Start: 2020-08-24 00:18:32 GMT [testing] Package: bio-rainbow Version: 2.0.4+dfsg-1 Installed-Size: 173 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), perl:any Description: clustering and assembling short reads for bioinformatics Homepage: http://sourceforge.net/projects/bio-rainbow/ Description-md5: 9923da0307e9697918f7aeba3ffbc7dd Section: science Priority: optional Filename: pool/main/b/bio-rainbow/bio-rainbow_2.0.4+dfsg-1_amd64.deb Size: 51780 MD5sum: 4ceeae6684053743fc943c08a399ce58 SHA256: 9423ca0d09be1cb509f3484528a2166eb8ab438ab19edf7dae8d5eb188759e84 [sid] Package: bio-rainbow Version: 2.0.4+dfsg-2 Installed-Size: 186 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), perl:any Description: clustering and assembling short reads for bioinformatics Homepage: http://sourceforge.net/projects/bio-rainbow/ Description-md5: 9923da0307e9697918f7aeba3ffbc7dd Section: science Priority: optional Filename: pool/main/b/bio-rainbow/bio-rainbow_2.0.4+dfsg-2_amd64.deb Size: 60260 MD5sum: 607596fbd7640f920eef3801f41a1568 SHA256: 283d67b39eb9b2accc77fea45eed43a8903113b4fe03add53e0d8ec8b2103ae9 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/bullseye_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt bio-rainbow=2.0.4+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 1.1.2~202004292038~1.1.1-19-g418151e2 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/bullseye_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt bio-rainbow=2.0.4+dfsg-2 0m0.0s INFO: Running on: Linux piu-slave-conova-01 4.19.0-10-amd64 #1 SMP Debian 4.19.132-1 (2020-07-24) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp6s677hzr 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp6s677hzr 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz'] 0m1.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye_amd64.tar.gz'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/proc'] 0m1.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/proc'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/dev/pts'] 0m1.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/dev/pts'] 0m1.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/dev/ptmx'] 0m1.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/dev/ptmx'] 0m1.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/dev/console'] 0m1.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/dev/console'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/dev/shm'] 0m1.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/dev/shm'] 0m1.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m1.4s DEBUG: Created policy-rc.d and chmodded it. 0m1.4s DEBUG: Created resolv.conf. 0m1.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp6s677hzr/tmp/scripts/ 0m1.4s INFO: Running scripts post_chroot_unpack 0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-get', 'update'] 0m4.3s DUMP: Get:1 http://deb.debian.org/debian bullseye InRelease [116 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 Packages [7675 kB] Get:3 http://deb.debian.org/debian bullseye/main Translation-en [5881 kB] Fetched 13.7 MB in 2s (5789 kB/s) Reading package lists... 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-get', 'update'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-get', '-yf', 'dist-upgrade'] 0m4.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: libsystemd0 libudev1 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 530 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 libsystemd0 amd64 246.2-1 [369 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libudev1 amd64 246.2-1 [162 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 530 kB in 0s (4679 kB/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 ... 6524 files and directories currently installed.) Preparing to unpack .../libsystemd0_246.2-1_amd64.deb ... Unpacking libsystemd0:amd64 (246.2-1) over (246.1-1) ... Setting up libsystemd0:amd64 (246.2-1) ... (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 ... 6524 files and directories currently installed.) Preparing to unpack .../libudev1_246.2-1_amd64.deb ... Unpacking libudev1:amd64 (246.2-1) over (246.1-1) ... Setting up libudev1:amd64 (246.2-1) ... Processing triggers for libc-bin (2.31-3) ... 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-get', '-yf', 'dist-upgrade'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.2s DUMP: 80d7900220ed03451670acba3e4a8371 - 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.2s INFO: Running scripts post_setup 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_setup_dummy_users'] 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_setup_dummy_users'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_setup_forbid_home'] 0m6.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_setup_forbid_home'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_setup_force-unsafe-io'] 0m6.3s 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' 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_setup_force-unsafe-io'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_setup_minimize'] 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_setup_minimize'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_setup_squeeze-backports'] 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_setup_squeeze-backports'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_setup_zz_backports'] 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_setup_zz_backports'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.4s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 2.1.10 install ok installed base-files base-files 11 install ok installed base-passwd base-passwd 3.5.47 install ok installed bash bash 5.0-7 install ok installed bsdutils bsdutils 1:2.36-2 install ok installed coreutils coreutils 8.30-3+b1 install ok installed dash dash 0.5.10.2-7 install ok installed debconf debconf 1.5.74 install ok installed debian-archive-keyring debian-archive-keyring 2019.1 install ok installed debianutils debianutils 4.9.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.20.5 install ok installed e2fsprogs e2fsprogs 1.45.6-1 install ok installed findutils findutils 4.7.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.0-5 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-15 install ok installed gpgv gpgv 2.2.20-1 install ok installed grep grep 3.4-1 install ok installed gzip gzip 1.10-2 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.58 install ok installed libacl1:amd64 libacl1 2.2.53-8 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.1.10 install ok installed libattr1:amd64 libattr1 1:2.4.48-5 install ok installed libaudit-common libaudit-common 1:2.8.5-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.5-3+b1 install ok installed libblkid1:amd64 libblkid1 2.36-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-3 install ok installed libc6:amd64 libc6 2.31-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2 install ok installed libcom-err2:amd64 libcom-err2 1.45.6-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.16-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.253 install ok installed libext2fs2:amd64 libext2fs2 1.45.6-1 install ok installed libffi7:amd64 libffi7 3.3-4 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.0-5 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.6-2 install ok installed libgmp10:amd64 libgmp10 2:6.2.0+dfsg-6 install ok installed libgnutls30:amd64 libgnutls30 3.6.14-2+b1 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libhogweed6:amd64 libhogweed6 3.6-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.2-2 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+b1 install ok installed libmount1:amd64 libmount1 2.36-2 install ok installed libnettle8:amd64 libnettle8 3.6-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.20-1 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.34-7 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.4.3-1+b1 install ok installed libselinux1:amd64 libselinux1 3.1-2 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36-2 install ok installed libss2:amd64 libss2 1.45.6-1 install ok installed libstdc++6:amd64 libstdc++6 10.2.0-5 install ok installed libsystemd0:amd64 libsystemd0 246.2-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.2-1 install ok installed libudev1:amd64 libudev1 246.2-1 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36-2 install ok installed libzstd1:amd64 libzstd1 1.4.5+dfsg-4 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.45.6-1 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36-2 install ok installed ncurses-base ncurses-base 6.2-1 install ok installed ncurses-bin ncurses-bin 6.2-1 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.30.3-4 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-4 install ok installed tar tar 1.30+dfsg-7 install ok installed tzdata tzdata 2020a-1 install ok installed util-linux util-linux 2.36-2 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.4s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m6.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6s677hzr'] 0m6.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6s677hzr'] 0m6.7s INFO: Running scripts is_testable 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/is_testable_uninstallable'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/is_testable_uninstallable'] 0m6.7s INFO: Running scripts pre_test 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_test_exceptions'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_test_exceptions'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_test_root_password'] 0m6.7s DUMP: New password: Retype new password: passwd: password updated successfully 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_test_root_password'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-cache', 'show', '--no-all-versions', 'bio-rainbow'] 0m6.9s DUMP: Package: bio-rainbow Version: 2.0.4+dfsg-1 Installed-Size: 173 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), perl:any Description-en: clustering and assembling short reads for bioinformatics Efficient tool for clustering and assembling short reads, especially for RAD. . Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like strategy to divide potential groups into haplotypes in a top-down manner. long a guided tree, it iteratively merges sibling leaves in a bottom-up manner if they are similar enough. Here, the similarity is defined by comparing the 2nd reads of a RAD segment. This approach tries to collapse heterozygote while discriminate repetitive sequences. At last, Rainbow uses a greedy algorithm to locally assemble merged reads into contigs. Rainbow not only outputs the optimal but also suboptimal assembly results. Based on simulation and a real guppy RAD-seq data, it is shown that Rainbow is more competent than the other tools in dealing with RAD-seq data. Description-md5: 9923da0307e9697918f7aeba3ffbc7dd Homepage: http://sourceforge.net/projects/bio-rainbow/ Section: science Priority: optional Filename: pool/main/b/bio-rainbow/bio-rainbow_2.0.4+dfsg-1_amd64.deb Size: 51780 MD5sum: 4ceeae6684053743fc943c08a399ce58 SHA256: 9423ca0d09be1cb509f3484528a2166eb8ab438ab19edf7dae8d5eb188759e84 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-cache', 'show', '--no-all-versions', 'bio-rainbow'] 0m6.9s INFO: apt-cache knows about the following packages: bio-rainbow 0m6.9s INFO: Running scripts pre_install 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_database-server'] 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_database-server'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_exceptions'] 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_exceptions'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_extras'] 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_extras'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-cache', 'policy'] 0m7.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release o=Debian,a=testing,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-cache', 'policy'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-cache', 'policy', 'bio-rainbow'] 0m7.0s DUMP: bio-rainbow: Installed: (none) Candidate: 2.0.4+dfsg-1 Version table: 2.0.4+dfsg-1 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-cache', 'policy', 'bio-rainbow'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-get', '-y', 'install', 'bio-rainbow'] 0m9.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libgdbm-compat4 libgdbm6 libperl5.30 perl perl-modules-5.30 Suggested packages: gdbm-l10n sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl Recommended packages: netbase The following NEW packages will be installed: bio-rainbow libgdbm-compat4 libgdbm6 libperl5.30 perl perl-modules-5.30 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. Need to get 7276 kB of archives. After this operation, 46.5 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 perl-modules-5.30 all 5.30.3-4 [2806 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libgdbm6 amd64 1.18.1-5 [64.5 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 libgdbm-compat4 amd64 1.18.1-5 [44.2 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 libperl5.30 amd64 5.30.3-4 [4019 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 perl amd64 5.30.3-4 [290 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 bio-rainbow amd64 2.0.4+dfsg-1 [51.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7276 kB in 0s (16.2 MB/s) Selecting previously unselected package perl-modules-5.30. (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 ... 6526 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.30_5.30.3-4_all.deb ... Unpacking perl-modules-5.30 (5.30.3-4) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.18.1-5_amd64.deb ... Unpacking libgdbm6:amd64 (1.18.1-5) ... Selecting previously unselected package libgdbm-compat4:amd64. Preparing to unpack .../2-libgdbm-compat4_1.18.1-5_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.18.1-5) ... Selecting previously unselected package libperl5.30:amd64. Preparing to unpack .../3-libperl5.30_5.30.3-4_amd64.deb ... Unpacking libperl5.30:amd64 (5.30.3-4) ... Selecting previously unselected package perl. Preparing to unpack .../4-perl_5.30.3-4_amd64.deb ... Unpacking perl (5.30.3-4) ... Selecting previously unselected package bio-rainbow. Preparing to unpack .../5-bio-rainbow_2.0.4+dfsg-1_amd64.deb ... Unpacking bio-rainbow (2.0.4+dfsg-1) ... Setting up perl-modules-5.30 (5.30.3-4) ... Setting up libgdbm6:amd64 (1.18.1-5) ... Setting up libgdbm-compat4:amd64 (1.18.1-5) ... Setting up libperl5.30:amd64 (5.30.3-4) ... Setting up perl (5.30.3-4) ... Setting up bio-rainbow (2.0.4+dfsg-1) ... Processing triggers for libc-bin (2.31-3) ... 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-get', '-y', 'install', 'bio-rainbow'] 0m9.0s INFO: Running scripts post_install 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_install_exceptions'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_install_exceptions'] 0m9.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6s677hzr'] 0m9.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6s677hzr'] 0m9.4s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp6s677hzr to sid 0m9.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m9.4s INFO: Running scripts pre_distupgrade 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_distupgrade_exceptions'] 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_distupgrade_exceptions'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-get', 'update'] 0m13.9s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [146 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [8373 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6302 kB] Fetched 14.8 MB in 4s (3905 kB/s) Reading package lists... 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-get', 'update'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-get', '-yf', 'dist-upgrade'] 0m16.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bio-rainbow coreutils debianutils gcc-9-base libgdbm-compat4 libgdbm6 libp11-kit0 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3641 kB of archives. After this operation, 1620 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 coreutils amd64 8.32-3 [2838 kB] Get:2 http://deb.debian.org/debian sid/main amd64 debianutils amd64 4.11.1 [101 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.23.21-2 [335 kB] Get:4 http://deb.debian.org/debian sid/main amd64 gcc-9-base amd64 9.3.0-17 [197 kB] Get:5 http://deb.debian.org/debian sid/main amd64 bio-rainbow amd64 2.0.4+dfsg-2 [60.3 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libgdbm6 amd64 1.18.1-5.1 [64.4 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4 amd64 1.18.1-5.1 [44.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3641 kB in 1s (6919 kB/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 ... 8495 files and directories currently installed.) Preparing to unpack .../coreutils_8.32-3_amd64.deb ... Unpacking coreutils (8.32-3) over (8.30-3+b1) ... Setting up coreutils (8.32-3) ... (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 ... 8583 files and directories currently installed.) Preparing to unpack .../debianutils_4.11.1_amd64.deb ... Unpacking debianutils (4.11.1) over (4.9.1) ... Setting up debianutils (4.11.1) ... (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 ... 8583 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.23.21-2_amd64.deb ... Unpacking libp11-kit0:amd64 (0.23.21-2) over (0.23.20-1) ... Setting up libp11-kit0:amd64 (0.23.21-2) ... (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 ... 8583 files and directories currently installed.) Preparing to unpack .../gcc-9-base_9.3.0-17_amd64.deb ... Unpacking gcc-9-base:amd64 (9.3.0-17) over (9.3.0-15) ... Preparing to unpack .../bio-rainbow_2.0.4+dfsg-2_amd64.deb ... Unpacking bio-rainbow (2.0.4+dfsg-2) over (2.0.4+dfsg-1) ... Preparing to unpack .../libgdbm6_1.18.1-5.1_amd64.deb ... Unpacking libgdbm6:amd64 (1.18.1-5.1) over (1.18.1-5) ... Preparing to unpack .../libgdbm-compat4_1.18.1-5.1_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.18.1-5.1) over (1.18.1-5) ... Setting up bio-rainbow (2.0.4+dfsg-2) ... Setting up libgdbm6:amd64 (1.18.1-5.1) ... Setting up gcc-9-base:amd64 (9.3.0-17) ... Setting up libgdbm-compat4:amd64 (1.18.1-5.1) ... Processing triggers for libc-bin (2.31-3) ... 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-get', '-yf', 'dist-upgrade'] 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m16.6s DUMP: e8c0dbc1f1c5bd238125d0ecac80ad65 - 0m16.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-cache', 'show', '--no-all-versions', 'bio-rainbow'] 0m16.9s DUMP: Package: bio-rainbow Version: 2.0.4+dfsg-2 Installed-Size: 186 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), perl:any Description-en: clustering and assembling short reads for bioinformatics Efficient tool for clustering and assembling short reads, especially for RAD. . Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like strategy to divide potential groups into haplotypes in a top-down manner. long a guided tree, it iteratively merges sibling leaves in a bottom-up manner if they are similar enough. Here, the similarity is defined by comparing the 2nd reads of a RAD segment. This approach tries to collapse heterozygote while discriminate repetitive sequences. At last, Rainbow uses a greedy algorithm to locally assemble merged reads into contigs. Rainbow not only outputs the optimal but also suboptimal assembly results. Based on simulation and a real guppy RAD-seq data, it is shown that Rainbow is more competent than the other tools in dealing with RAD-seq data. Description-md5: 9923da0307e9697918f7aeba3ffbc7dd Homepage: http://sourceforge.net/projects/bio-rainbow/ Section: science Priority: optional Filename: pool/main/b/bio-rainbow/bio-rainbow_2.0.4+dfsg-2_amd64.deb Size: 60260 MD5sum: 607596fbd7640f920eef3801f41a1568 SHA256: 283d67b39eb9b2accc77fea45eed43a8903113b4fe03add53e0d8ec8b2103ae9 0m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-cache', 'show', '--no-all-versions', 'bio-rainbow'] 0m16.9s INFO: apt-cache knows about the following packages: bio-rainbow 0m16.9s INFO: Running scripts pre_install 0m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_database-server'] 0m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_database-server'] 0m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_exceptions'] 0m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_exceptions'] 0m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_extras'] 0m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_extras'] 0m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_foreign_architecture'] 0m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_foreign_architecture'] 0m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-cache', 'policy'] 0m17.0s 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: 0m17.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-cache', 'policy'] 0m17.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-cache', 'policy', 'bio-rainbow'] 0m17.1s DUMP: bio-rainbow: Installed: 2.0.4+dfsg-2 Candidate: 2.0.4+dfsg-2 Version table: *** 2.0.4+dfsg-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m17.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-cache', 'policy', 'bio-rainbow'] 0m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-get', '-y', 'install', 'bio-rainbow'] 0m17.4s DUMP: Reading package lists... Building dependency tree... Reading state information... bio-rainbow is already the newest version (2.0.4+dfsg-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m17.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-get', '-y', 'install', 'bio-rainbow'] 0m17.4s INFO: Running scripts post_install 0m17.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_install_exceptions'] 0m17.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_install_exceptions'] 0m17.5s INFO: Running scripts post_distupgrade 0m17.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m17.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m17.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_distupgrade_exceptions'] 0m17.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_distupgrade_exceptions'] 0m17.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m17.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m17.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m17.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m17.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_distupgrade_zz_backports'] 0m17.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_distupgrade_zz_backports'] 0m17.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6s677hzr'] 0m18.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6s677hzr'] 0m18.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6s677hzr'] 0m18.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6s677hzr'] 0m18.8s INFO: Running scripts pre_install 0m18.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_database-server'] 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_database-server'] 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_exceptions'] 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_exceptions'] 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_extras'] 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_extras'] 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-cache', 'policy'] 0m19.0s 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: 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-cache', 'policy'] 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-cache', 'policy', 'bio-rainbow'] 0m19.0s DUMP: bio-rainbow: Installed: 2.0.4+dfsg-2 Candidate: 2.0.4+dfsg-2 Version table: *** 2.0.4+dfsg-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-cache', 'policy', 'bio-rainbow'] 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-get', '-y', 'install', 'bio-rainbow=2.0.4+dfsg-2'] 0m19.5s DUMP: Reading package lists... Building dependency tree... Reading state information... bio-rainbow is already the newest version (2.0.4+dfsg-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-get', '-y', 'install', 'bio-rainbow=2.0.4+dfsg-2'] 0m19.5s INFO: Running scripts post_install 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_install_exceptions'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_install_exceptions'] 0m19.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6s677hzr'] 0m19.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6s677hzr'] 0m20.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', '-ac', '--ignore-obsolete'] 0m21.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', '-ac', '--ignore-obsolete'] 0m21.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m21.2s DUMP: 0.15.2 0m21.2s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m21.2s INFO: Running adequate version 0.15.2 now. 0m21.2s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'bio-rainbow'] 0m21.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'bio-rainbow'] 0m21.2s INFO: Running scripts pre_remove 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m21.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m21.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m21.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m21.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m21.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m21.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m21.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m21.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m21.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m21.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_remove_exceptions'] 0m21.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/pre_remove_exceptions'] 0m21.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m22.0s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 2.1.10 install ok installed base-files base-files 11 install ok installed base-passwd base-passwd 3.5.47 install ok installed bash bash 5.0-7 install ok installed bio-rainbow bio-rainbow 2.0.4+dfsg-2 install ok installed bsdutils bsdutils 1:2.36-2 install ok installed coreutils coreutils 8.32-3 install ok installed dash dash 0.5.10.2-7 install ok installed debconf debconf 1.5.74 install ok installed debian-archive-keyring debian-archive-keyring 2019.1 install ok installed debianutils debianutils 4.11.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.20.5 install ok installed e2fsprogs e2fsprogs 1.45.6-1 install ok installed findutils findutils 4.7.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.0-5 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-17 install ok installed gpgv gpgv 2.2.20-1 install ok installed grep grep 3.4-1 install ok installed gzip gzip 1.10-2 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.58 install ok installed libacl1:amd64 libacl1 2.2.53-8 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.1.10 install ok installed libattr1:amd64 libattr1 1:2.4.48-5 install ok installed libaudit-common libaudit-common 1:2.8.5-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.5-3+b1 install ok installed libblkid1:amd64 libblkid1 2.36-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-3 install ok installed libc6:amd64 libc6 2.31-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2 install ok installed libcom-err2:amd64 libcom-err2 1.45.6-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.16-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.253 install ok installed libext2fs2:amd64 libext2fs2 1.45.6-1 install ok installed libffi7:amd64 libffi7 3.3-4 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.0-5 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.6-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.18.1-5.1 install ok installed libgdbm6:amd64 libgdbm6 1.18.1-5.1 install ok installed libgmp10:amd64 libgmp10 2:6.2.0+dfsg-6 install ok installed libgnutls30:amd64 libgnutls30 3.6.14-2+b1 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libhogweed6:amd64 libhogweed6 3.6-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.2-2 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+b1 install ok installed libmount1:amd64 libmount1 2.36-2 install ok installed libnettle8:amd64 libnettle8 3.6-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.21-2 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.34-7 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libperl5.30:amd64 libperl5.30 5.30.3-4 install ok installed libseccomp2:amd64 libseccomp2 2.4.3-1+b1 install ok installed libselinux1:amd64 libselinux1 3.1-2 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36-2 install ok installed libss2:amd64 libss2 1.45.6-1 install ok installed libstdc++6:amd64 libstdc++6 10.2.0-5 install ok installed libsystemd0:amd64 libsystemd0 246.2-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.2-1 install ok installed libudev1:amd64 libudev1 246.2-1 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36-2 install ok installed libzstd1:amd64 libzstd1 1.4.5+dfsg-4 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.45.6-1 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36-2 install ok installed ncurses-base ncurses-base 6.2-1 install ok installed ncurses-bin ncurses-bin 6.2-1 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl perl 5.30.3-4 install ok installed perl-base perl-base 5.30.3-4 install ok installed perl-modules-5.30 perl-modules-5.30 5.30.3-4 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-4 install ok installed tar tar 1.30+dfsg-7 install ok installed tzdata tzdata 2020a-1 install ok installed util-linux util-linux 2.36-2 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m22.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-get', 'remove', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libperl5.30:amd64', 'perl', 'perl-modules-5.30', 'bio-rainbow'] 0m22.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bio-rainbow libgdbm-compat4 libgdbm6 libperl5.30 perl perl-modules-5.30 0 upgraded, 0 newly installed, 6 to remove and 0 not upgraded. After this operation, 46.5 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 ... 8588 files and directories currently installed.) Removing bio-rainbow (2.0.4+dfsg-2) ... Removing perl (5.30.3-4) ... Removing libperl5.30:amd64 (5.30.3-4) ... Removing libgdbm-compat4:amd64 (1.18.1-5.1) ... Removing libgdbm6:amd64 (1.18.1-5.1) ... Removing perl-modules-5.30 (5.30.3-4) ... Processing triggers for libc-bin (2.31-3) ... 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-get', 'remove', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libperl5.30:amd64', 'perl', 'perl-modules-5.30', 'bio-rainbow'] 0m22.6s INFO: Running scripts post_remove 0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_remove_exceptions'] 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_remove_exceptions'] 0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'dpkg', '--purge', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libperl5.30:amd64', 'perl', 'perl-modules-5.30'] 0m22.6s DUMP: dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libperl5.30 which isn't installed (Reading database ... 6617 files and directories currently installed.) Purging configuration files for perl (5.30.3-4) ... dpkg: warning: ignoring request to remove perl-modules-5.30 which isn't installed 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'dpkg', '--purge', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libperl5.30:amd64', 'perl', 'perl-modules-5.30'] 0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'dpkg', '--purge', 'bio-rainbow'] 0m22.6s DUMP: dpkg: warning: ignoring request to remove bio-rainbow which isn't installed 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'dpkg', '--purge', 'bio-rainbow'] 0m22.6s INFO: Running scripts post_purge 0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_purge_exceptions'] 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_purge_exceptions'] 0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'dpkg', '--purge', '--pending'] 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'dpkg', '--purge', '--pending'] 0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'dpkg', '--remove', '--pending'] 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'dpkg', '--remove', '--pending'] 0m22.6s INFO: Running scripts post_test 0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_test_exceptions'] 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'tmp/scripts/post_test_exceptions'] 0m22.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6s677hzr'] 0m22.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6s677hzr'] 0m22.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'dpkg-divert', '--list'] 0m22.9s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m22.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'dpkg-divert', '--list'] 0m22.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-get', 'clean'] 0m22.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6s677hzr', 'apt-get', 'clean'] 0m22.9s DEBUG: Recording chroot state 0m23.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/dev/shm'] 0m23.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/dev/shm'] 0m23.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/dev/console'] 0m23.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/dev/console'] 0m23.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/dev/ptmx'] 0m23.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/dev/ptmx'] 0m23.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/dev/pts'] 0m23.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/dev/pts'] 0m23.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/proc'] 0m23.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp6s677hzr/proc'] 0m23.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp6s677hzr'] 0m23.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp6s677hzr'] 0m23.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp6s677hzr 0m23.9s INFO: PASS: Upgrading between Debian distributions. 0m23.9s INFO: PASS: All tests. 0m23.9s INFO: piuparts run ends. ret=0 End: 2020-08-24 00:18:56 GMT