Start: 2020-05-25 10:31:43 GMT 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/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --merged-usr -i /usr/lib32/ -i /usr/libx32/ --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_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 1.1.2~202004292038~1.1.1-19-g418151e2 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --merged-usr -i /usr/lib32/ -i /usr/libx32/ --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt metaphlan2-data=2.6.0+ds-4 0m0.0s INFO: Running on: Linux piu-slave-conova-01 4.19.0-9-amd64 #1 SMP Debian 4.19.118-2 (2020-04-29) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpknio0to7 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpknio0to7 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpknio0to7', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m1.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpknio0to7', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpknio0to7/proc'] 0m1.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpknio0to7/proc'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpknio0to7/dev/pts'] 0m1.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpknio0to7/dev/pts'] 0m1.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpknio0to7/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpknio0to7/dev/ptmx'] 0m1.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpknio0to7/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpknio0to7/dev/ptmx'] 0m1.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpknio0to7/dev/console'] 0m1.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpknio0to7/dev/console'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpknio0to7/dev/shm'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpknio0to7/dev/shm'] 0m1.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m1.5s DEBUG: Created policy-rc.d and chmodded it. 0m1.5s DEBUG: Created resolv.conf. 0m1.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpknio0to7/tmp/scripts/ 0m1.5s INFO: Running scripts post_chroot_unpack 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'apt-get', 'update'] 0m5.8s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [146 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [8226 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6188 kB] Fetched 14.6 MB in 3s (4352 kB/s) Reading package lists... 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'apt-get', 'update'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'apt-get', '-yf', 'dist-upgrade'] 0m6.7s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: debianutils 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 101 kB of archives. After this operation, 1024 B of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 debianutils amd64 4.10 [101 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 101 kB in 0s (1575 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6516 files and directories currently installed.) Preparing to unpack .../debianutils_4.10_amd64.deb ... Unpacking debianutils (4.10) over (4.9.3) ... Setting up debianutils (4.10) ... 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'apt-get', '-yf', 'dist-upgrade'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.2s DUMP: 02d58d06216e9791e9d7d84a9881d7d5 - 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.2s INFO: Running scripts post_setup 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/post_setup_dummy_users'] 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/post_setup_dummy_users'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/post_setup_forbid_home'] 0m8.8s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/post_setup_forbid_home'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.8s 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' 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/post_setup_minimize'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/post_setup_minimize'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/post_setup_zz_backports'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/post_setup_zz_backports'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'apt-get', 'clean'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'apt-get', 'clean'] 0m8.9s DEBUG: Recording chroot state 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.3s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 2.1.4 install ok installed base-files base-files 11 install ok installed base-passwd base-passwd 3.5.47 install ok installed bash bash 5.0-6 install ok installed bsdutils bsdutils 1:2.35.2-2 install ok installed coreutils coreutils 8.30-3+b1 install ok installed dash dash 0.5.10.2-7 install ok installed debconf debconf 1.5.74 install ok installed debian-archive-keyring debian-archive-keyring 2019.1 install ok installed debianutils debianutils 4.10 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.7 install ok installed e2fsprogs e2fsprogs 1.45.6-1 install ok installed findutils findutils 4.7.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.1.0-2 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-13 install ok installed gpgv gpgv 2.2.20-1 install ok installed grep grep 3.4-1 install ok installed gzip gzip 1.10-2 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.57 install ok installed libacl1:amd64 libacl1 2.2.53-8 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.1.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-5 install ok installed libaudit-common libaudit-common 1:2.8.5-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.5-3+b1 install ok installed libblkid1:amd64 libblkid1 2.35.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-2 install ok installed libc-bin libc-bin 2.30-8 install ok installed libc6:amd64 libc6 2.30-8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.1+b2 install ok installed libcom-err2:amd64 libcom-err2 1.45.6-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.16-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.252 install ok installed libext2fs2:amd64 libext2fs2 1.45.6-1 install ok installed libffi7:amd64 libffi7 3.3-4 install ok installed libgcc-s1:amd64 libgcc-s1 10.1.0-2 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.5-5 install ok installed libgmp10:amd64 libgmp10 2:6.2.0+dfsg-4 install ok installed libgnutls30:amd64 libgnutls30 3.6.13-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.37-1 install ok installed libhogweed5:amd64 libhogweed5 3.5.1+really3.5.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.2-2 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+b1 install ok installed libmount1:amd64 libmount1 2.35.2-2 install ok installed libnettle7:amd64 libnettle7 3.5.1+really3.5.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.20-1 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.34-7 install ok installed libpcre3:amd64 libpcre3 2:8.39-12+b1 install ok installed libseccomp2:amd64 libseccomp2 2.4.3-1+b1 install ok installed libselinux1:amd64 libselinux1 3.0-1+b3 install ok installed libsemanage-common libsemanage-common 3.0-1 install ok installed libsemanage1:amd64 libsemanage1 3.0-1+b3 install ok installed libsepol1:amd64 libsepol1 3.0-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.35.2-2 install ok installed libss2:amd64 libss2 1.45.6-1 install ok installed libstdc++6:amd64 libstdc++6 10.1.0-2 install ok installed libsystemd0:amd64 libsystemd0 245.5-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.2-1 install ok installed libudev1:amd64 libudev1 245.5-3 install ok installed libunistring2:amd64 libunistring2 0.9.10-2 install ok installed libuuid1:amd64 libuuid1 2.35.2-2 install ok installed libzstd1:amd64 libzstd1 1.4.4+dfsg-3 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.45.6-1 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.35.2-2 install ok installed ncurses-base ncurses-base 6.2-1 install ok installed ncurses-bin ncurses-bin 6.2-1 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.30.2-1 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-3 install ok installed tar tar 1.30+dfsg-7 install ok installed tzdata tzdata 2020a-1 install ok installed util-linux util-linux 2.35.2-2 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'dpkg-divert', '--list'] 0m9.3s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'dpkg-divert', '--list'] 0m9.3s INFO: Running scripts is_testable 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/is_testable_uninstallable'] 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/is_testable_uninstallable'] 0m9.3s INFO: apt-cache does not know about any of the requested packages 0m9.3s INFO: Running scripts pre_test 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/pre_test_exceptions'] 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/pre_test_exceptions'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/pre_test_root_password'] 0m9.4s DUMP: New password: Retype new password: passwd: password updated successfully 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/pre_test_root_password'] 0m9.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpknio0to7'] 0m9.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpknio0to7'] 0m10.6s DEBUG: No broken symlinks as far as we can find. 0m10.6s INFO: Running scripts pre_install 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/pre_install_database-server'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/pre_install_database-server'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/pre_install_exceptions'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/pre_install_exceptions'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/pre_install_extras'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/pre_install_extras'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/pre_install_foreign_architecture'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m10.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpknio0to7'] 0m11.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpknio0to7'] 0m11.9s DEBUG: No broken symlinks as far as we can find. 0m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'apt-cache', 'policy'] 0m12.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m12.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'apt-cache', 'policy'] 0m12.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'apt-cache', 'policy', 'metaphlan2-data'] 0m12.5s DUMP: metaphlan2-data: Installed: (none) Candidate: 2.6.0+ds-4 Version table: 2.6.0+ds-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m12.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'apt-cache', 'policy', 'metaphlan2-data'] 0m12.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'apt-get', '-y', 'install', 'metaphlan2-data=2.6.0+ds-4'] 12m37.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: bowtie2 libexpat1 libgdbm-compat4 libgdbm6 libmpdec2 libncursesw6 libperl5.30 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libreadline8 libsqlite3-0 libssl1.1 libtbb2 mime-support perl perl-modules-5.30 python3 python3-minimal python3.8 python3.8-minimal readline-common Suggested packages: bowtie2-examples gdbm-l10n sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libb-debug-perl liblocale-codes-perl libtap-harness-archive-perl python3-doc python3-tk python3-venv python3.8-venv python3.8-doc binutils binfmt-support readline-doc Recommended packages: libgpm2 bzip2 file xz-utils netbase The following NEW packages will be installed: bowtie2 libexpat1 libgdbm-compat4 libgdbm6 libmpdec2 libncursesw6 libperl5.30 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libreadline8 libsqlite3-0 libssl1.1 libtbb2 metaphlan2-data mime-support perl perl-modules-5.30 python3 python3-minimal python3.8 python3.8-minimal readline-common 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. Need to get 221 MB of archives. After this operation, 850 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 perl-modules-5.30 all 5.30.2-1 [2806 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libgdbm6 amd64 1.18.1-5 [64.5 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4 amd64 1.18.1-5 [44.2 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libperl5.30 amd64 5.30.2-1 [4024 kB] Get:5 http://deb.debian.org/debian sid/main amd64 perl amd64 5.30.2-1 [290 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libssl1.1 amd64 1.1.1g-1 [1543 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libpython3.8-minimal amd64 3.8.3-1 [760 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.2.9-1 [94.3 kB] Get:9 http://deb.debian.org/debian sid/main amd64 python3.8-minimal amd64 3.8.3-1 [1943 kB] Get:10 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.8.2-3 [37.6 kB] Get:11 http://deb.debian.org/debian sid/main amd64 mime-support all 3.64 [37.8 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libmpdec2 amd64 2.4.2-3 [84.1 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.2-1 [133 kB] Get:14 http://deb.debian.org/debian sid/main amd64 readline-common all 8.0-4 [72.5 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libreadline8 amd64 8.0-4 [160 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.32.0-2 [756 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libpython3.8-stdlib amd64 3.8.3-1 [1668 kB] Get:18 http://deb.debian.org/debian sid/main amd64 python3.8 amd64 3.8.3-1 [416 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.8.2-3 [20.8 kB] Get:20 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.8.2-3 [63.7 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libtbb2 amd64 2020.2-2 [160 kB] Get:22 http://deb.debian.org/debian sid/main amd64 bowtie2 amd64 2.4.1-4 [1338 kB] Get:23 http://deb.debian.org/debian sid/main amd64 metaphlan2-data all 2.6.0+ds-4 [204 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 221 MB in 2s (112 MB/s) Selecting previously unselected package perl-modules-5.30. 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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: 00:00:04 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:03 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: 00:00:05 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:08 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: 00:03:24 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: 00:06:04 Reading reference sizes Time reading reference sizes: 00:00:03 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:04 Time to reverse reference sequence: 00:00:00 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: 00:03:21 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: 00:05:57 Metaphlan2 data are properly created. Processing triggers for libc-bin (2.30-8) ... 12m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'apt-get', '-y', 'install', 'metaphlan2-data=2.6.0+ds-4'] 12m37.0s INFO: Running scripts post_install 12m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/post_install_exceptions'] 12m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpknio0to7', 'tmp/scripts/post_install_exceptions'] 12m37.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpknio0to7'] 12m37.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpknio0to7'] 12m38.3s DEBUG: No broken symlinks as far as we can find. 12m38.4s INFO: /bin converted to /usr/bin by /usr merge 12m38.4s INFO: /lib converted to /usr/lib by /usr merge 12m38.4s INFO: /lib/init converted to /usr/lib/init by /usr merge 12m38.4s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 12m38.4s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 12m38.4s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 12m38.4s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 12m38.4s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 12m38.4s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 12m38.4s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 12m38.4s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 12m38.4s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 12m38.4s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 12m38.4s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 12m38.4s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 12m38.4s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 12m38.4s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 12m38.4s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 12m38.4s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 12m38.4s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 12m38.4s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 12m38.4s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 12m38.4s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 12m38.4s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 12m38.4s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 12m38.4s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 12m38.4s INFO: /lib64 converted to /usr/lib64 by /usr merge 12m38.4s INFO: /sbin converted to /usr/sbin by /usr merge 12m38.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpknio0to7', '-ac', '--ignore-obsolete'] 12m40.7s DUMP: debsums: missing file /srv/piuparts.debian.org/tmp/tmpknio0to7/var/lib/metaphlan2-data/markers.fasta (from metaphlan2-data package) 12m40.7s DEBUG: Command failed (status=2), but ignoring error: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpknio0to7', '-ac', '--ignore-obsolete'] 12m40.7s ERROR: FAIL: debsums reports modifications inside the chroot: debsums: missing file /var/lib/metaphlan2-data/markers.fasta (from metaphlan2-data package) 12m41.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpknio0to7/dev/shm'] 12m41.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpknio0to7/dev/shm'] 12m41.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpknio0to7/dev/console'] 12m41.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpknio0to7/dev/console'] 12m41.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpknio0to7/dev/ptmx'] 12m41.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpknio0to7/dev/ptmx'] 12m41.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpknio0to7/dev/pts'] 12m41.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpknio0to7/dev/pts'] 12m41.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpknio0to7/proc'] 12m41.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpknio0to7/proc'] 12m41.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpknio0to7'] 12m41.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpknio0to7'] 12m41.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpknio0to7 12m41.6s ERROR: piuparts run ends. ret=1 End: 2020-05-25 10:44:25 GMT