Start: 2021-08-19 15:06:22 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-log-alternatives --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d bookworm --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 1.1.4 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 --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d bookworm --no-upgrade-test --apt metaphlan2-data=2.6.0+ds-4 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 4.19.0-17-amd64 #1 SMP Debian 4.19.194-3 (2021-07-18) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpvcdxnsw_ 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpvcdxnsw_ 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m1.7s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/proc'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/proc'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/dev/pts'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/dev/pts'] 0m1.7s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/dev/ptmx'] 0m1.8s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/dev/ptmx'] 0m1.8s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/dev/console'] 0m1.8s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/dev/console'] 0m1.8s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/dev/shm'] 0m1.8s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/dev/shm'] 0m1.8s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m1.8s DEBUG: Created policy-rc.d and chmodded it. 0m1.8s DEBUG: Created resolv.conf. 0m1.8s DEBUG: Copying scriptsdir /etc/piuparts/scripts-log-alternatives to /srv/piuparts.debian.org/tmp/tmpvcdxnsw_/tmp/scripts/ 0m1.8s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpvcdxnsw_/tmp/scripts/ 0m1.8s INFO: Running scripts post_chroot_unpack 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'apt-get', 'update'] 0m4.3s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [94.4 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8237 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [5661 kB] Fetched 14.0 MB in 2s (7813 kB/s) Reading package lists... 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'apt-get', 'update'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'apt-get', '-yf', 'dist-upgrade'] 0m5.1s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: libidn2-0 perl-base 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1724 kB of archives. After this operation, 50.2 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 perl-base amd64 5.32.1-5 [1629 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libidn2-0 amd64 2.3.2-2 [95.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1724 kB in 0s (30.3 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6653 files and directories currently installed.) Preparing to unpack .../perl-base_5.32.1-5_amd64.deb ... Unpacking perl-base (5.32.1-5) over (5.32.1-4) ... Setting up perl-base (5.32.1-5) ... (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 ... 6653 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.2-2_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.2-2) over (2.3.0-5) ... Setting up libidn2-0:amd64 (2.3.2-2) ... Processing triggers for libc-bin (2.31-13) ... 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'apt-get', '-yf', 'dist-upgrade'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.4s DUMP: 6378d4ed3f5863f20df468d1662028f6 - 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.4s INFO: Running scripts post_setup 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/post_setup_dummy_users'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/post_setup_dummy_users'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/post_setup_forbid_home'] 0m6.1s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/post_setup_forbid_home'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/post_setup_force-unsafe-io'] 0m6.1s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/post_setup_force-unsafe-io'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/post_setup_minimize'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/post_setup_minimize'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/post_setup_squeeze-backports'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/post_setup_squeeze-backports'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/post_setup_zz_backports'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/post_setup_zz_backports'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'apt-get', 'clean'] 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'apt-get', 'clean'] 0m6.2s DEBUG: Recording chroot state 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.5s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-3+b1 install ok installed bsdutils bsdutils 1:2.36.1-8 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20210120+802ebd4-1 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.9 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2 install ok installed grep grep 3.6-1 install ok installed gzip gzip 1.10-4 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13 install ok installed libc6:amd64 libc6 2.31-13 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.2-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2 install ok installed libmount1:amd64 libmount1 2.36.1-8 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9 install ok installed libpam-runtime libpam-runtime 1.4.0-9 install ok installed libpam0g:amd64 libpam0g 1.4.0-9 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1k-1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-6 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2 install ok installed libtirpc-common libtirpc-common 1.3.1-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1 install ok installed libudev1:amd64 libudev1 247.3-6 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8 install ok installed ncurses-base ncurses-base 6.2+20201114-2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-5 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2021a-1 install ok installed util-linux util-linux 2.36.1-8 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'dpkg-divert', '--list'] 0m6.5s 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 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'dpkg-divert', '--list'] 0m6.5s INFO: Running scripts is_testable 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/is_testable_uninstallable'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/is_testable_uninstallable'] 0m6.5s INFO: apt-cache does not know about any of the requested packages 0m6.5s INFO: Running scripts pre_test 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/pre_test_exceptions'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/pre_test_exceptions'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/pre_test_root_password'] 0m6.5s DUMP: New password: Retype new password: passwd: password updated successfully 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/pre_test_root_password'] 0m6.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_'] 0m6.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_'] 0m7.2s DEBUG: No broken symlinks as far as we can find. 0m7.2s INFO: Running scripts pre_install 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/pre_install_database-server'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/pre_install_database-server'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/pre_install_exceptions'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/pre_install_exceptions'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/pre_install_extras'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/pre_install_extras'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/pre_install_log_alternatives'] 0m7.3s DUMP: Adding 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' dpkg-divert: warning: diverting file '/usr/bin/update-alternatives' from an Essential package with rename is dangerous, use --no-rename 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/pre_install_log_alternatives'] 0m7.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_'] 0m7.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_'] 0m7.9s DEBUG: No broken symlinks as far as we can find. 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'apt-cache', 'policy'] 0m8.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release o=Debian,a=testing,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'apt-cache', 'policy'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'apt-cache', 'policy', 'metaphlan2-data'] 0m8.5s 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 bookworm/main amd64 Packages 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'apt-cache', 'policy', 'metaphlan2-data'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'apt-get', '-y', 'install', 'metaphlan2-data=2.6.0+ds-4'] 17m25.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: bowtie2 libexpat1 libgdbm-compat4 libgdbm6 libmpdec3 libncursesw6 libperl5.32 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 libsqlite3-0 libtbb2 media-types perl perl-modules-5.32 python3 python3-minimal python3.9 python3.9-minimal readline-common Suggested packages: bowtie2-examples gdbm-l10n sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv python3.9-venv python3.9-doc binutils binfmt-support readline-doc Recommended packages: libgpm2 ca-certificates netbase The following NEW packages will be installed: bowtie2 libexpat1 libgdbm-compat4 libgdbm6 libmpdec3 libncursesw6 libperl5.32 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 libsqlite3-0 libtbb2 media-types metaphlan2-data perl perl-modules-5.32 python3 python3-minimal python3.9 python3.9-minimal readline-common 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. Need to get 220 MB of archives. After this operation, 847 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 perl-modules-5.32 all 5.32.1-5 [2823 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libgdbm6 amd64 1.19-2 [64.9 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libgdbm-compat4 amd64 1.19-2 [44.7 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libperl5.32 amd64 5.32.1-5 [4125 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 perl amd64 5.32.1-5 [293 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 media-types all 4.0.0 [30.3 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 libmpdec3 amd64 2.5.1-2 [87.8 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.2+20201114-2 [132 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.1-2 [73.8 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.1-2 [168 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.34.1-3 [797 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libtbb2 amd64 2020.3-1 [161 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 bowtie2 amd64 2.4.2-2+b3 [1342 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 metaphlan2-data all 2.6.0+ds-4 [204 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 220 MB in 2s (141 MB/s) Selecting previously unselected package perl-modules-5.32. (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 ... 6656 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.32_5.32.1-5_all.deb ... Unpacking perl-modules-5.32 (5.32.1-5) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.19-2_amd64.deb ... Unpacking libgdbm6:amd64 (1.19-2) ... Selecting previously unselected package libgdbm-compat4:amd64. Preparing to unpack .../2-libgdbm-compat4_1.19-2_amd64.deb ... 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Setting up libperl5.32:amd64 (5.32.1-5) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up perl (5.32.1-5) ... Setting up python3.9 (3.9.2-1) ... Setting up python3 (3.9.2-3) ... Setting up bowtie2 (2.4.2-2+b3) ... Setting up metaphlan2-data (2.6.0+ds-4) ... 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: 00:00:05 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: 00:00:20 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: 00:00:10 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: 00:06:37 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: 00:09:24 Reading reference sizes Time reading reference sizes: 00:00:05 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: 00:00:16 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: 00:00:09 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: 00:05:10 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: 00:07:30 Metaphlan2 data are properly created. Processing triggers for libc-bin (2.31-13) ... 17m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'apt-get', '-y', 'install', 'metaphlan2-data=2.6.0+ds-4'] 17m25.7s INFO: Running scripts post_install 17m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/post_install_exceptions'] 17m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/post_install_exceptions'] 17m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/post_install_log_alternatives'] 17m25.7s DUMP: Removing 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' LOG-ALTERNATIVES: dpkg=python3: piuparts=metaphlan2-data=2.6.0+ds-4: /usr/bin/update-alternatives --auto /usr/bin/python3 LOG-ALTERNATIVES: dpkg=perl: piuparts=metaphlan2-data=2.6.0+ds-4: /usr/bin/update-alternatives --remove rename /usr/bin/prename 17m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', 'tmp/scripts/post_install_log_alternatives'] 17m25.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_'] 17m26.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_'] 17m27.1s DEBUG: No broken symlinks as far as we can find. 17m27.6s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', '-ac', '--ignore-obsolete'] 17m40.7s DUMP: debsums: missing file /srv/piuparts.debian.org/tmp/tmpvcdxnsw_/var/lib/metaphlan2-data/markers.fasta (from metaphlan2-data package) 17m40.7s DEBUG: Command failed (status=2), but ignoring error: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_', '-ac', '--ignore-obsolete'] 17m40.7s ERROR: FAIL: debsums reports modifications inside the chroot: debsums: missing file /var/lib/metaphlan2-data/markers.fasta (from metaphlan2-data package) 17m41.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/dev/shm'] 17m41.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/dev/shm'] 17m41.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/dev/console'] 17m41.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/dev/console'] 17m41.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/dev/ptmx'] 17m41.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/dev/ptmx'] 17m41.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/dev/pts'] 17m41.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/dev/pts'] 17m41.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/proc'] 17m41.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_/proc'] 17m41.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_'] 17m41.7s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpvcdxnsw_'] 17m41.7s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpvcdxnsw_ 17m41.7s ERROR: piuparts run ends. ret=1 End: 2021-08-19 15:24:03 GMT