuuid1:amd64 libuuid1 2.39.3-2 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-3 install ok installed logsave logsave 1.47.0-2+b1 install ok installed mawk mawk 1.3.4.20231126-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.39.3-2 install ok installed ncurses-base ncurses-base 6.4+20231209-1 install ok installed ncurses-bin ncurses-bin 6.4+20231209-1 install ok installed netbase netbase 6.4 install ok installed passwd passwd 1:4.13+dfsg1-3 install ok installed perl-base perl-base 5.36.0-10 install ok installed python3 python3 3.11.6-1 install ok installed python3-ete3 python3-ete3 3.1.3+dfsg-2 install ok installed python3-minimal python3-minimal 3.11.6-1 install ok installed python3-numpy python3-numpy 1:1.24.2-2 install ok installed python3-pkg-resources python3-pkg-resources 68.1.2-2 install ok installed python3-six python3-six 1.16.0-4 install ok installed python3.11 python3.11 3.11.7-2 install ok installed python3.11-minimal python3.11-minimal 3.11.7-2 install ok installed python3.12 python3.12 3.12.1-2 install ok installed python3.12-minimal python3.12-minimal 3.12.1-2 install ok installed readline-common readline-common 8.2-3 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.08-5 install ok installed tar tar 1.34+dfsg-1.3 install ok installed tzdata tzdata 2023c-11 install ok installed usr-is-merged usr-is-merged 38 install ok installed util-linux util-linux 2.39.3-2 install ok installed util-linux-extra util-linux-extra 2.39.3-2 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3 1m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-get', 'remove', 'libblas3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'netbase', 'python3', 'python3-minimal', 'python3-numpy', 'python3-pkg-resources', 'python3-six', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'readline-common', 'python3-ete3'] 1m4.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libblas3 libexpat1 libgfortran5 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libncursesw6 libnsl2 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libpython3.12-minimal libpython3.12-stdlib libquadmath0 libreadline8 libsqlite3-0 libtirpc-common libtirpc3 media-types netbase python3 python3-ete3 python3-minimal python3-numpy python3-pkg-resources python3-six python3.11 python3.11-minimal python3.12 python3.12-minimal readline-common 0 upgraded, 0 newly installed, 34 to remove and 0 not upgraded. After this operation, 107 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 ... 8192 files and directories currently installed.) Removing python3-ete3 (3.1.3+dfsg-2) ... Removing python3-numpy (1:1.24.2-2) ... Removing liblapack3:amd64 (3.11.0-2) ... Removing libblas3:amd64 (3.11.0-2) ... Removing python3.12 (3.12.1-2) ... Removing python3.12-minimal (3.12.1-2) ... Removing python3-six (1.16.0-4) ... Removing libgfortran5:amd64 (13.2.0-8) ... Removing libpython3.12-stdlib:amd64 (3.12.1-2) ... Removing libpython3.12-minimal:amd64 (3.12.1-2) ... Removing libquadmath0:amd64 (13.2.0-8) ... Removing python3-pkg-resources (68.1.2-2) ... Removing python3 (3.11.6-1) ... Removing python3.11 (3.11.7-2) ... Removing libpython3-stdlib:amd64 (3.11.6-1) ... Removing libpython3.11-stdlib:amd64 (3.11.7-2) ... find: '/usr/lib/python3': No such file or directory Removing libncursesw6:amd64 (6.4+20231209-1) ... Removing libnsl2:amd64 (1.3.0-3) ... Removing python3-minimal (3.11.6-1) ... Removing libreadline8:amd64 (8.2-3) ... Removing libsqlite3-0:amd64 (3.44.2-1) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-3) ... Removing python3.11-minimal (3.11.7-2) ... Removing libexpat1:amd64 (2.5.0-2) ... Removing libtirpc3:amd64 (1.3.4+ds-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-5) ... Removing libkrb5-3:amd64 (1.20.1-5) ... Removing libk5crypto3:amd64 (1.20.1-5) ... Removing libkeyutils1:amd64 (1.6.3-2) ... Removing libkrb5support0:amd64 (1.20.1-5) ... Removing libpython3.11-minimal:amd64 (3.11.7-2) ... find: '/usr/lib/python3': No such file or directory Removing libtirpc-common (1.3.4+ds-1) ... Processing triggers for libc-bin (2.37-13) ... 1m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-get', 'remove', 'libblas3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'netbase', 'python3', 'python3-minimal', 'python3-numpy', 'python3-pkg-resources', 'python3-six', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'readline-common', 'python3-ete3'] 1m4.3s INFO: Running scripts post_remove 1m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_remove_exceptions'] 1m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_remove_exceptions'] 1m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'dpkg', '--purge', 'libblas3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'netbase', 'python3', 'python3-minimal', 'python3-numpy', 'python3-pkg-resources', 'python3-six', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'readline-common'] 1m4.4s DUMP: dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed (Reading database ... 5336 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-5) ... 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 libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.7-2) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed Purging configuration files for libpython3.12-minimal:amd64 (3.12.1-2) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed Purging configuration files for libtirpc-common (1.3.4+ds-1) ... dpkg: warning: ignoring request to remove libtirpc3 which isn't installed Purging configuration files for media-types (10.1.0) ... Purging configuration files for netbase (6.4) ... Purging configuration files for python3 (3.11.6-1) ... dpkg: warning: ignoring request to remove python3-minimal 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-six which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed Purging configuration files for python3.11-minimal (3.11.7-2) ... dpkg: warning: ignoring request to remove python3.12 which isn't installed Purging configuration files for python3.12-minimal (3.12.1-2) ... Purging configuration files for readline-common (8.2-3) ... 1m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'dpkg', '--purge', 'libblas3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'netbase', 'python3', 'python3-minimal', 'python3-numpy', 'python3-pkg-resources', 'python3-six', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'readline-common'] 1m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'dpkg', '--purge', 'python3-ete3'] 1m4.4s DUMP: dpkg: warning: ignoring request to remove python3-ete3 which isn't installed 1m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'dpkg', '--purge', 'python3-ete3'] 1m4.4s INFO: Running scripts post_purge 1m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_purge_exceptions'] 1m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_purge_exceptions'] 1m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'dpkg', '--purge', '--pending'] 1m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'dpkg', '--purge', '--pending'] 1m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'dpkg', '--remove', '--pending'] 1m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'dpkg', '--remove', '--pending'] 1m4.5s INFO: Running scripts post_test 1m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_test_exceptions'] 1m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'tmp/scripts/post_test_exceptions'] 1m4.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_xkerg84'] 1m4.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_xkerg84'] 1m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'dpkg-divert', '--list'] 1m5.0s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 1m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'dpkg-divert', '--list'] 1m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-get', 'clean'] 1m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_xkerg84', 'apt-get', 'clean'] 1m5.0s DEBUG: Recording chroot state 1m6.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/dev/shm'] 1m6.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/dev/shm'] 1m6.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/dev/console'] 1m6.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/dev/console'] 1m6.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/dev/ptmx'] 1m6.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/dev/ptmx'] 1m6.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/dev/pts'] 1m6.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/dev/pts'] 1m6.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/proc'] 1m6.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp_xkerg84/proc'] 1m6.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp_xkerg84'] 1m6.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp_xkerg84'] 1m6.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp_xkerg84 1m6.6s INFO: PASS: Upgrading between Debian distributions. 1m6.6s INFO: PASS: All tests. 1m6.6s INFO: piuparts run ends. ret=0 End: 2023-12-14 21:45:39 GMT