Start: 2023-02-18 11:01:15 GMT Package: metaphlan2 Version: 2.6.0+ds-2 Installed-Size: 72138 Maintainer: Debian Med Packaging Team Architecture: all Depends: python:any (>= 2.7.5-5~), metaphlan2-data, python-biom-format, python-msgpack, python-pandas, bowtie2 Description: Metagenomic Phylogenetic Analysis Homepage: https://bitbucket.org/biobakery/metaphlan2 Description-md5: 3b2f7f0abf7727c8176639b50ed2f548 Section: science Priority: optional Filename: pool/main/m/metaphlan2/metaphlan2_2.6.0+ds-2_all.deb Size: 73315830 MD5sum: 1f9bece54faf2c7cd62ca02e4e5295f9 SHA256: 6e3bf1c4027039ec22b3341c2e51cdae7424953aa082814c3e08f8521d10551e 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-log-alternatives --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch --no-upgrade-test --apt metaphlan2=2.6.0+ds-2 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.5 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts-log-alternatives --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch --no-upgrade-test --apt metaphlan2=2.6.0+ds-2 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpww8kap73 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpww8kap73 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpww8kap73', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpww8kap73', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpww8kap73/proc'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpww8kap73/proc'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpww8kap73/dev/pts'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpww8kap73/dev/pts'] 0m1.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpww8kap73/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpww8kap73/dev/ptmx'] 0m1.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpww8kap73/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpww8kap73/dev/ptmx'] 0m1.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpww8kap73/dev/console'] 0m1.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpww8kap73/dev/console'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpww8kap73/dev/shm'] 0m1.6s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpww8kap73/dev/shm'] 0m1.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m1.6s DEBUG: Created policy-rc.d and chmodded it. 0m1.6s DEBUG: Created resolv.conf. 0m1.6s DEBUG: Copying scriptsdir /etc/piuparts/scripts-log-alternatives to /srv/piuparts.debian.org/tmp/tmpww8kap73/tmp/scripts/ 0m1.6s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpww8kap73/tmp/scripts/ 0m1.6s INFO: Running scripts post_chroot_unpack 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'apt-get', 'update'] 0m3.4s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'apt-get', 'update'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'apt-get', '-yf', 'dist-upgrade'] 0m3.7s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'apt-get', '-yf', 'dist-upgrade'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.3s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.3s INFO: Running scripts post_setup 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_setup_dummy_users'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_setup_dummy_users'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_setup_forbid_home'] 0m5.6s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_setup_forbid_home'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.6s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_setup_minimize'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_setup_minimize'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_setup_zz_backports'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_setup_zz_backports'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'apt-get', 'clean'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'apt-get', 'clean'] 0m5.6s DEBUG: Recording chroot state 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.1s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.10 install ok installed base-files base-files 9.9+deb9u13 install ok installed base-passwd base-passwd 3.5.43 install ok installed bash bash 4.4-5 install ok installed bsdutils bsdutils 1:2.29.2-1+deb9u1 install ok installed coreutils coreutils 8.26-3 install ok installed dash dash 0.5.8-2.4 install ok installed debconf debconf 1.5.61 install ok installed debian-archive-keyring debian-archive-keyring 2017.5+deb9u1 install ok installed debianutils debianutils 4.8.1.1 install ok installed diffutils diffutils 1:3.5-3 install ok installed dpkg dpkg 1.18.25 install ok installed e2fslibs:amd64 e2fslibs 1.43.4-2+deb9u1 install ok installed e2fsprogs e2fsprogs 1.43.4-2+deb9u1 install ok installed findutils findutils 4.6.0+git+20161106-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gpgv gpgv 2.1.18-8~deb9u4 install ok installed grep grep 2.27-2 install ok installed gzip gzip 1.6-5+b1 install ok installed hostname hostname 3.18+b1 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.4.10 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.6.7-2 install ok installed libaudit1:amd64 libaudit1 1:2.6.7-2 install ok installed libblkid1:amd64 libblkid1 2.29.2-1+deb9u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-8.1 install ok installed libc-bin libc-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 2.24-11+deb9u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2+deb9u1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+b1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+b1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.6 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.6 install ok installed libpam-runtime libpam-runtime 1.1.8-3.6 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.6 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libselinux1:amd64 libselinux1 2.6-3+b3 install ok installed libsemanage-common libsemanage-common 2.6-2 install ok installed libsemanage1:amd64 libsemanage1 2.6-2 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u1 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u12 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u12 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.29.2-1+deb9u1 install ok installed login login 1:4.4-4.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed ncurses-base ncurses-base 6.0+20161126-1+deb9u2 install ok installed ncurses-bin ncurses-bin 6.0+20161126-1+deb9u2 install ok installed passwd passwd 1:4.4-4.1 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59.9 install ok installed tar tar 1.29b-1.1 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'dpkg-divert', '--list'] 0m6.1s 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 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'dpkg-divert', '--list'] 0m6.1s INFO: Running scripts is_testable 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/is_testable_uninstallable'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/is_testable_uninstallable'] 0m6.1s INFO: apt-cache does not know about any of the requested packages 0m6.1s INFO: Running scripts pre_test 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_test_exceptions'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_test_exceptions'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_test_root_password'] 0m6.2s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_test_root_password'] 0m6.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpww8kap73'] 0m6.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpww8kap73'] 0m7.0s DEBUG: No broken symlinks as far as we can find. 0m7.0s INFO: Running scripts pre_install 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_install_database-server'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_install_database-server'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_install_exceptions'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_install_exceptions'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_install_extras'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_install_extras'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_install_log_alternatives'] 0m7.1s DUMP: Adding 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_install_log_alternatives'] 0m7.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpww8kap73'] 0m7.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpww8kap73'] 0m7.6s DEBUG: No broken symlinks as far as we can find. 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'apt-cache', 'policy'] 0m8.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian stretch/main amd64 Packages release v=9.13,o=Debian,a=oldoldstable,n=stretch,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'apt-cache', 'policy'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'apt-cache', 'policy', 'metaphlan2'] 0m8.3s DUMP: metaphlan2: Installed: (none) Candidate: 2.6.0+ds-2 Version table: 2.6.0+ds-2 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'apt-cache', 'policy', 'metaphlan2'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'apt-get', '-y', 'install', 'metaphlan2=2.6.0+ds-2'] 32m35.9s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: bowtie2 libatomic1 libblas-common libblas3 libexpat1 libffi6 libgfortran3 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 libsqlite3-0 libssl1.1 libtbb2 metaphlan2-data mime-support pyqi python python-biom-format python-click python-colorama python-configparser python-dateutil python-decorator python-future python-minimal python-msgpack python-numpy python-pandas python-pandas-lib python-pkg-resources python-scipy python-six python-tz python2.7 python2.7-minimal readline-common sphinx-common tzdata Suggested packages: bowtie2-examples python-doc python-tk python-biom-format-doc python-future-doc gcc gfortran python-dev python-nose python-numpy-dbg python-numpy-doc python-pandas-doc python-setuptools python-scipy-doc python2.7-doc binutils binfmt-support readline-doc Recommended packages: javascript-common bzip2 file xz-utils python-matplotlib python-tables python-numexpr python-xlrd python-statsmodels python-openpyxl python-xlwt python-bs4 python-html5lib python-lxml g++ | c++-compiler python-dev python-imaging python-sphinx | python3-sphinx The following NEW packages will be installed: bowtie2 libatomic1 libblas-common libblas3 libexpat1 libffi6 libgfortran3 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 libsqlite3-0 libssl1.1 libtbb2 metaphlan2 metaphlan2-data mime-support pyqi python python-biom-format python-click python-colorama python-configparser python-dateutil python-decorator python-future python-minimal python-msgpack python-numpy python-pandas python-pandas-lib python-pkg-resources python-scipy python-six python-tz python2.7 python2.7-minimal readline-common sphinx-common tzdata 0 upgraded, 45 newly installed, 0 to remove and 0 not upgraded. Need to get 305 MB of archives. After this operation, 979 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian stretch/main amd64 libpython2.7-minimal amd64 2.7.13-2+deb9u3 [389 kB] Get:2 http://deb.debian.org/debian stretch/main amd64 python2.7-minimal amd64 2.7.13-2+deb9u3 [1382 kB] Get:3 http://deb.debian.org/debian stretch/main amd64 python-minimal amd64 2.7.13-2 [40.5 kB] Get:4 http://deb.debian.org/debian stretch/main amd64 mime-support all 3.60 [36.7 kB] Get:5 http://deb.debian.org/debian stretch/main amd64 libexpat1 amd64 2.2.0-2+deb9u3 [83.7 kB] Get:6 http://deb.debian.org/debian stretch/main amd64 libffi6 amd64 3.2.1-6 [20.4 kB] Get:7 http://deb.debian.org/debian stretch/main amd64 readline-common all 7.0-3 [70.4 kB] Get:8 http://deb.debian.org/debian stretch/main amd64 libreadline7 amd64 7.0-3 [151 kB] Get:9 http://deb.debian.org/debian stretch/main amd64 libsqlite3-0 amd64 3.16.2-5+deb9u1 [572 kB] Get:10 http://deb.debian.org/debian stretch/main amd64 libssl1.1 amd64 1.1.0l-1~deb9u1 [1358 kB] Get:11 http://deb.debian.org/debian stretch/main amd64 libpython2.7-stdlib amd64 2.7.13-2+deb9u3 [1897 kB] Get:12 http://deb.debian.org/debian stretch/main amd64 python2.7 amd64 2.7.13-2+deb9u3 [285 kB] Get:13 http://deb.debian.org/debian stretch/main amd64 libpython-stdlib amd64 2.7.13-2 [20.0 kB] Get:14 http://deb.debian.org/debian stretch/main amd64 python amd64 2.7.13-2 [154 kB] Get:15 http://deb.debian.org/debian stretch/main amd64 tzdata all 2020a-0+deb9u1 [278 kB] Get:16 http://deb.debian.org/debian stretch/main amd64 libatomic1 amd64 6.3.0-18+deb9u1 [8966 B] Get:17 http://deb.debian.org/debian stretch/main amd64 libblas-common amd64 3.7.0-2 [14.2 kB] Get:18 http://deb.debian.org/debian stretch/main amd64 libquadmath0 amd64 6.3.0-18+deb9u1 [131 kB] Get:19 http://deb.debian.org/debian stretch/main amd64 libgfortran3 amd64 6.3.0-18+deb9u1 [265 kB] Get:20 http://deb.debian.org/debian stretch/main amd64 libblas3 amd64 3.7.0-2 [155 kB] Get:21 http://deb.debian.org/debian stretch/main amd64 libjs-jquery all 3.1.1-2+deb9u1 [154 kB] Get:22 http://deb.debian.org/debian stretch/main amd64 libjs-underscore all 1.8.3~dfsg-1 [63.8 kB] Get:23 http://deb.debian.org/debian stretch/main amd64 libjs-sphinxdoc all 1.4.9-2 [69.5 kB] Get:24 http://deb.debian.org/debian stretch/main amd64 liblapack3 amd64 3.7.0-2 [2141 kB] Get:25 http://deb.debian.org/debian stretch/main amd64 libtbb2 amd64 4.3~20150611-2 [136 kB] Get:26 http://deb.debian.org/debian stretch/main amd64 bowtie2 amd64 2.3.0-2 [1166 kB] Get:27 http://deb.debian.org/debian stretch/main amd64 metaphlan2-data all 2.6.0+ds-2 [204 MB] Get:28 http://deb.debian.org/debian stretch/main amd64 python-numpy amd64 1:1.12.1-3 [1936 kB] Get:29 http://deb.debian.org/debian stretch/main amd64 sphinx-common all 1.4.9-2 [350 kB] Get:30 http://deb.debian.org/debian stretch/main amd64 pyqi all 0.3.2+dfsg-2 [72.0 kB] Get:31 http://deb.debian.org/debian stretch/main amd64 python-colorama all 0.3.7-1 [25.7 kB] Get:32 http://deb.debian.org/debian stretch/main amd64 python-click all 6.6-1 [56.1 kB] Get:33 http://deb.debian.org/debian stretch/main amd64 python-configparser all 3.3.0r2-2 [62.1 kB] Get:34 http://deb.debian.org/debian stretch/main amd64 python-future all 0.15.2-4 [347 kB] Get:35 http://deb.debian.org/debian stretch/main amd64 python-decorator all 4.0.11-1 [13.3 kB] Get:36 http://deb.debian.org/debian stretch/main amd64 python-scipy amd64 0.18.1-2 [8933 kB] Get:37 http://deb.debian.org/debian stretch/main amd64 python-biom-format amd64 2.1.5+dfsg-7 [183 kB] Get:38 http://deb.debian.org/debian stretch/main amd64 python-msgpack amd64 0.4.8-1 [67.8 kB] Get:39 http://deb.debian.org/debian stretch/main amd64 python-six all 1.10.0-3 [14.4 kB] Get:40 http://deb.debian.org/debian stretch/main amd64 python-dateutil all 2.5.3-2 [51.3 kB] Get:41 http://deb.debian.org/debian stretch/main amd64 python-tz all 2016.7-0.3 [33.7 kB] Get:42 http://deb.debian.org/debian stretch/main amd64 python-pandas-lib amd64 0.19.2-5.1 [2275 kB] Get:43 http://deb.debian.org/debian stretch/main amd64 python-pkg-resources all 33.1.1-1 [166 kB] Get:44 http://deb.debian.org/debian stretch/main amd64 python-pandas all 0.19.2-5.1 [2616 kB] Get:45 http://deb.debian.org/debian stretch/main amd64 metaphlan2 all 2.6.0+ds-2 [73.3 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 305 MB in 20s (14.9 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 ... 4412 files and directories currently installed.) Preparing to unpack .../00-libpython2.7-minimal_2.7.13-2+deb9u3_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../01-python2.7-minimal_2.7.13-2+deb9u3_amd64.deb ... Unpacking python2.7-minimal (2.7.13-2+deb9u3) ... Selecting previously unselected package python-minimal. Preparing to unpack .../02-python-minimal_2.7.13-2_amd64.deb ... Unpacking python-minimal (2.7.13-2) ... Selecting previously unselected package mime-support. Preparing to unpack .../03-mime-support_3.60_all.deb ... Unpacking mime-support (3.60) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../04-libexpat1_2.2.0-2+deb9u3_amd64.deb ... Unpacking libexpat1:amd64 (2.2.0-2+deb9u3) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../05-libffi6_3.2.1-6_amd64.deb ... Unpacking libffi6:amd64 (3.2.1-6) ... Selecting previously unselected package readline-common. Preparing to unpack .../06-readline-common_7.0-3_all.deb ... Unpacking readline-common (7.0-3) ... Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../07-libreadline7_7.0-3_amd64.deb ... Unpacking libreadline7:amd64 (7.0-3) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../08-libsqlite3-0_3.16.2-5+deb9u1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../09-libssl1.1_1.1.0l-1~deb9u1_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Selecting previously unselected package libpython2.7-stdlib:amd64. Preparing to unpack .../10-libpython2.7-stdlib_2.7.13-2+deb9u3_amd64.deb ... Unpacking libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ... Selecting previously unselected package python2.7. Preparing to unpack .../11-python2.7_2.7.13-2+deb9u3_amd64.deb ... Unpacking python2.7 (2.7.13-2+deb9u3) ... Selecting previously unselected package libpython-stdlib:amd64. Preparing to unpack .../12-libpython-stdlib_2.7.13-2_amd64.deb ... Unpacking libpython-stdlib:amd64 (2.7.13-2) ... Setting up libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) ... Setting up python2.7-minimal (2.7.13-2+deb9u3) ... Setting up python-minimal (2.7.13-2) ... 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 ... 5238 files and directories currently installed.) Preparing to unpack .../00-python_2.7.13-2_amd64.deb ... Unpacking python (2.7.13-2) ... Selecting previously unselected package tzdata. Preparing to unpack .../01-tzdata_2020a-0+deb9u1_all.deb ... Unpacking tzdata (2020a-0+deb9u1) ... Selecting previously unselected package libatomic1:amd64. Preparing to unpack .../02-libatomic1_6.3.0-18+deb9u1_amd64.deb ... Unpacking libatomic1:amd64 (6.3.0-18+deb9u1) ... Selecting previously unselected package libblas-common. Preparing to unpack .../03-libblas-common_3.7.0-2_amd64.deb ... Unpacking libblas-common (3.7.0-2) ... Selecting previously unselected package libquadmath0:amd64. Preparing to unpack .../04-libquadmath0_6.3.0-18+deb9u1_amd64.deb ... Unpacking libquadmath0:amd64 (6.3.0-18+deb9u1) ... Selecting previously unselected package libgfortran3:amd64. Preparing to unpack .../05-libgfortran3_6.3.0-18+deb9u1_amd64.deb ... Unpacking libgfortran3:amd64 (6.3.0-18+deb9u1) ... Selecting previously unselected package libblas3. Preparing to unpack .../06-libblas3_3.7.0-2_amd64.deb ... Unpacking libblas3 (3.7.0-2) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../07-libjs-jquery_3.1.1-2+deb9u1_all.deb ... Unpacking libjs-jquery (3.1.1-2+deb9u1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../08-libjs-underscore_1.8.3~dfsg-1_all.deb ... Unpacking libjs-underscore (1.8.3~dfsg-1) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../09-libjs-sphinxdoc_1.4.9-2_all.deb ... Unpacking libjs-sphinxdoc (1.4.9-2) ... Selecting previously unselected package liblapack3. Preparing to unpack .../10-liblapack3_3.7.0-2_amd64.deb ... Unpacking liblapack3 (3.7.0-2) ... Selecting previously unselected package libtbb2:amd64. Preparing to unpack .../11-libtbb2_4.3~20150611-2_amd64.deb ... Unpacking libtbb2:amd64 (4.3~20150611-2) ... Selecting previously unselected package bowtie2. Preparing to unpack .../12-bowtie2_2.3.0-2_amd64.deb ... Unpacking bowtie2 (2.3.0-2) ... Selecting previously unselected package metaphlan2-data. Preparing to unpack .../13-metaphlan2-data_2.6.0+ds-2_all.deb ... Unpacking metaphlan2-data (2.6.0+ds-2) ... Selecting previously unselected package python-numpy. Preparing to unpack .../14-python-numpy_1%3a1.12.1-3_amd64.deb ... Unpacking python-numpy (1:1.12.1-3) ... Selecting previously unselected package sphinx-common. Preparing to unpack .../15-sphinx-common_1.4.9-2_all.deb ... Unpacking sphinx-common (1.4.9-2) ... Selecting previously unselected package pyqi. Preparing to unpack .../16-pyqi_0.3.2+dfsg-2_all.deb ... Unpacking pyqi (0.3.2+dfsg-2) ... Selecting previously unselected package python-colorama. Preparing to unpack .../17-python-colorama_0.3.7-1_all.deb ... Unpacking python-colorama (0.3.7-1) ... Selecting previously unselected package python-click. Preparing to unpack .../18-python-click_6.6-1_all.deb ... Unpacking python-click (6.6-1) ... Selecting previously unselected package python-configparser. Preparing to unpack .../19-python-configparser_3.3.0r2-2_all.deb ... Unpacking python-configparser (3.3.0r2-2) ... Selecting previously unselected package python-future. Preparing to unpack .../20-python-future_0.15.2-4_all.deb ... Unpacking python-future (0.15.2-4) ... Selecting previously unselected package python-decorator. Preparing to unpack .../21-python-decorator_4.0.11-1_all.deb ... Unpacking python-decorator (4.0.11-1) ... Selecting previously unselected package python-scipy. Preparing to unpack .../22-python-scipy_0.18.1-2_amd64.deb ... Unpacking python-scipy (0.18.1-2) ... Selecting previously unselected package python-biom-format. Preparing to unpack .../23-python-biom-format_2.1.5+dfsg-7_amd64.deb ... Unpacking python-biom-format (2.1.5+dfsg-7) ... Selecting previously unselected package python-msgpack. Preparing to unpack .../24-python-msgpack_0.4.8-1_amd64.deb ... Unpacking python-msgpack (0.4.8-1) ... Selecting previously unselected package python-six. Preparing to unpack .../25-python-six_1.10.0-3_all.deb ... Unpacking python-six (1.10.0-3) ... Selecting previously unselected package python-dateutil. Preparing to unpack .../26-python-dateutil_2.5.3-2_all.deb ... Unpacking python-dateutil (2.5.3-2) ... Selecting previously unselected package python-tz. Preparing to unpack .../27-python-tz_2016.7-0.3_all.deb ... Unpacking python-tz (2016.7-0.3) ... Selecting previously unselected package python-pandas-lib. Preparing to unpack .../28-python-pandas-lib_0.19.2-5.1_amd64.deb ... Unpacking python-pandas-lib (0.19.2-5.1) ... Selecting previously unselected package python-pkg-resources. Preparing to unpack .../29-python-pkg-resources_33.1.1-1_all.deb ... Unpacking python-pkg-resources (33.1.1-1) ... Selecting previously unselected package python-pandas. Preparing to unpack .../30-python-pandas_0.19.2-5.1_all.deb ... Unpacking python-pandas (0.19.2-5.1) ... Selecting previously unselected package metaphlan2. Preparing to unpack .../31-metaphlan2_2.6.0+ds-2_all.deb ... Unpacking metaphlan2 (2.6.0+ds-2) ... Setting up libquadmath0:amd64 (6.3.0-18+deb9u1) ... Setting up libjs-jquery (3.1.1-2+deb9u1) ... Setting up libatomic1:amd64 (6.3.0-18+deb9u1) ... Setting up readline-common (7.0-3) ... Setting up libexpat1:amd64 (2.2.0-2+deb9u3) ... Setting up libjs-underscore (1.8.3~dfsg-1) ... Setting up mime-support (3.60) ... Setting up libreadline7:amd64 (7.0-3) ... Setting up libblas-common (3.7.0-2) ... Setting up tzdata (2020a-0+deb9u1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Feb 18 11:02:05 UTC 2023. Universal Time is now: Sat Feb 18 11:02:05 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libtbb2:amd64 (4.3~20150611-2) ... Setting up libgfortran3:amd64 (6.3.0-18+deb9u1) ... Setting up libjs-sphinxdoc (1.4.9-2) ... Setting up libblas3 (3.7.0-2) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Setting up sphinx-common (1.4.9-2) ... Setting up libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Setting up libffi6:amd64 (3.2.1-6) ... Setting up libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ... Setting up liblapack3 (3.7.0-2) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up python2.7 (2.7.13-2+deb9u3) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up python (2.7.13-2) ... Setting up pyqi (0.3.2+dfsg-2) ... Setting up python-msgpack (0.4.8-1) ... Setting up python-tz (2016.7-0.3) ... Setting up python-colorama (0.3.7-1) ... Setting up python-pkg-resources (33.1.1-1) ... Setting up python-numpy (1:1.12.1-3) ... Setting up bowtie2 (2.3.0-2) ... Setting up python-configparser (3.3.0r2-2) ... Setting up python-six (1.10.0-3) ... Setting up python-pandas-lib (0.19.2-5.1) ... Setting up python-decorator (4.0.11-1) ... Setting up python-future (0.15.2-4) ... update-alternatives: using /usr/bin/python2-futurize to provide /usr/bin/futurize (futurize) in auto mode update-alternatives: using /usr/bin/python2-pasteurize to provide /usr/bin/pasteurize (pasteurize) in auto mode Setting up python-scipy (0.18.1-2) ... Setting up python-click (6.6-1) ... Setting up metaphlan2-data (2.6.0+ds-2) ... Settings: Output files: "/usr/share/metaphlan2/db_v20/mpa_v20_m200.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 4 Difference-cover sample period: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: /var/lib/metaphlan2-data/markers.fasta Building a SMALL index Reading reference sizes Time reading reference sizes: 00:00:07 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:06 bmax according to bmaxDivN setting: 177889396 Using parameters --bmax 133417047 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 133417047 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:14 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:06 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:10 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 7.11558e+08 (target: 133417046) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 1 No samples; assembling all-inclusive block Sorting block of length 711557587 for bucket 1 (Using difference cover) Sorting block time: 00:12:44 Returning block of 711557588 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 193247476 fchr[G]: 355349181 fchr[T]: 534730948 fchr[$]: 711557587 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 304203219 bytes to primary EBWT file: /usr/share/metaphlan2/db_v20/mpa_v20_m200.1.bt2 Wrote 177889404 bytes to secondary EBWT file: /usr/share/metaphlan2/db_v20/mpa_v20_m200.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 711557587 bwtLen: 711557588 sz: 177889397 bwtSz: 177889397 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 44472350 offsSz: 177889400 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 3706030 numLines: 3706030 ebwtTotLen: 237185920 ebwtTotSz: 237185920 color: 0 reverse: 0 Total time for call to driver() for forward index: 00:17:20 Reading reference sizes Time reading reference sizes: 00:00:12 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:06 Time to reverse reference sequence: 00:00:01 bmax according to bmaxDivN setting: 177889396 Using parameters --bmax 133417047 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 133417047 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:13 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:06 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:07 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 7.11558e+08 (target: 133417046) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 1 No samples; assembling all-inclusive block Sorting block of length 711557587 for bucket 1 (Using difference cover) Sorting block time: 00:10:56 Returning block of 711557588 for bucket 1 Exited Ebwt loop fchr[A]: 0 fchr[C]: 193247476 fchr[G]: 355349181 fchr[T]: 534730948 fchr[$]: 711557587 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 304203219 bytes to primary EBWT file: /usr/share/metaphlan2/db_v20/mpa_v20_m200.rev.1.bt2 Wrote 177889404 bytes to secondary EBWT file: /usr/share/metaphlan2/db_v20/mpa_v20_m200.rev.2.bt2 Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 711557587 bwtLen: 711557588 sz: 177889397 bwtSz: 177889397 lineRate: 6 offRate: 4 offMask: 0xfffffff0 ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 44472350 offsSz: 177889400 lineSz: 64 sideSz: 64 sideBwtSz: 48 sideBwtLen: 192 numSides: 3706030 numLines: 3706030 ebwtTotLen: 237185920 ebwtTotSz: 237185920 color: 0 reverse: 1 Total time for backward call to driver() for mirror index: 00:14:06 Metaphlan2 data are properly created. Setting up python-biom-format (2.1.5+dfsg-7) ... Setting up python-dateutil (2.5.3-2) ... Setting up python-pandas (0.19.2-5.1) ... Setting up metaphlan2 (2.6.0+ds-2) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 32m35.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'apt-get', '-y', 'install', 'metaphlan2=2.6.0+ds-2'] 32m35.9s INFO: Running scripts post_install 32m35.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_install_exceptions'] 32m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_install_exceptions'] 32m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_install_log_alternatives'] 32m36.0s DUMP: Removing 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' LOG-ALTERNATIVES: dpkg=python: piuparts=metaphlan2=2.6.0+ds-2: /usr/bin/update-alternatives --auto /usr/bin/python LOG-ALTERNATIVES: dpkg=python: piuparts=metaphlan2=2.6.0+ds-2: /usr/bin/update-alternatives --remove python /usr/bin/python1.5 LOG-ALTERNATIVES: dpkg=python: piuparts=metaphlan2=2.6.0+ds-2: /usr/bin/update-alternatives --remove python /usr/bin/python2.1 LOG-ALTERNATIVES: dpkg=python: piuparts=metaphlan2=2.6.0+ds-2: /usr/bin/update-alternatives --remove python /usr/bin/python2.2 LOG-ALTERNATIVES: dpkg=mime-support: piuparts=metaphlan2=2.6.0+ds-2: /usr/bin/update-alternatives --remove view /usr/bin/see LOG-ALTERNATIVES: dpkg=libblas3: piuparts=metaphlan2=2.6.0+ds-2: /usr/bin/update-alternatives --install /usr/lib/libblas.so.3 libblas.so.3 /usr/lib/libblas/libblas.so.3 10 LOG-ALTERNATIVES: dpkg=liblapack3: piuparts=metaphlan2=2.6.0+ds-2: /usr/bin/update-alternatives --install /usr/lib/liblapack.so.3 liblapack.so.3 /usr/lib/lapack/liblapack.so.3 10 LOG-ALTERNATIVES: dpkg=python-future: piuparts=metaphlan2=2.6.0+ds-2: /usr/bin/update-alternatives --install /usr/bin/futurize futurize /usr/bin/python2-futurize 300 LOG-ALTERNATIVES: dpkg=python-future: piuparts=metaphlan2=2.6.0+ds-2: /usr/bin/update-alternatives --install /usr/bin/pasteurize pasteurize /usr/bin/python2-pasteurize 300 32m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_install_log_alternatives'] 32m36.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpww8kap73'] 32m36.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpww8kap73'] 32m37.7s DEBUG: No broken symlinks as far as we can find. 32m38.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpww8kap73', '-ac', '--ignore-obsolete'] 32m44.3s DUMP: debsums: missing file /srv/piuparts.debian.org/tmp/tmpww8kap73/var/lib/metaphlan2-data/markers.fasta (from metaphlan2-data package) 32m44.3s DEBUG: Command failed (status=2), but ignoring error: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpww8kap73', '-ac', '--ignore-obsolete'] 32m44.3s ERROR: FAIL: debsums reports modifications inside the chroot: debsums: missing file /var/lib/metaphlan2-data/markers.fasta (from metaphlan2-data package) 32m44.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 32m44.3s DUMP: 0.15.6 32m44.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 32m44.3s INFO: Running adequate version 0.15.6 now. 32m44.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'metaphlan2'] 32m44.4s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'metaphlan2'] 32m44.4s INFO: Running scripts pre_remove 32m44.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 32m44.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 32m44.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 32m44.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 32m44.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 32m45.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 32m45.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 32m45.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 32m45.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 32m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 32m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_remove_exceptions'] 32m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/pre_remove_exceptions'] 32m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 32m45.3s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.10 install ok installed base-files base-files 9.9+deb9u13 install ok installed base-passwd base-passwd 3.5.43 install ok installed bash bash 4.4-5 install ok installed bowtie2 bowtie2 2.3.0-2 install ok installed bsdutils bsdutils 1:2.29.2-1+deb9u1 install ok installed coreutils coreutils 8.26-3 install ok installed dash dash 0.5.8-2.4 install ok installed debconf debconf 1.5.61 install ok installed debian-archive-keyring debian-archive-keyring 2017.5+deb9u1 install ok installed debianutils debianutils 4.8.1.1 install ok installed diffutils diffutils 1:3.5-3 install ok installed dpkg dpkg 1.18.25 install ok installed e2fslibs:amd64 e2fslibs 1.43.4-2+deb9u1 install ok installed e2fsprogs e2fsprogs 1.43.4-2+deb9u1 install ok installed findutils findutils 4.6.0+git+20161106-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gpgv gpgv 2.1.18-8~deb9u4 install ok installed grep grep 2.27-2 install ok installed gzip gzip 1.6-5+b1 install ok installed hostname hostname 3.18+b1 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.4.10 install ok installed libatomic1:amd64 libatomic1 6.3.0-18+deb9u1 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.6.7-2 install ok installed libaudit1:amd64 libaudit1 1:2.6.7-2 install ok installed libblas-common libblas-common 3.7.0-2 install ok installed libblas3 libblas3 3.7.0-2 install ok installed libblkid1:amd64 libblkid1 2.29.2-1+deb9u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-8.1 install ok installed libc-bin libc-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 2.24-11+deb9u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2+deb9u1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libexpat1:amd64 libexpat1 2.2.0-2+deb9u3 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libffi6:amd64 libffi6 3.2.1-6 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u3 install ok installed libgfortran3:amd64 libgfortran3 6.3.0-18+deb9u1 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed libjs-jquery libjs-jquery 3.1.1-2+deb9u1 install ok installed libjs-sphinxdoc libjs-sphinxdoc 1.4.9-2 install ok installed libjs-underscore libjs-underscore 1.8.3~dfsg-1 install ok installed liblapack3 liblapack3 3.7.0-2 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+b1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+b1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.6 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.6 install ok installed libpam-runtime libpam-runtime 1.1.8-3.6 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.6 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libpython-stdlib:amd64 libpython-stdlib 2.7.13-2 install ok installed libpython2.7-minimal:amd64 libpython2.7-minimal 2.7.13-2+deb9u3 install ok installed libpython2.7-stdlib:amd64 libpython2.7-stdlib 2.7.13-2+deb9u3 install ok installed libquadmath0:amd64 libquadmath0 6.3.0-18+deb9u1 install ok installed libreadline7:amd64 libreadline7 7.0-3 install ok installed libselinux1:amd64 libselinux1 2.6-3+b3 install ok installed libsemanage-common libsemanage-common 2.6-2 install ok installed libsemanage1:amd64 libsemanage1 2.6-2 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.16.2-5+deb9u1 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u1 install ok installed libssl1.1:amd64 libssl1.1 1.1.0l-1~deb9u1 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u12 install ok installed libtbb2:amd64 libtbb2 4.3~20150611-2 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u12 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.29.2-1+deb9u1 install ok installed login login 1:4.4-4.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed metaphlan2 metaphlan2 2.6.0+ds-2 install ok installed metaphlan2-data metaphlan2-data 2.6.0+ds-2 install ok installed mime-support mime-support 3.60 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed ncurses-base ncurses-base 6.0+20161126-1+deb9u2 install ok installed ncurses-bin ncurses-bin 6.0+20161126-1+deb9u2 install ok installed passwd passwd 1:4.4-4.1 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed pyqi pyqi 0.3.2+dfsg-2 install ok installed python python 2.7.13-2 install ok installed python-biom-format python-biom-format 2.1.5+dfsg-7 install ok installed python-click python-click 6.6-1 install ok installed python-colorama python-colorama 0.3.7-1 install ok installed python-configparser python-configparser 3.3.0r2-2 install ok installed python-dateutil python-dateutil 2.5.3-2 install ok installed python-decorator python-decorator 4.0.11-1 install ok installed python-future python-future 0.15.2-4 install ok installed python-minimal python-minimal 2.7.13-2 install ok installed python-msgpack python-msgpack 0.4.8-1 install ok installed python-numpy python-numpy 1:1.12.1-3 install ok installed python-pandas python-pandas 0.19.2-5.1 install ok installed python-pandas-lib python-pandas-lib 0.19.2-5.1 install ok installed python-pkg-resources python-pkg-resources 33.1.1-1 install ok installed python-scipy python-scipy 0.18.1-2 install ok installed python-six python-six 1.10.0-3 install ok installed python-tz python-tz 2016.7-0.3 install ok installed python2.7 python2.7 2.7.13-2+deb9u3 install ok installed python2.7-minimal python2.7-minimal 2.7.13-2+deb9u3 install ok installed readline-common readline-common 7.0-3 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed sphinx-common sphinx-common 1.4.9-2 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59.9 install ok installed tar tar 1.29b-1.1 install ok installed tzdata tzdata 2020a-0+deb9u1 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5 32m45.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 32m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'apt-get', 'remove', 'bowtie2', 'libatomic1:amd64', 'libblas-common', 'libblas3', 'libexpat1:amd64', 'libffi6:amd64', 'libgfortran3:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'libsqlite3-0:amd64', 'libssl1.1:amd64', 'libtbb2:amd64', 'metaphlan2-data', 'mime-support', 'pyqi', 'python', 'python-biom-format', 'python-click', 'python-colorama', 'python-configparser', 'python-dateutil', 'python-decorator', 'python-future', 'python-minimal', 'python-msgpack', 'python-numpy', 'python-pandas', 'python-pandas-lib', 'python-pkg-resources', 'python-scipy', 'python-six', 'python-tz', 'python2.7', 'python2.7-minimal', 'readline-common', 'sphinx-common', 'tzdata', 'metaphlan2'] 32m47.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bowtie2 libatomic1 libblas-common libblas3 libexpat1 libffi6 libgfortran3 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 libsqlite3-0 libssl1.1 libtbb2 metaphlan2 metaphlan2-data mime-support pyqi python python-biom-format python-click python-colorama python-configparser python-dateutil python-decorator python-future python-minimal python-msgpack python-numpy python-pandas python-pandas-lib python-pkg-resources python-scipy python-six python-tz python2.7 python2.7-minimal readline-common sphinx-common tzdata 0 upgraded, 0 newly installed, 45 to remove and 0 not upgraded. After this operation, 979 MB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 10486 files and directories currently installed.) Removing metaphlan2 (2.6.0+ds-2) ... dpkg: warning: while removing metaphlan2, directory '/usr/share/metaphlan2/db_v20' not empty so not removed Removing metaphlan2-data (2.6.0+ds-2) ... Removing bowtie2 (2.3.0-2) ... Removing libtbb2:amd64 (4.3~20150611-2) ... Removing libatomic1:amd64 (6.3.0-18+deb9u1) ... Removing python-biom-format (2.1.5+dfsg-7) ... Removing python-scipy (0.18.1-2) ... Removing python-pandas (0.19.2-5.1) ... Removing python-pandas-lib (0.19.2-5.1) ... Removing python-numpy (1:1.12.1-3) ... Removing liblapack3 (3.7.0-2) ... Removing libblas3 (3.7.0-2) ... Removing libblas-common (3.7.0-2) ... Removing pyqi (0.3.2+dfsg-2) ... Removing python-dateutil (2.5.3-2) ... Removing python-six (1.10.0-3) ... Removing python-msgpack (0.4.8-1) ... Removing python-tz (2016.7-0.3) ... Removing libgfortran3:amd64 (6.3.0-18+deb9u1) ... Removing sphinx-common (1.4.9-2) ... Removing python-future (0.15.2-4) ... Removing python-configparser (3.3.0r2-2) ... Removing libjs-sphinxdoc (1.4.9-2) ... Removing libjs-jquery (3.1.1-2+deb9u1) ... Removing libjs-underscore (1.8.3~dfsg-1) ... Removing libquadmath0:amd64 (6.3.0-18+deb9u1) ... Removing python-click (6.6-1) ... Removing python-colorama (0.3.7-1) ... Removing python-decorator (4.0.11-1) ... Removing python-pkg-resources (33.1.1-1) ... Removing tzdata (2020a-0+deb9u1) ... Removing python (2.7.13-2) ... Removing python2.7 (2.7.13-2+deb9u3) ... Removing libpython-stdlib:amd64 (2.7.13-2) ... Removing libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ... Removing libexpat1:amd64 (2.2.0-2+deb9u3) ... Removing libffi6:amd64 (3.2.1-6) ... Removing python-minimal (2.7.13-2) ... Removing python2.7-minimal (2.7.13-2+deb9u3) ... Removing libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) ... Removing libreadline7:amd64 (7.0-3) ... Removing libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Removing libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Removing mime-support (3.60) ... Removing readline-common (7.0-3) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 32m47.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'apt-get', 'remove', 'bowtie2', 'libatomic1:amd64', 'libblas-common', 'libblas3', 'libexpat1:amd64', 'libffi6:amd64', 'libgfortran3:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'libsqlite3-0:amd64', 'libssl1.1:amd64', 'libtbb2:amd64', 'metaphlan2-data', 'mime-support', 'pyqi', 'python', 'python-biom-format', 'python-click', 'python-colorama', 'python-configparser', 'python-dateutil', 'python-decorator', 'python-future', 'python-minimal', 'python-msgpack', 'python-numpy', 'python-pandas', 'python-pandas-lib', 'python-pkg-resources', 'python-scipy', 'python-six', 'python-tz', 'python2.7', 'python2.7-minimal', 'readline-common', 'sphinx-common', 'tzdata', 'metaphlan2'] 32m47.0s INFO: Running scripts post_remove 32m47.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_remove_exceptions'] 32m47.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_remove_exceptions'] 32m47.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'dpkg', '--purge', 'bowtie2', 'libatomic1:amd64', 'libblas-common', 'libblas3', 'libexpat1:amd64', 'libffi6:amd64', 'libgfortran3:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'libsqlite3-0:amd64', 'libssl1.1:amd64', 'libtbb2:amd64', 'metaphlan2-data', 'mime-support', 'pyqi', 'python', 'python-biom-format', 'python-click', 'python-colorama', 'python-configparser', 'python-dateutil', 'python-decorator', 'python-future', 'python-minimal', 'python-msgpack', 'python-numpy', 'python-pandas', 'python-pandas-lib', 'python-pkg-resources', 'python-scipy', 'python-six', 'python-tz', 'python2.7', 'python2.7-minimal', 'readline-common', 'sphinx-common', 'tzdata'] 32m47.2s DUMP: dpkg: warning: ignoring request to remove bowtie2 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libblas-common which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libffi6 which isn't installed dpkg: warning: ignoring request to remove libgfortran3 which isn't installed dpkg: warning: ignoring request to remove libjs-jquery which isn't installed dpkg: warning: ignoring request to remove libjs-sphinxdoc which isn't installed dpkg: warning: ignoring request to remove libjs-underscore which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove libpython-stdlib which isn't installed (Reading database ... 4415 files and directories currently installed.) Purging configuration files for libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) ... dpkg: warning: ignoring request to remove libpython2.7-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline7 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed Purging configuration files for libssl1.1:amd64 (1.1.0l-1~deb9u1) ... dpkg: warning: ignoring request to remove libtbb2 which isn't installed Purging configuration files for metaphlan2-data (2.6.0+ds-2) ... Purging configuration files for mime-support (3.60) ... dpkg: warning: ignoring request to remove pyqi which isn't installed Purging configuration files for python (2.7.13-2) ... dpkg: warning: ignoring request to remove python-biom-format which isn't installed dpkg: warning: ignoring request to remove python-click which isn't installed dpkg: warning: ignoring request to remove python-colorama which isn't installed dpkg: warning: ignoring request to remove python-configparser which isn't installed dpkg: warning: ignoring request to remove python-dateutil which isn't installed dpkg: warning: ignoring request to remove python-decorator which isn't installed dpkg: warning: ignoring request to remove python-future which isn't installed dpkg: warning: ignoring request to remove python-minimal which isn't installed dpkg: warning: ignoring request to remove python-msgpack which isn't installed dpkg: warning: ignoring request to remove python-numpy which isn't installed dpkg: warning: ignoring request to remove python-pandas which isn't installed dpkg: warning: ignoring request to remove python-pandas-lib which isn't installed dpkg: warning: ignoring request to remove python-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python-scipy which isn't installed dpkg: warning: ignoring request to remove python-six which isn't installed dpkg: warning: ignoring request to remove python-tz which isn't installed dpkg: warning: ignoring request to remove python2.7 which isn't installed Purging configuration files for python2.7-minimal (2.7.13-2+deb9u3) ... Purging configuration files for readline-common (7.0-3) ... dpkg: warning: ignoring request to remove sphinx-common which isn't installed Purging configuration files for tzdata (2020a-0+deb9u1) ... 32m47.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'dpkg', '--purge', 'bowtie2', 'libatomic1:amd64', 'libblas-common', 'libblas3', 'libexpat1:amd64', 'libffi6:amd64', 'libgfortran3:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'libsqlite3-0:amd64', 'libssl1.1:amd64', 'libtbb2:amd64', 'metaphlan2-data', 'mime-support', 'pyqi', 'python', 'python-biom-format', 'python-click', 'python-colorama', 'python-configparser', 'python-dateutil', 'python-decorator', 'python-future', 'python-minimal', 'python-msgpack', 'python-numpy', 'python-pandas', 'python-pandas-lib', 'python-pkg-resources', 'python-scipy', 'python-six', 'python-tz', 'python2.7', 'python2.7-minimal', 'readline-common', 'sphinx-common', 'tzdata'] 32m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'dpkg', '--purge', 'metaphlan2'] 32m47.2s DUMP: dpkg: warning: ignoring request to remove metaphlan2 which isn't installed 32m47.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'dpkg', '--purge', 'metaphlan2'] 32m47.2s INFO: Running scripts post_purge 32m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_purge_exceptions'] 32m47.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_purge_exceptions'] 32m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'dpkg', '--purge', '--pending'] 32m47.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'dpkg', '--purge', '--pending'] 32m47.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'dpkg', '--remove', '--pending'] 32m47.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'dpkg', '--remove', '--pending'] 32m47.3s INFO: Running scripts post_test 32m47.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_test_exceptions'] 32m47.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'tmp/scripts/post_test_exceptions'] 32m47.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpww8kap73'] 32m47.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpww8kap73'] 32m47.9s DEBUG: No broken symlinks as far as we can find. 32m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'dpkg-divert', '--list'] 32m47.9s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 32m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'dpkg-divert', '--list'] 32m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'apt-get', 'clean'] 32m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpww8kap73', 'apt-get', 'clean'] 32m48.0s DEBUG: Recording chroot state 32m48.5s INFO: Warning: Package purging left files on system: /usr/share/metaphlan2/ owned by: metaphlan2 /usr/share/metaphlan2/db_v20/ owned by: metaphlan2 32m48.5s INFO: PASS: Installation and purging test. 32m48.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpww8kap73/dev/shm'] 32m48.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpww8kap73/dev/shm'] 32m48.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpww8kap73/dev/console'] 32m48.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpww8kap73/dev/console'] 32m48.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpww8kap73/dev/ptmx'] 32m48.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpww8kap73/dev/ptmx'] 32m48.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpww8kap73/dev/pts'] 32m48.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpww8kap73/dev/pts'] 32m48.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpww8kap73/proc'] 32m48.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpww8kap73/proc'] 32m48.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpww8kap73'] 32m48.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpww8kap73'] 32m48.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpww8kap73 32m48.9s INFO: PASS: All tests. 32m48.9s INFO: piuparts run ends. ret=0 End: 2023-02-18 11:34:04 GMT