Start: 2018-12-11 17:56:52 UTC Package: metaphlan2-data Version: 2.6.0+ds-4 Installed-Size: 753107 Maintainer: Debian Med Packaging Team Architecture: all Depends: debconf (>= 0.5) | debconf-2.0, bowtie2 Description: data package for Metagenomic Phylogenetic Analysis Homepage: https://bitbucket.org/biobakery/metaphlan2 Description-md5: f0775409e41de9fba49cda4590c73ce4 Section: science Priority: optional Filename: pool/main/m/metaphlan2-data/metaphlan2-data_2.6.0+ds-4_all.deb Size: 204323768 MD5sum: de685246213a02dcedfee6e464f7ac11 SHA256: f38a6e3f49d7b03ba80d9fdd5647b9f9f2dfb38d43b28618053e8ef2c60db7d7 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python2.7/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts-log-alternatives --warn-on-others --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://mirror.bm.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid_amd64.tar.gz -d sid --no-upgrade-test --apt metaphlan2-data=2.6.0+ds-4 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 0.95~201811291053~0.94-24-g107b4297 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts-log-alternatives --warn-on-others --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://mirror.bm.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid_amd64.tar.gz -d sid --no-upgrade-test --apt metaphlan2-data=2.6.0+ds-4 0m0.0s INFO: Running on: Linux piu-slave-bm-a 4.9.0-8-amd64 #1 SMP Debian 4.9.130-2 (2018-10-27) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpsdaAAB 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpsdaAAB 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/sid_amd64.tar.gz'] 0m2.6s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/sid_amd64.tar.gz'] 0m2.6s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/proc'] 0m2.6s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/proc'] 0m2.6s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/dev/pts'] 0m2.6s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/dev/pts'] 0m2.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/dev/ptmx'] 0m2.7s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/dev/ptmx'] 0m2.7s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/dev/console'] 0m2.7s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/dev/console'] 0m2.7s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/dev/shm'] 0m2.7s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/dev/shm'] 0m2.7s DEBUG: sources.list: deb http://mirror.bm.debian.org/debian/ sid main 0m2.7s DEBUG: Created policy-rc.d and chmodded it. 0m2.7s DEBUG: Created resolv.conf. 0m2.7s DEBUG: Copying scriptsdir /etc/piuparts/scripts-log-alternatives to /srv/piuparts.debian.org/tmp/tmpsdaAAB/tmp/scripts/ 0m2.7s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpsdaAAB/tmp/scripts/ 0m2.8s INFO: Running scripts post_chroot_unpack 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'apt-get', 'update'] 0m10.0s DUMP: Get:1 http://mirror.bm.debian.org/debian sid InRelease [237 kB] Get:2 http://mirror.bm.debian.org/debian sid/main amd64 Packages [8310 kB] Get:3 http://mirror.bm.debian.org/debian sid/main Translation-en [6243 kB] Fetched 14.8 MB in 5s (2758 kB/s) Reading package lists... 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'apt-get', 'update'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'apt-get', '-yf', 'dist-upgrade'] 0m11.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'apt-get', '-yf', 'dist-upgrade'] 0m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m12.8s DUMP: c7119af3b216443ffd059d6b161c0063 - 0m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m12.8s INFO: Running scripts post_setup 0m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/post_setup_dummy_users'] 0m14.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/post_setup_dummy_users'] 0m14.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/post_setup_experimental'] 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/post_setup_experimental'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/post_setup_forbid_home'] 0m14.8s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/post_setup_forbid_home'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/post_setup_force-unsafe-io'] 0m14.8s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/post_setup_force-unsafe-io'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/post_setup_minimize'] 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/post_setup_minimize'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/post_setup_squeeze-backports'] 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/post_setup_squeeze-backports'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/post_setup_zz_backports'] 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/post_setup_zz_backports'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'apt-get', 'clean'] 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'apt-get', 'clean'] 0m14.9s DEBUG: Recording chroot state 0m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m17.1s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.0~alpha2 install ok installed base-files base-files 10.1 install ok installed base-passwd base-passwd 3.5.45 install ok installed bash bash 4.4.18-3.1 install ok installed bsdutils bsdutils 1:2.33-0.2 install ok installed coreutils coreutils 8.30-1 install ok installed dash dash 0.5.10.2-1 install ok installed debconf debconf 1.5.69 install ok installed debian-archive-keyring debian-archive-keyring 2018.1 install ok installed debianutils debianutils 4.8.6 install ok installed diffutils diffutils 1:3.6-1 install ok installed dpkg dpkg 1.19.2 install ok installed e2fsprogs e2fsprogs 1.44.4-2 install ok installed fdisk fdisk 2.33-0.2 install ok installed findutils findutils 4.6.0+git+20181018-1 install ok installed gcc-8-base:amd64 gcc-8-base 8.2.0-12 install ok installed gpgv gpgv 2.2.11-1 install ok installed grep grep 3.1-3 install ok installed gzip gzip 1.9-2.1 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.0~alpha2 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.8.4-2 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-2 install ok installed libblkid1:amd64 libblkid1 2.33-0.2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-9 install ok installed libc-bin libc-bin 2.28-2 install ok installed libc6:amd64 libc6 2.28-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-1+b1 install ok installed libcom-err2:amd64 libcom-err2 1.44.4-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.2 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.245 install ok installed libext2fs2:amd64 libext2fs2 1.44.4-2 install ok installed libfdisk1:amd64 libfdisk1 2.33-0.2 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libgcc1:amd64 libgcc1 1:8.2.0-12 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-4 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4 install ok installed libgnutls30:amd64 libgnutls30 3.5.19-1+b1 install ok installed libgpg-error0:amd64 libgpg-error0 1.32-3 install ok installed libhogweed4:amd64 libhogweed4 3.4.1~rc1-1 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1 install ok installed liblz4-1:amd64 liblz4-1 1.8.2-1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.3 install ok installed libmount1:amd64 libmount1 2.33-0.2 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-1 install ok installed libnettle6:amd64 libnettle6 3.4.1~rc1-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.14-2 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.8 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.8 install ok installed libpam-runtime libpam-runtime 1.1.8-3.8 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.8 install ok installed libpcre3:amd64 libpcre3 2:8.39-11 install ok installed libseccomp2:amd64 libseccomp2 2.3.3-3 install ok installed libselinux1:amd64 libselinux1 2.8-1+b1 install ok installed libsemanage-common libsemanage-common 2.8-1 install ok installed libsemanage1:amd64 libsemanage1 2.8-1+b1 install ok installed libsepol1:amd64 libsepol1 2.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.33-0.2 install ok installed libss2:amd64 libss2 1.44.4-2 install ok installed libstdc++6:amd64 libstdc++6 8.2.0-12 install ok installed libsystemd0:amd64 libsystemd0 239-15 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-1 install ok installed libudev1:amd64 libudev1 239-15 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libuuid1:amd64 libuuid1 2.33-0.2 install ok installed libzstd1:amd64 libzstd1 1.3.5+dfsg-1 install ok installed login login 1:4.5-1.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.33-0.2 install ok installed ncurses-base ncurses-base 6.1+20181013-1 install ok installed ncurses-bin ncurses-bin 6.1+20181013-1 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl-base perl-base 5.28.1-3 install ok installed sed sed 4.5-2 install ok installed sysvinit-utils sysvinit-utils 2.93-1 install ok installed tar tar 1.30+dfsg-3 install ok installed util-linux util-linux 2.33-0.2 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1 0m17.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m17.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'dpkg-divert', '--list'] 0m17.2s 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 0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'dpkg-divert', '--list'] 0m17.2s INFO: Running scripts is_testable 0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/is_testable_uninstallable'] 0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/is_testable_uninstallable'] 0m17.2s INFO: apt-cache does not know about any of the requested packages 0m17.2s INFO: Running scripts pre_test 0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/pre_test_exceptions'] 0m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/pre_test_exceptions'] 0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/pre_test_root_password'] 0m17.3s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/pre_test_root_password'] 0m17.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpsdaAAB'] 0m18.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpsdaAAB'] 0m19.7s DEBUG: No broken symlinks as far as we can find. 0m19.7s INFO: Running scripts pre_install 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/pre_install_database-server'] 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/pre_install_database-server'] 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/pre_install_exceptions'] 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/pre_install_exceptions'] 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/pre_install_extras'] 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/pre_install_extras'] 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/pre_install_log_alternatives'] 0m19.8s DUMP: Adding 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' dpkg-divert: warning: diverting file '/usr/bin/update-alternatives' from an Essential package with rename is dangerous, use --no-rename 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'tmp/scripts/pre_install_log_alternatives'] 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'apt-cache', 'show', '--no-all-versions', 'metaphlan2-data=2.6.0+ds-4'] 0m22.2s DUMP: Package: metaphlan2-data Version: 2.6.0+ds-4 Installed-Size: 753107 Maintainer: Debian Med Packaging Team Architecture: all Depends: debconf (>= 0.5) | debconf-2.0, bowtie2 Description-en: data package for Metagenomic Phylogenetic Analysis MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. From version 2.0, MetaPhlAn is also able to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species. . MetaPhlAn 2.0 relies on ~1M unique clade-specific marker genes (the marker information file can be found at src/utils/markers_info.txt.bz2 or here) identified from ~17,000 reference genomes (~13,500 bacterial and archaeal, ~3,500 viral, and ~110 eukaryotic), allowing: . * unambiguous taxonomic assignments; * accurate estimation of organismal relative abundance; * species-level resolution for bacteria, archaea, eukaryotes and viruses; * strain identification and tracking * orders of magnitude speedups compared to existing methods. * metagenomic strain-level population genomics . This package contains the data for metaphlan2. Description-md5: f0775409e41de9fba49cda4590c73ce4 Homepage: https://bitbucket.org/biobakery/metaphlan2 Section: science Priority: optional Filename: pool/main/m/metaphlan2-data/metaphlan2-data_2.6.0+ds-4_all.deb Size: 204323768 MD5sum: de685246213a02dcedfee6e464f7ac11 SHA256: f38a6e3f49d7b03ba80d9fdd5647b9f9f2dfb38d43b28618053e8ef2c60db7d7 0m22.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'apt-cache', 'show', '--no-all-versions', 'metaphlan2-data=2.6.0+ds-4'] 0m22.2s DEBUG: metapackage: Package: piuparts-depends-dummy Version: 0.invalid.0 Architecture: all Maintainer: piuparts developers team Description: Dummy package to satisfy dependencies - created by piuparts This package was created automatically by piuparts and can safely be removed Depends: debconf (>= 0.5) | debconf-2.0, bowtie2 0m22.2s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpZhC1vH/piuparts-depends-dummy'] 0m22.2s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmpZhC1vH/piuparts-depends-dummy.deb'. 0m22.2s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpZhC1vH/piuparts-depends-dummy'] 0m22.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m22.2s DUMP: 1.8.0~alpha2 0m22.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m22.2s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmpZhC1vH/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmpsdaAAB/tmp 0m22.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'apt-get', '-y', '--allow-downgrades', 'install', './tmp/piuparts-depends-dummy.deb'] 0m29.4s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: bowtie2 libatomic1 libexpat1 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 libsqlite3-0 libssl1.1 libtbb2 mime-support python python-minimal python2 python2-minimal python2.7 python2.7-minimal readline-common Suggested packages: bowtie2-examples python-doc python-tk python2-doc python2.7-doc binutils binfmt-support readline-doc Recommended packages: bzip2 file xz-utils The following NEW packages will be installed: bowtie2 libatomic1 libexpat1 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 libsqlite3-0 libssl1.1 libtbb2 mime-support piuparts-depends-dummy python python-minimal python2 python2-minimal python2.7 python2.7-minimal readline-common 0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded. Need to get 8004 kB/8005 kB of archives. After this operation, 28.9 MB of additional disk space will be used. Get:1 /tmp/piuparts-depends-dummy.deb piuparts-depends-dummy all 0.invalid.0 [656 B] Get:2 http://mirror.bm.debian.org/debian sid/main amd64 libpython2.7-minimal amd64 2.7.15-5 [394 kB] Get:3 http://mirror.bm.debian.org/debian sid/main amd64 python2.7-minimal amd64 2.7.15-5 [1365 kB] Get:4 http://mirror.bm.debian.org/debian sid/main amd64 python2-minimal amd64 2.7.15-3 [41.3 kB] Get:5 http://mirror.bm.debian.org/debian sid/main amd64 python-minimal amd64 2.7.15-3 [20.9 kB] Get:6 http://mirror.bm.debian.org/debian sid/main amd64 mime-support all 3.61 [37.1 kB] Get:7 http://mirror.bm.debian.org/debian sid/main amd64 libexpat1 amd64 2.2.6-1 [105 kB] Get:8 http://mirror.bm.debian.org/debian sid/main amd64 readline-common all 7.0-5 [70.6 kB] Get:9 http://mirror.bm.debian.org/debian sid/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:10 http://mirror.bm.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.26.0-3 [634 kB] Get:11 http://mirror.bm.debian.org/debian sid/main amd64 libssl1.1 amd64 1.1.1a-1 [1527 kB] Get:12 http://mirror.bm.debian.org/debian sid/main amd64 libpython2.7-stdlib amd64 2.7.15-5 [1909 kB] Get:13 http://mirror.bm.debian.org/debian sid/main amd64 python2.7 amd64 2.7.15-5 [299 kB] Get:14 http://mirror.bm.debian.org/debian sid/main amd64 libpython2-stdlib amd64 2.7.15-3 [20.7 kB] Get:15 http://mirror.bm.debian.org/debian sid/main amd64 libpython-stdlib amd64 2.7.15-3 [20.7 kB] Get:16 http://mirror.bm.debian.org/debian sid/main amd64 python2 amd64 2.7.15-3 [41.5 kB] Get:17 http://mirror.bm.debian.org/debian sid/main amd64 python amd64 2.7.15-3 [22.7 kB] Get:18 http://mirror.bm.debian.org/debian sid/main amd64 libatomic1 amd64 8.2.0-12 [8896 B] Get:19 http://mirror.bm.debian.org/debian sid/main amd64 libtbb2 amd64 2018~U6-2 [147 kB] Get:20 http://mirror.bm.debian.org/debian sid/main amd64 bowtie2 amd64 2.3.4.3-1 [1188 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 8004 kB in 0s (52.0 MB/s) Selecting previously unselected package libpython2.7-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4461 files and directories currently installed.) Preparing to unpack .../00-libpython2.7-minimal_2.7.15-5_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.15-5) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../01-python2.7-minimal_2.7.15-5_amd64.deb ... Unpacking python2.7-minimal (2.7.15-5) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../02-python2-minimal_2.7.15-3_amd64.deb ... Unpacking python2-minimal (2.7.15-3) ... Selecting previously unselected package python-minimal. Preparing to unpack .../03-python-minimal_2.7.15-3_amd64.deb ... Unpacking python-minimal (2.7.15-3) ... Selecting previously unselected package mime-support. Preparing to unpack .../04-mime-support_3.61_all.deb ... Unpacking mime-support (3.61) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../05-libexpat1_2.2.6-1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../06-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../07-libreadline7_7.0-5_amd64.deb ... Unpacking libreadline7:amd64 (7.0-5) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../08-libsqlite3-0_3.26.0-3_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.26.0-3) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../09-libssl1.1_1.1.1a-1_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1a-1) ... Selecting previously unselected package libpython2.7-stdlib:amd64. Preparing to unpack .../10-libpython2.7-stdlib_2.7.15-5_amd64.deb ... Unpacking libpython2.7-stdlib:amd64 (2.7.15-5) ... Selecting previously unselected package python2.7. Preparing to unpack .../11-python2.7_2.7.15-5_amd64.deb ... Unpacking python2.7 (2.7.15-5) ... Selecting previously unselected package libpython2-stdlib:amd64. Preparing to unpack .../12-libpython2-stdlib_2.7.15-3_amd64.deb ... Unpacking libpython2-stdlib:amd64 (2.7.15-3) ... Selecting previously unselected package libpython-stdlib:amd64. Preparing to unpack .../13-libpython-stdlib_2.7.15-3_amd64.deb ... Unpacking libpython-stdlib:amd64 (2.7.15-3) ... Setting up libpython2.7-minimal:amd64 (2.7.15-5) ... Setting up python2.7-minimal (2.7.15-5) ... Setting up python2-minimal (2.7.15-3) ... Selecting previously unselected package python2. (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 ... 5298 files and directories currently installed.) Preparing to unpack .../python2_2.7.15-3_amd64.deb ... Unpacking python2 (2.7.15-3) ... Setting up python-minimal (2.7.15-3) ... Selecting previously unselected package python. (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 ... 5331 files and directories currently installed.) Preparing to unpack .../python_2.7.15-3_amd64.deb ... Unpacking python (2.7.15-3) ... Selecting previously unselected package libatomic1:amd64. Preparing to unpack .../libatomic1_8.2.0-12_amd64.deb ... Unpacking libatomic1:amd64 (8.2.0-12) ... Selecting previously unselected package libtbb2:amd64. Preparing to unpack .../libtbb2_2018~U6-2_amd64.deb ... Unpacking libtbb2:amd64 (2018~U6-2) ... Selecting previously unselected package bowtie2. Preparing to unpack .../bowtie2_2.3.4.3-1_amd64.deb ... Unpacking bowtie2 (2.3.4.3-1) ... Selecting previously unselected package piuparts-depends-dummy. Preparing to unpack .../tmp/piuparts-depends-dummy.deb ... Unpacking piuparts-depends-dummy (0.invalid.0) ... Setting up libatomic1:amd64 (8.2.0-12) ... Setting up readline-common (7.0-5) ... Setting up libexpat1:amd64 (2.2.6-1) ... Setting up mime-support (3.61) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libtbb2:amd64 (2018~U6-2) ... Processing triggers for libc-bin (2.28-2) ... Setting up libssl1.1:amd64 (1.1.1a-1) ... Setting up libsqlite3-0:amd64 (3.26.0-3) ... Setting up libpython2.7-stdlib:amd64 (2.7.15-5) ... Setting up python2.7 (2.7.15-5) ... Setting up libpython2-stdlib:amd64 (2.7.15-3) ... Setting up python2 (2.7.15-3) ... Setting up libpython-stdlib:amd64 (2.7.15-3) ... Setting up python (2.7.15-3) ... Setting up bowtie2 (2.3.4.3-1) ... Setting up piuparts-depends-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.28-2) ... 0m29.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'apt-get', '-y', '--allow-downgrades', 'install', './tmp/piuparts-depends-dummy.deb'] 0m29.4s INFO: Installation of ['./tmp/piuparts-depends-dummy.deb'] ok 0m29.4s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmpsdaAAB/./tmp/piuparts-depends-dummy.deb 0m29.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m29.4s DUMP: piuparts-depends-dummy install ok installed 0m29.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m29.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m29.5s DUMP: (Reading database ... 5383 files and directories currently installed.) Removing piuparts-depends-dummy (0.invalid.0) ... 0m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'apt-get', 'clean'] 0m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'apt-get', 'clean'] 0m29.5s DEBUG: Recording chroot state 0m31.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpsdaAAB'] 0m32.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpsdaAAB'] 0m34.1s DEBUG: No broken symlinks as far as we can find. 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'apt-cache', 'policy'] 0m36.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror.bm.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin mirror.bm.debian.org Pinned packages: 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'apt-cache', 'policy'] 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'apt-cache', 'policy', 'metaphlan2-data'] 0m36.1s DUMP: metaphlan2-data: Installed: (none) Candidate: 2.6.0+ds-4 Version table: 2.6.0+ds-4 500 500 http://mirror.bm.debian.org/debian sid/main amd64 Packages 0m36.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'apt-cache', 'policy', 'metaphlan2-data'] 0m36.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'apt-get', '-y', 'install', 'metaphlan2-data=2.6.0+ds-4'] 60m37.0s ERROR: Terminating command due to excessive runtime 60m37.8s DUMP: ***** Command was terminated after exceeding runtime limit (3600 s) ***** 60m37.9s ERROR: Command failed (status=-15): ['chroot', '/srv/piuparts.debian.org/tmp/tmpsdaAAB', 'apt-get', '-y', 'install', 'metaphlan2-data=2.6.0+ds-4'] ***** Command was terminated after exceeding runtime limit (3600 s) ***** 60m39.8s DEBUG: kill -15 28061 60m40.1s DEBUG: kill -15 28045 60m40.3s DEBUG: kill -15 28042 60m40.6s DEBUG: kill -15 28039 60m47.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/dev/shm'] 60m47.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/dev/shm'] 60m47.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/dev/console'] 60m47.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/dev/console'] 60m47.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/dev/ptmx'] 60m47.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/dev/ptmx'] 60m47.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/dev/pts'] 60m47.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/dev/pts'] 60m47.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/proc'] 60m47.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpsdaAAB/proc'] 60m47.6s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpsdaAAB'] 60m48.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpsdaAAB'] 60m48.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpsdaAAB 60m48.1s ERROR: piuparts run ends. ret=1 End: 2018-12-11 18:57:43 UTC