Start: 2022-10-13 19:12:48 GMT [jessie] Package: mira-assembler Source: mira (4.0.2-1) Version: 4.0.2-1+b1 Installed-Size: 4096 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libboost-filesystem1.55.0, libboost-iostreams1.55.0, libboost-regex1.55.0, libboost-system1.55.0, libboost-thread1.55.0, libbz2-1.0, libc6 (>= 2.14), libexpat1 (>= 2.0.1), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.8), libtcmalloc-minimal4, zlib1g (>= 1:1.1.4) Suggests: mira-examples, mira-doc Description: Whole Genome Shotgun and EST Sequence Assembler Homepage: http://chevreux.org/projects_mira.html Description-md5: 82b6240df7e707dae67c440269ca669f Tag: role::program Section: science Priority: optional Filename: pool/main/m/mira/mira-assembler_4.0.2-1+b1_amd64.deb Size: 1403168 MD5sum: 52a53e6a4447705386f1b7ec86acecc8 SHA1: f4b80fb52658600ecbc71f92452127327445075e SHA256: 869ecdd0415a88c8b4872184b8914afc7e755eaf143cdce377f33cc34ecb374f [jessie-lts] Package: mira-assembler Source: mira (4.0.2-1) Version: 4.0.2-1+b1 Installed-Size: 4096 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libboost-filesystem1.55.0, libboost-iostreams1.55.0, libboost-regex1.55.0, libboost-system1.55.0, libboost-thread1.55.0, libbz2-1.0, libc6 (>= 2.14), libexpat1 (>= 2.0.1), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.8), libtcmalloc-minimal4, zlib1g (>= 1:1.1.4) Suggests: mira-examples, mira-doc Description: Whole Genome Shotgun and EST Sequence Assembler Homepage: http://chevreux.org/projects_mira.html Description-md5: 82b6240df7e707dae67c440269ca669f Tag: role::program Section: science Priority: optional Filename: pool/main/m/mira/mira-assembler_4.0.2-1+b1_amd64.deb Size: 1403168 MD5sum: 52a53e6a4447705386f1b7ec86acecc8 SHA1: f4b80fb52658600ecbc71f92452127327445075e SHA256: 869ecdd0415a88c8b4872184b8914afc7e755eaf143cdce377f33cc34ecb374f 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 --scriptsdir /etc/piuparts/scripts-jessie --skip-logrotatefiles-test --warn-on-debsums-errors --warn-on-install-over-symlink --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz -d jessie -d jessie-lts -B /srv/piuparts.debian.org/slave/refchroot/jessie2lts/reference-chroot-metadata.dat --apt mira-assembler=4.0.2-1+b1 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 1.1.5 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 --scriptsdir /etc/piuparts/scripts-jessie --skip-logrotatefiles-test --warn-on-debsums-errors --warn-on-install-over-symlink --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz -d jessie -d jessie-lts -B /srv/piuparts.debian.org/slave/refchroot/jessie2lts/reference-chroot-metadata.dat --apt mira-assembler=4.0.2-1+b1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-18-amd64 #1 SMP Debian 5.10.140-1 (2022-09-02) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp6pumkvj9 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp6pumkvj9 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz'] 0m1.8s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz'] 0m1.8s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/proc'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/proc'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/dev/pts'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/dev/pts'] 0m1.9s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/dev/ptmx'] 0m1.9s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/dev/ptmx'] 0m1.9s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/dev/console'] 0m1.9s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/dev/console'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/dev/shm'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/dev/shm'] 0m1.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ jessie main 0m1.9s DEBUG: Created policy-rc.d and chmodded it. 0m1.9s DEBUG: Created resolv.conf. 0m1.9s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp6pumkvj9/tmp/scripts/ 0m1.9s DEBUG: Copying scriptsdir /etc/piuparts/scripts-jessie to /srv/piuparts.debian.org/tmp/tmp6pumkvj9/tmp/scripts/ 0m1.9s INFO: Running scripts post_chroot_unpack 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-get', 'update'] 0m4.2s DUMP: Ign http://deb.debian.org jessie InRelease Hit http://deb.debian.org jessie Release.gpg Hit http://deb.debian.org jessie Release Hit http://deb.debian.org jessie/main amd64 Packages Hit http://deb.debian.org jessie/main Translation-en Reading package lists... 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-get', 'update'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-get', '-yf', 'dist-upgrade'] 0m4.4s DUMP: Reading package lists... Building dependency tree... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-get', '-yf', 'dist-upgrade'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.6s DUMP: c58dd1ad19dd97acb5ff8b7cd65de431 - 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.6s INFO: Running scripts post_setup 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_setup_dummy_users'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_setup_dummy_users'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_setup_forbid_home'] 0m5.4s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_setup_forbid_home'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.4s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_setup_jessie-fake-essential'] 0m6.0s DUMP: *** Adding fake essential packages *** Reading package lists... Building dependency tree... The following NEW packages will be installed: init-system-helpers ucf 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 83.7 kB of archives. After this operation, 334 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian/ jessie/main init-system-helpers all 1.22 [14.0 kB] Get:2 http://deb.debian.org/debian/ jessie/main ucf all 3.0030 [69.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 83.7 kB in 0s (1551 kB/s) Selecting previously unselected package init-system-helpers. (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 ... 7449 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.22_all.deb ... Unpacking init-system-helpers (1.22) ... Selecting previously unselected package ucf. Preparing to unpack .../archives/ucf_3.0030_all.deb ... Moving old data out of the way Unpacking ucf (3.0030) ... Setting up init-system-helpers (1.22) ... Setting up ucf (3.0030) ... 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_setup_jessie-fake-essential'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_setup_minimize'] 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_setup_minimize'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_setup_squeeze-backports'] 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_setup_squeeze-backports'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_setup_zz_backports'] 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_setup_zz_backports'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.0s DUMP: install ok installed acl acl 2.2.52-2 install ok installed adduser adduser 3.113+nmu3 install ok installed apt apt 1.0.9.8.4 install ok installed base-files base-files 8+deb8u11 install ok installed base-passwd base-passwd 3.5.37 install ok installed bash bash 4.3-11+deb8u1 install ok installed bsdutils bsdutils 1:2.25.2-6 install ok installed coreutils coreutils 8.23-4 install ok installed dash dash 0.5.7-4+b1 install ok installed debconf debconf 1.5.56+deb8u1 install ok installed debconf-i18n debconf-i18n 1.5.56+deb8u1 install ok installed debian-archive-keyring debian-archive-keyring 2017.5~deb8u1 install ok installed debianutils debianutils 4.4+b1 install ok installed diffutils diffutils 1:3.3-1+b1 install ok installed dmsetup dmsetup 2:1.02.90-2.2+deb8u1 install ok installed dpkg dpkg 1.17.27 install ok installed e2fslibs:amd64 e2fslibs 1.42.12-2+b1 install ok installed e2fsprogs e2fsprogs 1.42.12-2+b1 install ok installed findutils findutils 4.4.2-9+b1 install ok installed gcc-4.9-base:amd64 gcc-4.9-base 4.9.2-10+deb8u1 install ok installed gnupg gnupg 1.4.18-7+deb8u5 install ok installed gpgv gpgv 1.4.18-7+deb8u5 install ok installed grep grep 2.20-4.1 install ok installed gzip gzip 1.6-4 install ok installed hostname hostname 3.15 install ok installed init init 1.22 install ok installed init-system-helpers init-system-helpers 1.22 install ok installed initscripts initscripts 2.88dsf-59 install ok installed insserv insserv 1.14.0-5 install ok installed libacl1:amd64 libacl1 2.2.52-2 install ok installed libapt-pkg4.12:amd64 libapt-pkg4.12 1.0.9.8.4 install ok installed libattr1:amd64 libattr1 1:2.4.47-2 install ok installed libaudit-common libaudit-common 1:2.4-1 install ok installed libaudit1:amd64 libaudit1 1:2.4-1+b1 install ok installed libblkid1:amd64 libblkid1 2.25.2-6 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-7+b3 install ok installed libc-bin libc-bin 2.19-18+deb8u10 install ok installed libc6:amd64 libc6 2.19-18+deb8u10 install ok installed libcap2:amd64 libcap2 1:2.24-8 install ok installed libcap2-bin libcap2-bin 1:2.24-8 install ok installed libcomerr2:amd64 libcomerr2 1.42.12-2+b1 install ok installed libcryptsetup4:amd64 libcryptsetup4 2:1.6.6-5 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-9+deb8u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.192 install ok installed libdevmapper1.02.1:amd64 libdevmapper1.02.1 2:1.02.90-2.2+deb8u1 install ok installed libgcc1:amd64 libgcc1 1:4.9.2-10+deb8u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.6.3-2+deb8u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.17-3 install ok installed libkmod2:amd64 libkmod2 18-3 install ok installed liblocale-gettext-perl liblocale-gettext-perl 1.05-8+b1 install ok installed liblzma5:amd64 liblzma5 5.1.1alpha+20120614-2+b3 install ok installed libmount1:amd64 libmount1 2.25.2-6 install ok installed libncurses5:amd64 libncurses5 5.9+20140913-1+deb8u3 install ok installed libncursesw5:amd64 libncursesw5 5.9+20140913-1+deb8u3 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.1+deb8u2+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.1+deb8u2+b1 install ok installed libpam-runtime libpam-runtime 1.1.8-3.1+deb8u2 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.1+deb8u2+b1 install ok installed libpcre3:amd64 libpcre3 2:8.35-3.3+deb8u4 install ok installed libprocps3:amd64 libprocps3 2:3.3.9-9+deb8u1 install ok installed libreadline6:amd64 libreadline6 6.3-8+b3 install ok installed libselinux1:amd64 libselinux1 2.3-2 install ok installed libsemanage-common libsemanage-common 2.3-1 install ok installed libsemanage1:amd64 libsemanage1 2.3-1+b1 install ok installed libsepol1:amd64 libsepol1 2.3-2 install ok installed libslang2:amd64 libslang2 2.3.0-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.25.2-6 install ok installed libss2:amd64 libss2 1.42.12-2+b1 install ok installed libstdc++6:amd64 libstdc++6 4.9.2-10+deb8u1 install ok installed libsystemd0:amd64 libsystemd0 215-17+deb8u7 install ok installed libtext-charwidth-perl libtext-charwidth-perl 0.04-7+b3 install ok installed libtext-iconv-perl libtext-iconv-perl 1.7-5+b2 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-7 install ok installed libtinfo5:amd64 libtinfo5 5.9+20140913-1+deb8u3 install ok installed libudev1:amd64 libudev1 215-17+deb8u7 install ok installed libusb-0.1-4:amd64 libusb-0.1-4 2:0.1.12-25 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-3+b2 install ok installed libuuid1:amd64 libuuid1 2.25.2-6 install ok installed login login 1:4.2-3+deb8u4 install ok installed lsb-base lsb-base 4.1+Debian13+nmu1 install ok installed mawk mawk 1.3.3-17 install ok installed mount mount 2.25.2-6 install ok installed multiarch-support multiarch-support 2.19-18+deb8u10 install ok installed ncurses-base ncurses-base 5.9+20140913-1+deb8u3 install ok installed ncurses-bin ncurses-bin 5.9+20140913-1+deb8u3 install ok installed passwd passwd 1:4.2-3+deb8u4 install ok installed perl-base perl-base 5.20.2-3+deb8u11 install ok installed procps procps 2:3.3.9-9+deb8u1 install ok installed readline-common readline-common 6.3-8 install ok installed sed sed 4.2.2-4+deb8u1 install ok installed sensible-utils sensible-utils 0.0.9+deb8u1 install ok installed startpar startpar 0.59-3 install ok installed systemd systemd 215-17+deb8u7 install ok installed systemd-sysv systemd-sysv 215-17+deb8u7 install ok installed sysv-rc sysv-rc 2.88dsf-59 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59 install ok installed tar tar 1.27.1-2+deb8u1 install ok installed tzdata tzdata 2018e-0+deb8u1 install ok installed ucf ucf 3.0030 install ok installed udev udev 215-17+deb8u7 install ok installed util-linux util-linux 2.25.2-6 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-2+b1 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.0s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/jessie2lts/reference-chroot-metadata.dat 0m6.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9'] 0m6.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9'] 0m6.3s INFO: Running scripts is_testable 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/is_testable_uninstallable'] 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/is_testable_uninstallable'] 0m6.3s INFO: Running scripts pre_test 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_test_exceptions'] 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_test_exceptions'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_test_root_password'] 0m6.3s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_test_root_password'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-cache', 'show', '--no-all-versions', 'mira-assembler'] 0m6.3s DUMP: Package: mira-assembler Source: mira (4.0.2-1) Version: 4.0.2-1+b1 Installed-Size: 4096 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libboost-filesystem1.55.0, libboost-iostreams1.55.0, libboost-regex1.55.0, libboost-system1.55.0, libboost-thread1.55.0, libbz2-1.0, libc6 (>= 2.14), libexpat1 (>= 2.0.1), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.8), libtcmalloc-minimal4, zlib1g (>= 1:1.1.4) Suggests: mira-examples, mira-doc Description-en: Whole Genome Shotgun and EST Sequence Assembler The mira genome fragment assembler is a specialised assembler for sequencing projects classified as 'hard' due to high number of similar repeats. For expressed sequence tags (ESTs) transcripts, miraEST is specialised on reconstructing pristine mRNA transcripts while detecting and classifying single nucleotide polymorphisms (SNP) occuring in different variations thereof. . The assembler is routinely used for such various tasks as mutation detection in different cell types, similarity analysis of transcripts between organisms, and pristine assembly of sequences from various sources for oligo design in clinical microarray experiments. . The package provides the following executables: Binaries provided: * mira: for assembly of genome sequences * miramem: estimating memory needed to assemble projects. Realised through link to mira. * convert_project: for converting project file types into other types * caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some frequently used file converters (realised through links to convert_project) * scftool: set of tools useful when working with SCF trace files * fastatool: set of tools useful when working with FASTA trace files . Scripts provided: * fasta2frag: fragmenting sequences into smaller, overlapping subsequences. Useful for simulating shotgun sequences. Can create subsequences in both directions (/default) and also paired-end sequences. * fastaselect: given a FASTA file (and possibly a FASTA quality file) and a file with names of reads, select the sequences from the input FASTA (and quality file) and writes them to an output FASTA * fastqselect: like fastaselect, only for FASTQ * fixACE4consed: Consed has a bug which incapacitates it from reading consensus tags in ACE files written by the MIRA assembler (and possibly other programs). This script massages an ACE file so that consed can read the consensus tags. Description-md5: 82b6240df7e707dae67c440269ca669f Homepage: http://chevreux.org/projects_mira.html Tag: role::program Section: science Priority: optional Filename: pool/main/m/mira/mira-assembler_4.0.2-1+b1_amd64.deb Size: 1403168 MD5sum: 52a53e6a4447705386f1b7ec86acecc8 SHA1: f4b80fb52658600ecbc71f92452127327445075e SHA256: 869ecdd0415a88c8b4872184b8914afc7e755eaf143cdce377f33cc34ecb374f 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-cache', 'show', '--no-all-versions', 'mira-assembler'] 0m6.3s INFO: apt-cache knows about the following packages: mira-assembler 0m6.3s INFO: Running scripts pre_install 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_database-server'] 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_database-server'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_exceptions'] 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_exceptions'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_extras'] 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_extras'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-cache', 'policy'] 0m6.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian/ jessie/main Translation-en 500 http://deb.debian.org/debian/ jessie/main amd64 Packages release v=8.11,o=Debian,a=oldoldstable,n=jessie,l=Debian,c=main origin deb.debian.org Pinned packages: 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-cache', 'policy'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-cache', 'policy', 'mira-assembler'] 0m6.4s DUMP: mira-assembler: Installed: (none) Candidate: 4.0.2-1+b1 Version table: 4.0.2-1+b1 0 500 http://deb.debian.org/debian/ jessie/main amd64 Packages 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-cache', 'policy', 'mira-assembler'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-get', '-y', 'install', 'mira-assembler'] 0m9.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libboost-filesystem1.55.0 libboost-iostreams1.55.0 libboost-regex1.55.0 libboost-system1.55.0 libboost-thread1.55.0 libexpat1 libicu52 libtcmalloc-minimal4 Suggested packages: mira-examples mira-doc The following NEW packages will be installed: libboost-filesystem1.55.0 libboost-iostreams1.55.0 libboost-regex1.55.0 libboost-system1.55.0 libboost-thread1.55.0 libexpat1 libicu52 libtcmalloc-minimal4 mira-assembler 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. Need to get 8904 kB of archives. After this operation, 35.0 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian/ jessie/main libboost-iostreams1.55.0 amd64 1.55.0+dfsg-3 [48.9 kB] Get:2 http://deb.debian.org/debian/ jessie/main libboost-system1.55.0 amd64 1.55.0+dfsg-3 [30.2 kB] Get:3 http://deb.debian.org/debian/ jessie/main libboost-filesystem1.55.0 amd64 1.55.0+dfsg-3 [58.8 kB] Get:4 http://deb.debian.org/debian/ jessie/main libicu52 amd64 52.1-8+deb8u7 [6807 kB] Get:5 http://deb.debian.org/debian/ jessie/main libboost-regex1.55.0 amd64 1.55.0+dfsg-3 [293 kB] Get:6 http://deb.debian.org/debian/ jessie/main libboost-thread1.55.0 amd64 1.55.0+dfsg-3 [53.4 kB] Get:7 http://deb.debian.org/debian/ jessie/main libexpat1 amd64 2.1.0-6+deb8u4 [80.2 kB] Get:8 http://deb.debian.org/debian/ jessie/main libtcmalloc-minimal4 amd64 2.2.1-0.2 [128 kB] Get:9 http://deb.debian.org/debian/ jessie/main mira-assembler amd64 4.0.2-1+b1 [1403 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 8904 kB in 1s (7012 kB/s) Selecting previously unselected package libboost-iostreams1.55.0: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 ... 7475 files and directories currently installed.) Preparing to unpack .../libboost-iostreams1.55.0_1.55.0+dfsg-3_amd64.deb ... Unpacking libboost-iostreams1.55.0:amd64 (1.55.0+dfsg-3) ... Selecting previously unselected package libboost-system1.55.0:amd64. Preparing to unpack .../libboost-system1.55.0_1.55.0+dfsg-3_amd64.deb ... Unpacking libboost-system1.55.0:amd64 (1.55.0+dfsg-3) ... Selecting previously unselected package libboost-filesystem1.55.0:amd64. Preparing to unpack .../libboost-filesystem1.55.0_1.55.0+dfsg-3_amd64.deb ... Unpacking libboost-filesystem1.55.0:amd64 (1.55.0+dfsg-3) ... Selecting previously unselected package libicu52:amd64. Preparing to unpack .../libicu52_52.1-8+deb8u7_amd64.deb ... Unpacking libicu52:amd64 (52.1-8+deb8u7) ... Selecting previously unselected package libboost-regex1.55.0:amd64. Preparing to unpack .../libboost-regex1.55.0_1.55.0+dfsg-3_amd64.deb ... Unpacking libboost-regex1.55.0:amd64 (1.55.0+dfsg-3) ... Selecting previously unselected package libboost-thread1.55.0:amd64. Preparing to unpack .../libboost-thread1.55.0_1.55.0+dfsg-3_amd64.deb ... Unpacking libboost-thread1.55.0:amd64 (1.55.0+dfsg-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.1.0-6+deb8u4_amd64.deb ... Unpacking libexpat1:amd64 (2.1.0-6+deb8u4) ... Selecting previously unselected package libtcmalloc-minimal4. Preparing to unpack .../libtcmalloc-minimal4_2.2.1-0.2_amd64.deb ... Unpacking libtcmalloc-minimal4 (2.2.1-0.2) ... Selecting previously unselected package mira-assembler. Preparing to unpack .../mira-assembler_4.0.2-1+b1_amd64.deb ... Unpacking mira-assembler (4.0.2-1+b1) ... Setting up libboost-iostreams1.55.0:amd64 (1.55.0+dfsg-3) ... Setting up libboost-system1.55.0:amd64 (1.55.0+dfsg-3) ... Setting up libboost-filesystem1.55.0:amd64 (1.55.0+dfsg-3) ... Setting up libicu52:amd64 (52.1-8+deb8u7) ... Setting up libboost-regex1.55.0:amd64 (1.55.0+dfsg-3) ... Setting up libboost-thread1.55.0:amd64 (1.55.0+dfsg-3) ... Setting up libexpat1:amd64 (2.1.0-6+deb8u4) ... Setting up libtcmalloc-minimal4 (2.2.1-0.2) ... Setting up mira-assembler (4.0.2-1+b1) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-get', '-y', 'install', 'mira-assembler'] 0m9.7s INFO: Running scripts post_install 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_install_exceptions'] 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_install_exceptions'] 0m9.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9'] 0m10.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9'] 0m10.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp6pumkvj9 to jessie-lts 0m10.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ jessie main deb http://security.debian.org jessie/updates main 0m10.0s INFO: Running scripts pre_distupgrade 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_distupgrade_exceptions'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_distupgrade_exceptions'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-get', 'update'] 0m13.0s DUMP: Get:1 http://security.debian.org jessie/updates InRelease [44.9 kB] Ign http://deb.debian.org jessie InRelease Get:2 http://security.debian.org jessie/updates/main amd64 Packages [781 kB] Hit http://deb.debian.org jessie Release.gpg Get:3 http://security.debian.org jessie/updates/main Translation-en [401 kB] Hit http://deb.debian.org jessie Release Hit http://deb.debian.org jessie/main amd64 Packages Hit http://deb.debian.org jessie/main Translation-en Fetched 1227 kB in 1s (632 kB/s) Reading package lists... 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-get', 'update'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-get', '-yf', 'dist-upgrade'] 0m19.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: apt bash e2fslibs e2fsprogs gcc-4.9-base libapt-pkg4.12 libbz2-1.0 libcomerr2 libexpat1 libgcc1 libgcrypt20 libicu52 libss2 libstdc++6 libsystemd0 libudev1 perl-base systemd systemd-sysv tar tzdata udev zlib1g 23 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 17.8 MB of archives. After this operation, 3841 kB of additional disk space will be used. Get:1 http://security.debian.org/ jessie/updates/main bash amd64 4.3-11+deb8u2 [1173 kB] Get:2 http://security.debian.org/ jessie/updates/main e2fslibs amd64 1.42.12-2+deb8u2 [186 kB] Get:3 http://security.debian.org/ jessie/updates/main e2fsprogs amd64 1.42.12-2+deb8u2 [751 kB] Get:4 http://security.debian.org/ jessie/updates/main perl-base amd64 5.20.2-3+deb8u12 [1231 kB] Get:5 http://security.debian.org/ jessie/updates/main tar amd64 1.27.1-2+deb8u2 [676 kB] Get:6 http://security.debian.org/ jessie/updates/main libbz2-1.0 amd64 1.0.6-7+deb8u2 [43.3 kB] Get:7 http://security.debian.org/ jessie/updates/main gcc-4.9-base amd64 4.9.2-10+deb8u2 [160 kB] Get:8 http://security.debian.org/ jessie/updates/main libgcc1 amd64 1:4.9.2-10+deb8u2 [39.4 kB] Get:9 http://security.debian.org/ jessie/updates/main libstdc++6 amd64 4.9.2-10+deb8u2 [273 kB] Get:10 http://security.debian.org/ jessie/updates/main zlib1g amd64 1:1.2.8.dfsg-2+deb8u1 [88.3 kB] Get:11 http://security.debian.org/ jessie/updates/main libapt-pkg4.12 amd64 1.0.9.8.6 [794 kB] Get:12 http://security.debian.org/ jessie/updates/main apt amd64 1.0.9.8.6 [1109 kB] Get:13 http://security.debian.org/ jessie/updates/main libudev1 amd64 215-17+deb8u13 [58.8 kB] Get:14 http://security.debian.org/ jessie/updates/main udev amd64 215-17+deb8u13 [878 kB] Get:15 http://security.debian.org/ jessie/updates/main libcomerr2 amd64 1.42.12-2+deb8u2 [60.6 kB] Get:16 http://security.debian.org/ jessie/updates/main libss2 amd64 1.42.12-2+deb8u2 [64.9 kB] Get:17 http://security.debian.org/ jessie/updates/main libgcrypt20 amd64 1.6.3-2+deb8u8 [394 kB] Get:18 http://security.debian.org/ jessie/updates/main libsystemd0 amd64 215-17+deb8u13 [90.5 kB] Get:19 http://security.debian.org/ jessie/updates/main systemd amd64 215-17+deb8u13 [2555 kB] Get:20 http://security.debian.org/ jessie/updates/main systemd-sysv amd64 215-17+deb8u13 [37.5 kB] Get:21 http://security.debian.org/ jessie/updates/main libexpat1 amd64 2.1.0-6+deb8u6 [80.3 kB] Get:22 http://security.debian.org/ jessie/updates/main libicu52 amd64 52.1-8+deb8u8 [6791 kB] Get:23 http://security.debian.org/ jessie/updates/main tzdata all 2019c-0+deb8u1 [234 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 17.8 MB in 0s (27.3 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 7576 files and directories currently installed.) Preparing to unpack .../bash_4.3-11+deb8u2_amd64.deb ... Unpacking bash (4.3-11+deb8u2) over (4.3-11+deb8u1) ... Setting up bash (4.3-11+deb8u2) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (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 ... 7573 files and directories currently installed.) Preparing to unpack .../libgcc1_1%3a4.9.2-10+deb8u2_amd64.deb ... Unpacking libgcc1:amd64 (1:4.9.2-10+deb8u2) over (1:4.9.2-10+deb8u1) ... Setting up libgcc1:amd64 (1:4.9.2-10+deb8u2) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7573 files and directories currently installed.) Preparing to unpack .../libstdc++6_4.9.2-10+deb8u2_amd64.deb ... Unpacking libstdc++6:amd64 (4.9.2-10+deb8u2) over (4.9.2-10+deb8u1) ... Setting up libstdc++6:amd64 (4.9.2-10+deb8u2) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7573 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.2.8.dfsg-2+deb8u1_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.8.dfsg-2+deb8u1) over (1:1.2.8.dfsg-2+b1) ... Setting up zlib1g:amd64 (1:1.2.8.dfsg-2+deb8u1) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7572 files and directories currently installed.) Preparing to unpack .../libapt-pkg4.12_1.0.9.8.6_amd64.deb ... Unpacking libapt-pkg4.12:amd64 (1.0.9.8.6) over (1.0.9.8.4) ... Setting up libapt-pkg4.12:amd64 (1.0.9.8.6) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7572 files and directories currently installed.) Preparing to unpack .../apt_1.0.9.8.6_amd64.deb ... Unpacking apt (1.0.9.8.6) over (1.0.9.8.4) ... Setting up apt (1.0.9.8.6) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7572 files and directories currently installed.) Preparing to unpack .../libudev1_215-17+deb8u13_amd64.deb ... Unpacking libudev1:amd64 (215-17+deb8u13) over (215-17+deb8u7) ... Setting up libudev1:amd64 (215-17+deb8u13) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7572 files and directories currently installed.) Preparing to unpack .../udev_215-17+deb8u13_amd64.deb ... Unpacking udev (215-17+deb8u13) over (215-17+deb8u7) ... Processing triggers for systemd (215-17+deb8u7) ... Setting up udev (215-17+deb8u13) ... addgroup: The group `input' already exists as a system group. Exiting. A chroot environment has been detected, udev not started. A chroot environment has been detected, udev not started. (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 ... 7572 files and directories currently installed.) Preparing to unpack .../libcomerr2_1.42.12-2+deb8u2_amd64.deb ... Unpacking libcomerr2:amd64 (1.42.12-2+deb8u2) over (1.42.12-2+b1) ... Setting up libcomerr2:amd64 (1.42.12-2+deb8u2) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7571 files and directories currently installed.) Preparing to unpack .../libss2_1.42.12-2+deb8u2_amd64.deb ... Unpacking libss2:amd64 (1.42.12-2+deb8u2) over (1.42.12-2+b1) ... Setting up libss2:amd64 (1.42.12-2+deb8u2) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7570 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.6.3-2+deb8u8_amd64.deb ... Unpacking libgcrypt20:amd64 (1.6.3-2+deb8u8) over (1.6.3-2+deb8u4) ... Setting up libgcrypt20:amd64 (1.6.3-2+deb8u8) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7570 files and directories currently installed.) Preparing to unpack .../libsystemd0_215-17+deb8u13_amd64.deb ... Unpacking libsystemd0:amd64 (215-17+deb8u13) over (215-17+deb8u7) ... Setting up libsystemd0:amd64 (215-17+deb8u13) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... (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 ... 7570 files and directories currently installed.) Preparing to unpack .../systemd_215-17+deb8u13_amd64.deb ... Unpacking systemd (215-17+deb8u13) over (215-17+deb8u7) ... Setting up systemd (215-17+deb8u13) ... addgroup: The group `systemd-journal' already exists as a system group. Exiting. (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 ... 7570 files and directories currently installed.) Preparing to unpack .../systemd-sysv_215-17+deb8u13_amd64.deb ... Unpacking systemd-sysv (215-17+deb8u13) over (215-17+deb8u7) ... Setting up systemd-sysv (215-17+deb8u13) ... (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 ... 7570 files and directories currently installed.) Preparing to unpack .../libexpat1_2.1.0-6+deb8u6_amd64.deb ... Unpacking libexpat1:amd64 (2.1.0-6+deb8u6) over (2.1.0-6+deb8u4) ... Preparing to unpack .../libicu52_52.1-8+deb8u8_amd64.deb ... Unpacking libicu52:amd64 (52.1-8+deb8u8) over (52.1-8+deb8u7) ... Preparing to unpack .../tzdata_2019c-0+deb8u1_all.deb ... Unpacking tzdata (2019c-0+deb8u1) over (2018e-0+deb8u1) ... Setting up tzdata (2019c-0+deb8u1) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Oct 13 19:13:07 UTC 2022. Universal Time is now: Thu Oct 13 19:13:07 UTC 2022. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libexpat1:amd64 (2.1.0-6+deb8u6) ... Setting up libicu52:amd64 (52.1-8+deb8u8) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-get', '-yf', 'dist-upgrade'] 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m19.5s DUMP: ea587cb5da6f95fbc79bf1681671e909 - 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-cache', 'show', '--no-all-versions', 'mira-assembler'] 0m19.5s DUMP: Package: mira-assembler Source: mira (4.0.2-1) Version: 4.0.2-1+b1 Installed-Size: 4096 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libboost-filesystem1.55.0, libboost-iostreams1.55.0, libboost-regex1.55.0, libboost-system1.55.0, libboost-thread1.55.0, libbz2-1.0, libc6 (>= 2.14), libexpat1 (>= 2.0.1), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.8), libtcmalloc-minimal4, zlib1g (>= 1:1.1.4) Suggests: mira-examples, mira-doc Description-en: Whole Genome Shotgun and EST Sequence Assembler The mira genome fragment assembler is a specialised assembler for sequencing projects classified as 'hard' due to high number of similar repeats. For expressed sequence tags (ESTs) transcripts, miraEST is specialised on reconstructing pristine mRNA transcripts while detecting and classifying single nucleotide polymorphisms (SNP) occuring in different variations thereof. . The assembler is routinely used for such various tasks as mutation detection in different cell types, similarity analysis of transcripts between organisms, and pristine assembly of sequences from various sources for oligo design in clinical microarray experiments. . The package provides the following executables: Binaries provided: * mira: for assembly of genome sequences * miramem: estimating memory needed to assemble projects. Realised through link to mira. * convert_project: for converting project file types into other types * caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some frequently used file converters (realised through links to convert_project) * scftool: set of tools useful when working with SCF trace files * fastatool: set of tools useful when working with FASTA trace files . Scripts provided: * fasta2frag: fragmenting sequences into smaller, overlapping subsequences. Useful for simulating shotgun sequences. Can create subsequences in both directions (/default) and also paired-end sequences. * fastaselect: given a FASTA file (and possibly a FASTA quality file) and a file with names of reads, select the sequences from the input FASTA (and quality file) and writes them to an output FASTA * fastqselect: like fastaselect, only for FASTQ * fixACE4consed: Consed has a bug which incapacitates it from reading consensus tags in ACE files written by the MIRA assembler (and possibly other programs). This script massages an ACE file so that consed can read the consensus tags. Description-md5: 82b6240df7e707dae67c440269ca669f Homepage: http://chevreux.org/projects_mira.html Tag: role::program Section: science Priority: optional Filename: pool/main/m/mira/mira-assembler_4.0.2-1+b1_amd64.deb Size: 1403168 MD5sum: 52a53e6a4447705386f1b7ec86acecc8 SHA1: f4b80fb52658600ecbc71f92452127327445075e SHA256: 869ecdd0415a88c8b4872184b8914afc7e755eaf143cdce377f33cc34ecb374f 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-cache', 'show', '--no-all-versions', 'mira-assembler'] 0m19.5s INFO: apt-cache knows about the following packages: mira-assembler 0m19.5s INFO: Running scripts pre_install 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_database-server'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_database-server'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_exceptions'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_exceptions'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_extras'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_extras'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-cache', 'policy'] 0m19.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://security.debian.org/ jessie/updates/main Translation-en 500 http://security.debian.org/ jessie/updates/main amd64 Packages release v=8,o=Debian,a=oldoldstable,n=jessie,l=Debian-Security,c=main origin security.debian.org 500 http://deb.debian.org/debian/ jessie/main Translation-en 500 http://deb.debian.org/debian/ jessie/main amd64 Packages release v=8.11,o=Debian,a=oldoldstable,n=jessie,l=Debian,c=main origin deb.debian.org Pinned packages: 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-cache', 'policy'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-cache', 'policy', 'mira-assembler'] 0m19.7s DUMP: mira-assembler: Installed: 4.0.2-1+b1 Candidate: 4.0.2-1+b1 Version table: *** 4.0.2-1+b1 0 500 http://deb.debian.org/debian/ jessie/main amd64 Packages 100 /var/lib/dpkg/status 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-cache', 'policy', 'mira-assembler'] 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-get', '-y', 'install', 'mira-assembler'] 0m20.0s DUMP: Reading package lists... Building dependency tree... Reading state information... mira-assembler is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-get', '-y', 'install', 'mira-assembler'] 0m20.0s INFO: Running scripts post_install 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_install_exceptions'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_install_exceptions'] 0m20.0s INFO: Running scripts post_distupgrade 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_distupgrade_exceptions'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_distupgrade_exceptions'] 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_distupgrade_zz_backports'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_distupgrade_zz_backports'] 0m20.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9'] 0m20.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9'] 0m20.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9'] 0m20.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9'] 0m20.6s INFO: Running scripts pre_install 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_database-server'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_database-server'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_exceptions'] 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_exceptions'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_extras'] 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_extras'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-cache', 'policy'] 0m20.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://security.debian.org/ jessie/updates/main Translation-en 500 http://security.debian.org/ jessie/updates/main amd64 Packages release v=8,o=Debian,a=oldoldstable,n=jessie,l=Debian-Security,c=main origin security.debian.org 500 http://deb.debian.org/debian/ jessie/main Translation-en 500 http://deb.debian.org/debian/ jessie/main amd64 Packages release v=8.11,o=Debian,a=oldoldstable,n=jessie,l=Debian,c=main origin deb.debian.org Pinned packages: 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-cache', 'policy'] 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-cache', 'policy', 'mira-assembler'] 0m20.8s DUMP: mira-assembler: Installed: 4.0.2-1+b1 Candidate: 4.0.2-1+b1 Version table: *** 4.0.2-1+b1 0 500 http://deb.debian.org/debian/ jessie/main amd64 Packages 100 /var/lib/dpkg/status 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-cache', 'policy', 'mira-assembler'] 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-get', '-y', 'install', 'mira-assembler=4.0.2-1+b1'] 0m21.0s DUMP: Reading package lists... Building dependency tree... Reading state information... mira-assembler is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-get', '-y', 'install', 'mira-assembler=4.0.2-1+b1'] 0m21.0s INFO: Running scripts post_install 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_install_exceptions'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_install_exceptions'] 0m21.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9'] 0m21.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9'] 0m21.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', '-ac', '--ignore-obsolete'] 0m22.5s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', '-ac', '--ignore-obsolete'] 0m22.5s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m22.5s DUMP: 0.15.6 0m22.5s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m22.5s INFO: Running adequate version 0.15.6 now. 0m22.5s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'mira-assembler'] 0m22.6s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'mira-assembler'] 0m22.7s INFO: Running scripts pre_remove 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_remove_exceptions'] 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/pre_remove_exceptions'] 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m24.2s DUMP: install ok installed acl acl 2.2.52-2 install ok installed adduser adduser 3.113+nmu3 install ok installed apt apt 1.0.9.8.6 install ok installed base-files base-files 8+deb8u11 install ok installed base-passwd base-passwd 3.5.37 install ok installed bash bash 4.3-11+deb8u2 install ok installed bsdutils bsdutils 1:2.25.2-6 install ok installed coreutils coreutils 8.23-4 install ok installed dash dash 0.5.7-4+b1 install ok installed debconf debconf 1.5.56+deb8u1 install ok installed debconf-i18n debconf-i18n 1.5.56+deb8u1 install ok installed debian-archive-keyring debian-archive-keyring 2017.5~deb8u1 install ok installed debianutils debianutils 4.4+b1 install ok installed diffutils diffutils 1:3.3-1+b1 install ok installed dmsetup dmsetup 2:1.02.90-2.2+deb8u1 install ok installed dpkg dpkg 1.17.27 install ok installed e2fslibs:amd64 e2fslibs 1.42.12-2+deb8u2 install ok installed e2fsprogs e2fsprogs 1.42.12-2+deb8u2 install ok installed findutils findutils 4.4.2-9+b1 install ok installed gcc-4.9-base:amd64 gcc-4.9-base 4.9.2-10+deb8u2 install ok installed gnupg gnupg 1.4.18-7+deb8u5 install ok installed gpgv gpgv 1.4.18-7+deb8u5 install ok installed grep grep 2.20-4.1 install ok installed gzip gzip 1.6-4 install ok installed hostname hostname 3.15 install ok installed init init 1.22 install ok installed init-system-helpers init-system-helpers 1.22 install ok installed initscripts initscripts 2.88dsf-59 install ok installed insserv insserv 1.14.0-5 install ok installed libacl1:amd64 libacl1 2.2.52-2 install ok installed libapt-pkg4.12:amd64 libapt-pkg4.12 1.0.9.8.6 install ok installed libattr1:amd64 libattr1 1:2.4.47-2 install ok installed libaudit-common libaudit-common 1:2.4-1 install ok installed libaudit1:amd64 libaudit1 1:2.4-1+b1 install ok installed libblkid1:amd64 libblkid1 2.25.2-6 install ok installed libboost-filesystem1.55.0:amd64 libboost-filesystem1.55.0 1.55.0+dfsg-3 install ok installed libboost-iostreams1.55.0:amd64 libboost-iostreams1.55.0 1.55.0+dfsg-3 install ok installed libboost-regex1.55.0:amd64 libboost-regex1.55.0 1.55.0+dfsg-3 install ok installed libboost-system1.55.0:amd64 libboost-system1.55.0 1.55.0+dfsg-3 install ok installed libboost-thread1.55.0:amd64 libboost-thread1.55.0 1.55.0+dfsg-3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-7+deb8u2 install ok installed libc-bin libc-bin 2.19-18+deb8u10 install ok installed libc6:amd64 libc6 2.19-18+deb8u10 install ok installed libcap2:amd64 libcap2 1:2.24-8 install ok installed libcap2-bin libcap2-bin 1:2.24-8 install ok installed libcomerr2:amd64 libcomerr2 1.42.12-2+deb8u2 install ok installed libcryptsetup4:amd64 libcryptsetup4 2:1.6.6-5 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-9+deb8u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.192 install ok installed libdevmapper1.02.1:amd64 libdevmapper1.02.1 2:1.02.90-2.2+deb8u1 install ok installed libexpat1:amd64 libexpat1 2.1.0-6+deb8u6 install ok installed libgcc1:amd64 libgcc1 1:4.9.2-10+deb8u2 install ok installed libgcrypt20:amd64 libgcrypt20 1.6.3-2+deb8u8 install ok installed libgpg-error0:amd64 libgpg-error0 1.17-3 install ok installed libicu52:amd64 libicu52 52.1-8+deb8u8 install ok installed libkmod2:amd64 libkmod2 18-3 install ok installed liblocale-gettext-perl liblocale-gettext-perl 1.05-8+b1 install ok installed liblzma5:amd64 liblzma5 5.1.1alpha+20120614-2+b3 install ok installed libmount1:amd64 libmount1 2.25.2-6 install ok installed libncurses5:amd64 libncurses5 5.9+20140913-1+deb8u3 install ok installed libncursesw5:amd64 libncursesw5 5.9+20140913-1+deb8u3 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.1+deb8u2+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.1+deb8u2+b1 install ok installed libpam-runtime libpam-runtime 1.1.8-3.1+deb8u2 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.1+deb8u2+b1 install ok installed libpcre3:amd64 libpcre3 2:8.35-3.3+deb8u4 install ok installed libprocps3:amd64 libprocps3 2:3.3.9-9+deb8u1 install ok installed libreadline6:amd64 libreadline6 6.3-8+b3 install ok installed libselinux1:amd64 libselinux1 2.3-2 install ok installed libsemanage-common libsemanage-common 2.3-1 install ok installed libsemanage1:amd64 libsemanage1 2.3-1+b1 install ok installed libsepol1:amd64 libsepol1 2.3-2 install ok installed libslang2:amd64 libslang2 2.3.0-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.25.2-6 install ok installed libss2:amd64 libss2 1.42.12-2+deb8u2 install ok installed libstdc++6:amd64 libstdc++6 4.9.2-10+deb8u2 install ok installed libsystemd0:amd64 libsystemd0 215-17+deb8u13 install ok installed libtcmalloc-minimal4 libtcmalloc-minimal4 2.2.1-0.2 install ok installed libtext-charwidth-perl libtext-charwidth-perl 0.04-7+b3 install ok installed libtext-iconv-perl libtext-iconv-perl 1.7-5+b2 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-7 install ok installed libtinfo5:amd64 libtinfo5 5.9+20140913-1+deb8u3 install ok installed libudev1:amd64 libudev1 215-17+deb8u13 install ok installed libusb-0.1-4:amd64 libusb-0.1-4 2:0.1.12-25 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-3+b2 install ok installed libuuid1:amd64 libuuid1 2.25.2-6 install ok installed login login 1:4.2-3+deb8u4 install ok installed lsb-base lsb-base 4.1+Debian13+nmu1 install ok installed mawk mawk 1.3.3-17 install ok installed mira-assembler mira-assembler 4.0.2-1+b1 install ok installed mount mount 2.25.2-6 install ok installed multiarch-support multiarch-support 2.19-18+deb8u10 install ok installed ncurses-base ncurses-base 5.9+20140913-1+deb8u3 install ok installed ncurses-bin ncurses-bin 5.9+20140913-1+deb8u3 install ok installed passwd passwd 1:4.2-3+deb8u4 install ok installed perl-base perl-base 5.20.2-3+deb8u12 install ok installed procps procps 2:3.3.9-9+deb8u1 install ok installed readline-common readline-common 6.3-8 install ok installed sed sed 4.2.2-4+deb8u1 install ok installed sensible-utils sensible-utils 0.0.9+deb8u1 install ok installed startpar startpar 0.59-3 install ok installed systemd systemd 215-17+deb8u13 install ok installed systemd-sysv systemd-sysv 215-17+deb8u13 install ok installed sysv-rc sysv-rc 2.88dsf-59 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59 install ok installed tar tar 1.27.1-2+deb8u2 install ok installed tzdata tzdata 2019c-0+deb8u1 install ok installed ucf ucf 3.0030 install ok installed udev udev 215-17+deb8u13 install ok installed util-linux util-linux 2.25.2-6 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-2+deb8u1 0m24.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m24.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-get', 'remove', 'libboost-filesystem1.55.0:amd64', 'libboost-iostreams1.55.0:amd64', 'libboost-regex1.55.0:amd64', 'libboost-system1.55.0:amd64', 'libboost-thread1.55.0:amd64', 'libexpat1:amd64', 'libicu52:amd64', 'libtcmalloc-minimal4', 'mira-assembler'] 0m24.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libboost-filesystem1.55.0 libboost-iostreams1.55.0 libboost-regex1.55.0 libboost-system1.55.0 libboost-thread1.55.0 libexpat1 libicu52 libtcmalloc-minimal4 mira-assembler 0 upgraded, 0 newly installed, 9 to remove and 0 not upgraded. After this operation, 35.0 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 ... 7573 files and directories currently installed.) Removing mira-assembler (4.0.2-1+b1) ... Removing libboost-filesystem1.55.0:amd64 (1.55.0+dfsg-3) ... Removing libboost-iostreams1.55.0:amd64 (1.55.0+dfsg-3) ... Removing libboost-regex1.55.0:amd64 (1.55.0+dfsg-3) ... Removing libboost-thread1.55.0:amd64 (1.55.0+dfsg-3) ... Removing libboost-system1.55.0:amd64 (1.55.0+dfsg-3) ... Removing libexpat1:amd64 (2.1.0-6+deb8u6) ... Removing libicu52:amd64 (52.1-8+deb8u8) ... Removing libtcmalloc-minimal4 (2.2.1-0.2) ... Processing triggers for libc-bin (2.19-18+deb8u10) ... 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-get', 'remove', 'libboost-filesystem1.55.0:amd64', 'libboost-iostreams1.55.0:amd64', 'libboost-regex1.55.0:amd64', 'libboost-system1.55.0:amd64', 'libboost-thread1.55.0:amd64', 'libexpat1:amd64', 'libicu52:amd64', 'libtcmalloc-minimal4', 'mira-assembler'] 0m24.9s INFO: Running scripts post_remove 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_remove_exceptions'] 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_remove_exceptions'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'dpkg', '--purge', 'libboost-filesystem1.55.0:amd64', 'libboost-iostreams1.55.0:amd64', 'libboost-regex1.55.0:amd64', 'libboost-system1.55.0:amd64', 'libboost-thread1.55.0:amd64', 'libexpat1:amd64', 'libicu52:amd64', 'libtcmalloc-minimal4'] 0m24.9s DUMP: (Reading database ... 7472 files and directories currently installed.) Removing libboost-filesystem1.55.0:amd64 (1.55.0+dfsg-3) ... Purging configuration files for libboost-filesystem1.55.0:amd64 (1.55.0+dfsg-3) ... Removing libboost-iostreams1.55.0:amd64 (1.55.0+dfsg-3) ... Purging configuration files for libboost-iostreams1.55.0:amd64 (1.55.0+dfsg-3) ... Removing libboost-regex1.55.0:amd64 (1.55.0+dfsg-3) ... Purging configuration files for libboost-regex1.55.0:amd64 (1.55.0+dfsg-3) ... Removing libboost-system1.55.0:amd64 (1.55.0+dfsg-3) ... Purging configuration files for libboost-system1.55.0:amd64 (1.55.0+dfsg-3) ... Removing libboost-thread1.55.0:amd64 (1.55.0+dfsg-3) ... Purging configuration files for libboost-thread1.55.0:amd64 (1.55.0+dfsg-3) ... Removing libexpat1:amd64 (2.1.0-6+deb8u6) ... Purging configuration files for libexpat1:amd64 (2.1.0-6+deb8u6) ... Removing libicu52:amd64 (52.1-8+deb8u8) ... Purging configuration files for libicu52:amd64 (52.1-8+deb8u8) ... Removing libtcmalloc-minimal4 (2.2.1-0.2) ... Purging configuration files for libtcmalloc-minimal4 (2.2.1-0.2) ... 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'dpkg', '--purge', 'libboost-filesystem1.55.0:amd64', 'libboost-iostreams1.55.0:amd64', 'libboost-regex1.55.0:amd64', 'libboost-system1.55.0:amd64', 'libboost-thread1.55.0:amd64', 'libexpat1:amd64', 'libicu52:amd64', 'libtcmalloc-minimal4'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'dpkg', '--purge', 'mira-assembler'] 0m25.0s DUMP: dpkg: warning: ignoring request to remove mira-assembler which isn't installed 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'dpkg', '--purge', 'mira-assembler'] 0m25.0s INFO: Running scripts post_purge 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_purge_exceptions'] 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_purge_exceptions'] 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'dpkg', '--purge', '--pending'] 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'dpkg', '--purge', '--pending'] 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'dpkg', '--remove', '--pending'] 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'dpkg', '--remove', '--pending'] 0m25.0s INFO: Running scripts post_test 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_test_exceptions'] 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'tmp/scripts/post_test_exceptions'] 0m25.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9'] 0m25.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9'] 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'dpkg-divert', '--list'] 0m25.3s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'dpkg-divert', '--list'] 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-get', 'clean'] 0m25.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9', 'apt-get', 'clean'] 0m25.4s DEBUG: Recording chroot state 0m26.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/dev/shm'] 0m26.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/dev/shm'] 0m26.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/dev/console'] 0m26.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/dev/console'] 0m26.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/dev/ptmx'] 0m26.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/dev/ptmx'] 0m26.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/dev/pts'] 0m26.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/dev/pts'] 0m26.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/proc'] 0m26.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9/proc'] 0m26.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9'] 0m26.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp6pumkvj9'] 0m26.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp6pumkvj9 0m26.3s INFO: PASS: Upgrading between Debian distributions. 0m26.3s INFO: PASS: All tests. 0m26.3s INFO: piuparts run ends. ret=0 End: 2022-10-13 19:13:14 GMT