Start: 2023-01-30 07:52:55 GMT [stretch] Package: smrtanalysis Version: 0~20161126 Installed-Size: 9 Maintainer: Debian Med Packaging Team Architecture: all Depends: pbbamtools, pbh5tools, pbbarcode, pbalign, blasr, pbdagcon, pbgenomicconsensus, kineticstools, falcon Description: software suite for single molecule, real-time sequencing Homepage: http://www.pacb.com/products-and-services/analytical-software/smrt-analysis/ Description-md5: 07f41ceb2de8cc7b1a670a30f40ef08a Section: science Priority: optional Filename: pool/main/s/smrtanalysis/smrtanalysis_0~20161126_all.deb Size: 2518 MD5sum: d83fc2b339ff007ad9f20ef104729b0f SHA256: 2f75de7e8c1b732b3a82eb4802f1de3cfc20cd93e43af90440ccc24102ada7e8 [buster] Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --upgrade-before-dist-upgrade --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/stretch_amd64.tar.gz -d stretch -d buster -B /srv/piuparts.debian.org/slave/refchroot/stretch2Xbuster/reference-chroot-metadata.dat --apt smrtanalysis=None 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 --upgrade-before-dist-upgrade --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/stretch_amd64.tar.gz -d stretch -d buster -B /srv/piuparts.debian.org/slave/refchroot/stretch2Xbuster/reference-chroot-metadata.dat --apt smrtanalysis=None 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/tmptp7cv_q0 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmptp7cv_q0 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/proc'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/proc'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/dev/pts'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/dev/pts'] 0m1.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/dev/ptmx'] 0m1.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/dev/ptmx'] 0m1.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/dev/console'] 0m1.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/dev/console'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/dev/shm'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/dev/shm'] 0m1.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m1.3s DEBUG: Created policy-rc.d and chmodded it. 0m1.3s DEBUG: Created resolv.conf. 0m1.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmptp7cv_q0/tmp/scripts/ 0m1.3s INFO: Running scripts post_chroot_unpack 0m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-get', 'update'] 0m2.0s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-get', 'update'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.7s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.7s INFO: Running scripts post_setup 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_setup_dummy_users'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_setup_dummy_users'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_setup_forbid_home'] 0m3.4s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_setup_forbid_home'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.4s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_setup_minimize'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_setup_minimize'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_setup_zz_backports'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_setup_zz_backports'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.4s 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 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.4s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stretch2Xbuster/reference-chroot-metadata.dat 0m3.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0'] 0m3.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0'] 0m3.8s INFO: Running scripts is_testable 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/is_testable_uninstallable'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/is_testable_uninstallable'] 0m3.8s INFO: Running scripts pre_test 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_test_exceptions'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_test_exceptions'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_test_root_password'] 0m3.8s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_test_root_password'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-cache', 'show', '--no-all-versions', 'smrtanalysis'] 0m4.0s DUMP: Package: smrtanalysis Version: 0~20161126 Installed-Size: 9 Maintainer: Debian Med Packaging Team Architecture: all Depends: pbbamtools, pbh5tools, pbbarcode, pbalign, blasr, pbdagcon, pbgenomicconsensus, kineticstools, falcon Description-en: software suite for single molecule, real-time sequencing SMRT? Analysis is a powerful, open-source bioinformatics software suite available for analysis of DNA sequencing data from Pacific Biosciences?? SMRT technology. Users can choose from a variety of analysis protocols that utilize PacBio? and third-party tools. Analysis protocols include de novo genome assembly, cDNA mapping, DNA base-modification detection, and long-amplicon analysis to determine phased consensus sequences. . This is a metapackage that depends on the components of SMRT Analysis. Description-md5: 07f41ceb2de8cc7b1a670a30f40ef08a Homepage: http://www.pacb.com/products-and-services/analytical-software/smrt-analysis/ Section: science Priority: optional Filename: pool/main/s/smrtanalysis/smrtanalysis_0~20161126_all.deb Size: 2518 MD5sum: d83fc2b339ff007ad9f20ef104729b0f SHA256: 2f75de7e8c1b732b3a82eb4802f1de3cfc20cd93e43af90440ccc24102ada7e8 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-cache', 'show', '--no-all-versions', 'smrtanalysis'] 0m4.0s INFO: apt-cache knows about the following packages: smrtanalysis 0m4.0s INFO: Running scripts pre_install 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_install_database-server'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_install_database-server'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_install_exceptions'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_install_exceptions'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_install_extras'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_install_extras'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-cache', 'policy'] 0m4.1s 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: 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-cache', 'policy'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-cache', 'policy', 'smrtanalysis'] 0m4.1s DUMP: smrtanalysis: Installed: (none) Candidate: 0~20161126 Version table: 0~20161126 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-cache', 'policy', 'smrtanalysis'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-get', '-y', 'install', 'smrtanalysis'] 0m20.8s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: blasr ca-certificates falcon kineticstools kineticstools-data libaec0 libblas-common libblas3 libblasr libcurl3-gnutls libexpat1 libffi6 libgfortran3 libgmp10 libgnutls30 libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100 libhogweed4 libhts1 libidn11 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common libnettle6 libnghttp2-14 libp11-kit0 libpbbam libpbdata libpbihdf libpbseq libpopt0 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libsz2 libtasn1-6 libunistring0 lsb-base mime-support openssl pbalign pbbamtools pbbarcode pbdagcon pbgenomicconsensus pbh5tools python python-avro python-chardet python-decorator python-h5py python-iso8601 python-kineticstools python-minimal python-networkx python-numpy python-pbalign python-pbcommand python-pbconsensuscore python-pbcore python-pbgenomicconsensus python-pbh5tools python-pkg-resources python-pysam python-requests python-scipy python-six python-urllib3 python2.7 python2.7-minimal readline-common rsync time Suggested packages: gnutls-bin krb5-doc krb5-user bowtie2 gmap pbalign-doc python-doc python-tk python-h5py-doc python-pybigwig python-networkx-doc gcc gfortran python-dev python-nose python-numpy-dbg python-numpy-doc python-pbcore-doc python-consensuscore2 python-setuptools python-cryptography python-idna python-openssl python-socks python-scipy-doc python-ntlm python2.7-doc binutils binfmt-support readline-doc openssh-client openssh-server Recommended packages: krb5-locales publicsuffix libsasl2-modules bzip2 file xz-utils hdf5-tools samtools python-consensuscore2 python-matplotlib python-pygraphviz | python-pydot python-yaml g++ | c++-compiler python-dev python-imaging python-cryptography python-idna python-ipaddress python-openssl The following NEW packages will be installed: blasr ca-certificates falcon kineticstools kineticstools-data libaec0 libblas-common libblas3 libblasr libcurl3-gnutls libexpat1 libffi6 libgfortran3 libgmp10 libgnutls30 libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100 libhogweed4 libhts1 libidn11 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common libnettle6 libnghttp2-14 libp11-kit0 libpbbam libpbdata libpbihdf libpbseq libpopt0 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libsz2 libtasn1-6 libunistring0 lsb-base mime-support openssl pbalign pbbamtools pbbarcode pbdagcon pbgenomicconsensus pbh5tools python python-avro python-chardet python-decorator python-h5py python-iso8601 python-kineticstools python-minimal python-networkx python-numpy python-pbalign python-pbcommand python-pbconsensuscore python-pbcore python-pbgenomicconsensus python-pbh5tools python-pkg-resources python-pysam python-requests python-scipy python-six python-urllib3 python2.7 python2.7-minimal readline-common rsync smrtanalysis time 0 upgraded, 89 newly installed, 0 to remove and 0 not upgraded. Need to get 145 MB of archives. After this operation, 257 MB of additional disk space will be used. 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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 lsb-base all 9.20161125 [27.9 kB] Get:16 http://deb.debian.org/debian stretch/main amd64 libpopt0 amd64 1.16-10+b2 [49.4 kB] Get:17 http://deb.debian.org/debian stretch/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1 [253 kB] Get:18 http://deb.debian.org/debian stretch/main amd64 libnettle6 amd64 3.3-1+b2 [192 kB] Get:19 http://deb.debian.org/debian stretch/main amd64 libhogweed4 amd64 3.3-1+b2 [136 kB] Get:20 http://deb.debian.org/debian stretch/main amd64 libidn11 amd64 1.33-1+deb9u1 [115 kB] Get:21 http://deb.debian.org/debian stretch/main amd64 libp11-kit0 amd64 0.23.3-2 [111 kB] Get:22 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0.10.0+ds-2 [1301 kB] Get:74 http://deb.debian.org/debian stretch/main amd64 python-pbcore all 1.2.11+dfsg-1 [9087 kB] Get:75 http://deb.debian.org/debian stretch/main amd64 python-scipy amd64 0.18.1-2 [8933 kB] Get:76 http://deb.debian.org/debian stretch/main amd64 kineticstools-data all 0.6.1+20161222-1 [102 MB] Get:77 http://deb.debian.org/debian stretch/main amd64 python-kineticstools amd64 0.6.1+20161222-1 [49.3 kB] Get:78 http://deb.debian.org/debian stretch/main amd64 kineticstools all 0.6.1+20161222-1 [13.3 kB] Get:79 http://deb.debian.org/debian stretch/main amd64 python-pbalign all 0.3.0-1 [37.2 kB] Get:80 http://deb.debian.org/debian stretch/main amd64 pbalign all 0.3.0-1 [7482 B] Get:81 http://deb.debian.org/debian stretch/main amd64 pbbamtools amd64 0.7.4+ds-1 [116 kB] Get:82 http://deb.debian.org/debian stretch/main amd64 pbbarcode amd64 0.8.0-4 [26.5 kB] Get:83 http://deb.debian.org/debian stretch/main amd64 pbdagcon amd64 0.3+20161121+ds-1 [322 kB] Get:84 http://deb.debian.org/debian stretch/main amd64 python-pbconsensuscore amd64 1.0.2-2 [651 kB] Get:85 http://deb.debian.org/debian stretch/main amd64 python-pbgenomicconsensus all 2.1.0-1 [45.7 kB] Get:86 http://deb.debian.org/debian stretch/main amd64 pbgenomicconsensus all 2.1.0-1 [26.6 kB] Get:87 http://deb.debian.org/debian stretch/main amd64 python-pbh5tools amd64 0.8.0+dfsg-5 [29.0 kB] Get:88 http://deb.debian.org/debian stretch/main amd64 pbh5tools all 0.8.0+dfsg-5 [8282 B] Get:89 http://deb.debian.org/debian stretch/main amd64 smrtanalysis all 0~20161126 [2518 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 145 MB in 1s (137 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 ... 4411 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. 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Unpacking libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Selecting previously unselected package libquadmath0:amd64. Preparing to unpack .../19-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 .../20-libgfortran3_6.3.0-18+deb9u1_amd64.deb ... Unpacking libgfortran3:amd64 (6.3.0-18+deb9u1) ... Selecting previously unselected package libaec0:amd64. Preparing to unpack .../21-libaec0_0.3.2-1_amd64.deb ... Unpacking libaec0:amd64 (0.3.2-1) ... Selecting previously unselected package libsz2:amd64. Preparing to unpack .../22-libsz2_0.3.2-1_amd64.deb ... Unpacking libsz2:amd64 (0.3.2-1) ... Selecting previously unselected package libhdf5-100:amd64. Preparing to unpack .../23-libhdf5-100_1.10.0-patch1+docs-3+deb9u1_amd64.deb ... Unpacking libhdf5-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Selecting previously unselected package libhdf5-cpp-100:amd64. 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Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../30-libssh2-1_1.7.0-1+deb9u1_amd64.deb ... Unpacking libssh2-1:amd64 (1.7.0-1+deb9u1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../31-libcurl3-gnutls_7.52.1-5+deb9u10_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Selecting previously unselected package libhts1:amd64. Preparing to unpack .../32-libhts1_1.3.2-2_amd64.deb ... Unpacking libhts1:amd64 (1.3.2-2) ... Selecting previously unselected package libpbbam:amd64. Preparing to unpack .../33-libpbbam_0.7.4+ds-1_amd64.deb ... Unpacking libpbbam:amd64 (0.7.4+ds-1) ... Selecting previously unselected package libpbdata:amd64. Preparing to unpack .../34-libpbdata_0~20161219-1_amd64.deb ... Unpacking libpbdata:amd64 (0~20161219-1) ... Selecting previously unselected package libpbihdf:amd64. Preparing to unpack .../35-libpbihdf_0~20161219-1_amd64.deb ... Unpacking libpbihdf:amd64 (0~20161219-1) ... Selecting previously unselected package libblasr:amd64. Preparing to unpack .../36-libblasr_0~20161219-1_amd64.deb ... Unpacking libblasr:amd64 (0~20161219-1) ... Selecting previously unselected package libpbseq. Preparing to unpack .../37-libpbseq_0~20161219-1_all.deb ... Unpacking libpbseq (0~20161219-1) ... Selecting previously unselected package blasr. Preparing to unpack .../38-blasr_5.3+0-1_amd64.deb ... Unpacking blasr (5.3+0-1) ... Selecting previously unselected package openssl. Preparing to unpack .../39-openssl_1.1.0l-1~deb9u1_amd64.deb ... Unpacking openssl (1.1.0l-1~deb9u1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../40-ca-certificates_20200601~deb9u1_all.deb ... Unpacking ca-certificates (20200601~deb9u1) ... Selecting previously unselected package python-pkg-resources. Preparing to unpack .../41-python-pkg-resources_33.1.1-1_all.deb ... Unpacking python-pkg-resources (33.1.1-1) ... Selecting previously unselected package python-decorator. Preparing to unpack .../42-python-decorator_4.0.11-1_all.deb ... Unpacking python-decorator (4.0.11-1) ... Selecting previously unselected package python-networkx. Preparing to unpack .../43-python-networkx_1.11-2_all.deb ... Unpacking python-networkx (1.11-2) ... Selecting previously unselected package rsync. Preparing to unpack .../44-rsync_3.1.2-1+deb9u2_amd64.deb ... Unpacking rsync (3.1.2-1+deb9u2) ... Selecting previously unselected package time. Preparing to unpack .../45-time_1.7-25.1+b1_amd64.deb ... Unpacking time (1.7-25.1+b1) ... Selecting previously unselected package falcon. Preparing to unpack .../46-falcon_1.8.6-1.1_amd64.deb ... Unpacking falcon (1.8.6-1.1) ... Selecting previously unselected package libblas-common. Preparing to unpack .../47-libblas-common_3.7.0-2_amd64.deb ... Unpacking libblas-common (3.7.0-2) ... Selecting previously unselected package libblas3. Preparing to unpack .../48-libblas3_3.7.0-2_amd64.deb ... Unpacking libblas3 (3.7.0-2) ... Selecting previously unselected package liblapack3. Preparing to unpack .../49-liblapack3_3.7.0-2_amd64.deb ... Unpacking liblapack3 (3.7.0-2) ... Selecting previously unselected package python-numpy. Preparing to unpack .../50-python-numpy_1%3a1.12.1-3_amd64.deb ... Unpacking python-numpy (1:1.12.1-3) ... Selecting previously unselected package python-six. Preparing to unpack .../51-python-six_1.10.0-3_all.deb ... Unpacking python-six (1.10.0-3) ... Selecting previously unselected package python-h5py. Preparing to unpack .../52-python-h5py_2.7.0-1_amd64.deb ... Unpacking python-h5py (2.7.0-1) ... Selecting previously unselected package python-avro. Preparing to unpack .../53-python-avro_1.8.1+dfsg-1_all.deb ... Unpacking python-avro (1.8.1+dfsg-1) ... Selecting previously unselected package python-iso8601. Preparing to unpack .../54-python-iso8601_0.1.11-1_all.deb ... Unpacking python-iso8601 (0.1.11-1) ... Selecting previously unselected package python-urllib3. Preparing to unpack .../55-python-urllib3_1.19.1-1_all.deb ... Unpacking python-urllib3 (1.19.1-1) ... Selecting previously unselected package python-chardet. Preparing to unpack .../56-python-chardet_2.3.0-2_all.deb ... Unpacking python-chardet (2.3.0-2) ... Selecting previously unselected package python-requests. Preparing to unpack .../57-python-requests_2.12.4-1_all.deb ... Unpacking python-requests (2.12.4-1) ... Selecting previously unselected package python-pbcommand. Preparing to unpack .../58-python-pbcommand_0.5.3-1_all.deb ... Unpacking python-pbcommand (0.5.3-1) ... Selecting previously unselected package python-pysam. Preparing to unpack .../59-python-pysam_0.10.0+ds-2_amd64.deb ... Unpacking python-pysam (0.10.0+ds-2) ... Selecting previously unselected package python-pbcore. Preparing to unpack .../60-python-pbcore_1.2.11+dfsg-1_all.deb ... Unpacking python-pbcore (1.2.11+dfsg-1) ... Selecting previously unselected package python-scipy. Preparing to unpack .../61-python-scipy_0.18.1-2_amd64.deb ... Unpacking python-scipy (0.18.1-2) ... Selecting previously unselected package kineticstools-data. Preparing to unpack .../62-kineticstools-data_0.6.1+20161222-1_all.deb ... Unpacking kineticstools-data (0.6.1+20161222-1) ... Selecting previously unselected package python-kineticstools. Preparing to unpack .../63-python-kineticstools_0.6.1+20161222-1_amd64.deb ... Unpacking python-kineticstools (0.6.1+20161222-1) ... Selecting previously unselected package kineticstools. Preparing to unpack .../64-kineticstools_0.6.1+20161222-1_all.deb ... Unpacking kineticstools (0.6.1+20161222-1) ... Selecting previously unselected package python-pbalign. Preparing to unpack .../65-python-pbalign_0.3.0-1_all.deb ... Unpacking python-pbalign (0.3.0-1) ... Selecting previously unselected package pbalign. Preparing to unpack .../66-pbalign_0.3.0-1_all.deb ... Unpacking pbalign (0.3.0-1) ... Selecting previously unselected package pbbamtools. Preparing to unpack .../67-pbbamtools_0.7.4+ds-1_amd64.deb ... Unpacking pbbamtools (0.7.4+ds-1) ... Selecting previously unselected package pbbarcode. Preparing to unpack .../68-pbbarcode_0.8.0-4_amd64.deb ... Unpacking pbbarcode (0.8.0-4) ... Selecting previously unselected package pbdagcon. Preparing to unpack .../69-pbdagcon_0.3+20161121+ds-1_amd64.deb ... Unpacking pbdagcon (0.3+20161121+ds-1) ... Selecting previously unselected package python-pbconsensuscore. Preparing to unpack .../70-python-pbconsensuscore_1.0.2-2_amd64.deb ... Unpacking python-pbconsensuscore (1.0.2-2) ... Selecting previously unselected package python-pbgenomicconsensus. Preparing to unpack .../71-python-pbgenomicconsensus_2.1.0-1_all.deb ... Unpacking python-pbgenomicconsensus (2.1.0-1) ... Selecting previously unselected package pbgenomicconsensus. Preparing to unpack .../72-pbgenomicconsensus_2.1.0-1_all.deb ... Unpacking pbgenomicconsensus (2.1.0-1) ... Selecting previously unselected package python-pbh5tools. Preparing to unpack .../73-python-pbh5tools_0.8.0+dfsg-5_amd64.deb ... Unpacking python-pbh5tools (0.8.0+dfsg-5) ... Selecting previously unselected package pbh5tools. Preparing to unpack .../74-pbh5tools_0.8.0+dfsg-5_all.deb ... Unpacking pbh5tools (0.8.0+dfsg-5) ... Selecting previously unselected package smrtanalysis. Preparing to unpack .../75-smrtanalysis_0~20161126_all.deb ... Unpacking smrtanalysis (0~20161126) ... Setting up libquadmath0:amd64 (6.3.0-18+deb9u1) ... Setting up readline-common (7.0-3) ... Setting up libnettle6:amd64 (3.3-1+b2) ... Setting up libpopt0:amd64 (1.16-10+b2) ... Setting up libaec0:amd64 (0.3.2-1) ... Setting up libexpat1:amd64 (2.2.0-2+deb9u3) ... Setting up libnghttp2-14:amd64 (1.18.1-1+deb9u1) ... Setting up time (1.7-25.1+b1) ... Setting up mime-support (3.60) ... Setting up libldap-common (2.4.44+dfsg-5+deb9u4) ... Setting up kineticstools-data (0.6.1+20161222-1) ... Setting up libreadline7:amd64 (7.0-3) ... Setting up libblas-common (3.7.0-2) ... Setting up libgfortran3:amd64 (6.3.0-18+deb9u1) ... Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Setting up lsb-base (9.20161125) ... Setting up rsync (3.1.2-1+deb9u2) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up libgmp10:amd64 (2:6.1.2+dfsg-1) ... 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 Setting up libssh2-1:amd64 (1.7.0-1+deb9u1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Setting up libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Setting up openssl (1.1.0l-1~deb9u1) ... Setting up libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Setting up libffi6:amd64 (3.2.1-6) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up ca-certificates (20200601~deb9u1) ... Updating certificates in /etc/ssl/certs... 126 added, 0 removed; done. Setting up libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ... Setting up libidn11:amd64 (1.33-1+deb9u1) ... Setting up libsz2:amd64 (0.3.2-1) ... Setting up libidn2-0:amd64 (0.16-1+deb9u1) ... Setting up libhdf5-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Setting up libpsl5:amd64 (0.17.0-3) ... 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 libkrb5support0:amd64 (1.15-1+deb9u1) ... Setting up libhogweed4:amd64 (3.3-1+b2) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up libp11-kit0:amd64 (0.23.3-2) ... Setting up python (2.7.13-2) ... Setting up libk5crypto3:amd64 (1.15-1+deb9u1) ... Setting up libhdf5-cpp-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Setting up libgnutls30:amd64 (3.5.8-5+deb9u5) ... Setting up python-avro (1.8.1+dfsg-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Setting up python-pkg-resources (33.1.1-1) ... Setting up python-numpy (1:1.12.1-3) ... Setting up python-six (1.10.0-3) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Setting up python-iso8601 (0.1.11-1) ... Setting up libkrb5-3:amd64 (1.15-1+deb9u1) ... Setting up python-decorator (4.0.11-1) ... Setting up python-pbconsensuscore (1.0.2-2) ... Setting up python-urllib3 (1.19.1-1) ... Setting up python-h5py (2.7.0-1) ... Setting up python-networkx (1.11-2) ... Setting up python-chardet (2.3.0-2) ... Setting up python-scipy (0.18.1-2) ... Setting up libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Setting up python-requests (2.12.4-1) ... Setting up python-pbcommand (0.5.3-1) ... Setting up falcon (1.8.6-1.1) ... Setting up libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Setting up libhts1:amd64 (1.3.2-2) ... Setting up python-pysam (0.10.0+ds-2) ... Setting up python-pbcore (1.2.11+dfsg-1) ... Setting up libpbbam:amd64 (0.7.4+ds-1) ... Setting up python-kineticstools (0.6.1+20161222-1) ... Setting up kineticstools (0.6.1+20161222-1) ... Setting up python-pbh5tools (0.8.0+dfsg-5) ... Setting up pbbarcode (0.8.0-4) ... Setting up pbh5tools (0.8.0+dfsg-5) ... Setting up python-pbgenomicconsensus (2.1.0-1) ... Setting up pbbamtools (0.7.4+ds-1) ... Setting up libpbdata:amd64 (0~20161219-1) ... Setting up libpbihdf:amd64 (0~20161219-1) ... Setting up pbgenomicconsensus (2.1.0-1) ... Setting up libblasr:amd64 (0~20161219-1) ... Setting up libpbseq (0~20161219-1) ... Setting up pbdagcon (0.3+20161121+ds-1) ... Setting up blasr (5.3+0-1) ... Setting up python-pbalign (0.3.0-1) ... Setting up pbalign (0.3.0-1) ... Setting up smrtanalysis (0~20161126) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Processing triggers for ca-certificates (20200601~deb9u1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-get', '-y', 'install', 'smrtanalysis'] 0m20.8s INFO: Running scripts post_install 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_install_exceptions'] 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_install_exceptions'] 0m20.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0'] 0m21.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0'] 0m21.3s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmptp7cv_q0 to buster 0m21.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main 0m21.3s INFO: Running scripts pre_distupgrade 0m21.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m21.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m21.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_distupgrade_exceptions'] 0m21.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_distupgrade_exceptions'] 0m21.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m21.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m21.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m21.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m21.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m21.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m21.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-get', 'update'] 0m24.0s DUMP: Get:1 http://deb.debian.org/debian buster InRelease [122 kB] Get:2 http://deb.debian.org/debian buster/main amd64 Packages [7909 kB] Get:3 http://deb.debian.org/debian buster/main Translation-en [5969 kB] Fetched 14.0 MB in 2s (6735 kB/s) Reading package lists... 0m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-get', 'update'] 0m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-get', '-y', 'upgrade'] 0m43.4s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages have been kept back: apt bash blasr dash dpkg e2fslibs e2fsprogs libapt-pkg5.0 libblas3 libblasr libcomerr2 libcurl3-gnutls libgcc1 libgnutls30 libgssapi-krb5-2 libidn2-0 libk5crypto3 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libncursesw5 libpbdata libpbihdf libpbseq libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 libss2 libstdc++6 libtinfo5 login mount ncurses-base ncurses-bin pbbamtools pbdagcon python python-h5py python-minimal python-pbcommand python-pysam python-requests python-scipy python-urllib3 python2.7 python2.7-minimal util-linux The following packages will be upgraded: adduser base-files base-passwd bsdutils ca-certificates coreutils debconf debian-archive-keyring debianutils diffutils findutils gpgv grep gzip hostname init-system-helpers kineticstools kineticstools-data libacl1 libaec0 libattr1 libaudit-common libaudit1 libblkid1 libbz2-1.0 libc-bin libc6 libcap-ng0 libdb5.3 libdebconfclient0 libexpat1 libfdisk1 libffi6 libgcrypt20 libgmp10 libgpg-error0 libhogweed4 libidn11 libkeyutils1 libldap-common liblz4-1 liblzma5 libmount1 libnettle6 libnghttp2-14 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre3 libpopt0 librtmp1 libsasl2-2 libsasl2-modules-db libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libssh2-1 libssl1.1 libsystemd0 libsz2 libtasn1-6 libudev1 libuuid1 lsb-base mime-support multiarch-support openssl passwd pbalign pbbarcode pbgenomicconsensus pbh5tools perl-base python-avro python-chardet python-decorator python-kineticstools python-networkx python-numpy python-pbalign python-pbconsensuscore python-pbcore python-pbgenomicconsensus python-pbh5tools python-pkg-resources python-six readline-common rsync sed sensible-utils sysvinit-utils tar zlib1g 98 upgraded, 0 newly installed, 0 to remove and 51 not upgraded. Need to get 140 MB of archives. After this operation, 19.0 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian buster/main amd64 base-files amd64 10.3+deb10u13 [69.9 kB] Get:2 http://deb.debian.org/debian buster/main amd64 bsdutils amd64 1:2.33.1-0.1 [121 kB] Get:3 http://deb.debian.org/debian buster/main amd64 libc6 amd64 2.28-10+deb10u1 [2863 kB] Get:4 http://deb.debian.org/debian buster/main amd64 libc-bin amd64 2.28-10+deb10u1 [795 kB] Get:5 http://deb.debian.org/debian buster/main amd64 coreutils amd64 8.30-3 [2708 kB] Get:6 http://deb.debian.org/debian buster/main amd64 debianutils amd64 4.8.6.1 [100 kB] Get:7 http://deb.debian.org/debian buster/main amd64 diffutils amd64 1:3.7-3 [371 kB] Get:8 http://deb.debian.org/debian buster/main amd64 findutils amd64 4.6.0+git+20190209-2 [684 kB] Get:9 http://deb.debian.org/debian buster/main amd64 grep amd64 3.3-1 [373 kB] Get:10 http://deb.debian.org/debian buster/main amd64 gzip amd64 1.9-3+deb10u1 [128 kB] Get:11 http://deb.debian.org/debian buster/main amd64 hostname amd64 3.21 [14.8 kB] Get:12 http://deb.debian.org/debian buster/main amd64 perl-base amd64 5.28.1-6+deb10u1 [1514 kB] Get:13 http://deb.debian.org/debian buster/main amd64 sed amd64 4.7-1 [310 kB] Get:14 http://deb.debian.org/debian buster/main amd64 tar amd64 1.30+dfsg-6 [780 kB] Get:15 http://deb.debian.org/debian buster/main amd64 libdebconfclient0 amd64 0.249 [49.1 kB] Get:16 http://deb.debian.org/debian buster/main amd64 base-passwd amd64 3.5.46 [56.7 kB] Get:17 http://deb.debian.org/debian buster/main amd64 init-system-helpers all 1.56+nmu1 [46.8 kB] Get:18 http://deb.debian.org/debian buster/main amd64 sysvinit-utils amd64 2.93-8 [78.4 kB] Get:19 http://deb.debian.org/debian buster/main amd64 debconf all 1.5.71+deb10u1 [145 kB] Get:20 http://deb.debian.org/debian buster/main amd64 libaudit-common all 1:2.8.4-3 [22.4 kB] Get:21 http://deb.debian.org/debian buster/main amd64 libcap-ng0 amd64 0.7.9-2 [14.3 kB] Get:22 http://deb.debian.org/debian buster/main amd64 libaudit1 amd64 1:2.8.4-3 [57.3 kB] Get:23 http://deb.debian.org/debian buster/main amd64 libpam0g amd64 1.3.1-5 [126 kB] Get:24 http://deb.debian.org/debian buster/main amd64 libpcre3 amd64 2:8.39-12 [341 kB] Get:25 http://deb.debian.org/debian buster/main amd64 libselinux1 amd64 2.8-1+b1 [86.9 kB] Get:26 http://deb.debian.org/debian buster/main amd64 libpam-modules-bin amd64 1.3.1-5 [107 kB] Get:27 http://deb.debian.org/debian buster/main amd64 libpam-modules amd64 1.3.1-5 [309 kB] Get:28 http://deb.debian.org/debian buster/main amd64 libgpg-error0 amd64 1.35-1 [71.1 kB] Get:29 http://deb.debian.org/debian buster/main amd64 libgcrypt20 amd64 1.8.4-5+deb10u1 [556 kB] Get:30 http://deb.debian.org/debian buster/main amd64 libsystemd0 amd64 241-7~deb10u8 [331 kB] Get:31 http://deb.debian.org/debian buster/main amd64 libpam-runtime all 1.3.1-5 [211 kB] Get:32 http://deb.debian.org/debian buster/main amd64 libsepol1 amd64 2.8-1 [263 kB] Get:33 http://deb.debian.org/debian buster/main amd64 libsemanage-common all 2.8-2 [17.7 kB] Get:34 http://deb.debian.org/debian buster/main amd64 libsemanage1 amd64 2.8-2 [96.5 kB] Get:35 http://deb.debian.org/debian buster/main amd64 libbz2-1.0 amd64 1.0.6-9.2~deb10u1 [45.3 kB] Get:36 http://deb.debian.org/debian buster/main amd64 passwd amd64 1:4.5-1.1 [1005 kB] Get:37 http://deb.debian.org/debian buster/main amd64 adduser all 3.118 [240 kB] Get:38 http://deb.debian.org/debian buster/main amd64 debian-archive-keyring all 2019.1+deb10u1 [93.5 kB] Get:39 http://deb.debian.org/debian buster/main amd64 zlib1g amd64 1:1.2.11.dfsg-1+deb10u1 [90.8 kB] Get:40 http://deb.debian.org/debian buster/main amd64 gpgv amd64 2.2.12-1+deb10u2 [584 kB] Get:41 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:42 http://deb.debian.org/debian buster/main amd64 libattr1 amd64 1:2.4.48-4 [21.3 kB] Get:43 http://deb.debian.org/debian buster/main amd64 libacl1 amd64 2.2.53-4 [30.4 kB] Get:44 http://deb.debian.org/debian buster/main amd64 libuuid1 amd64 2.33.1-0.1 [78.3 kB] Get:45 http://deb.debian.org/debian buster/main amd64 libblkid1 amd64 2.33.1-0.1 [195 kB] Get:46 http://deb.debian.org/debian buster/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.5 [683 kB] Get:47 http://deb.debian.org/debian buster/main amd64 libfdisk1 amd64 2.33.1-0.1 [234 kB] Get:48 http://deb.debian.org/debian buster/main amd64 liblz4-1 amd64 1.8.3-1+deb10u1 [53.3 kB] Get:49 http://deb.debian.org/debian buster/main amd64 liblzma5 amd64 5.2.4-1+deb10u1 [153 kB] Get:50 http://deb.debian.org/debian buster/main amd64 libmount1 amd64 2.33.1-0.1 [207 kB] Get:51 http://deb.debian.org/debian buster/main amd64 libsmartcols1 amd64 2.33.1-0.1 [150 kB] Get:52 http://deb.debian.org/debian buster/main amd64 libudev1 amd64 241-7~deb10u8 [151 kB] Get:53 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get:54 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get:55 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1n-0+deb10u3 [1551 kB] Get:56 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1n-0+deb10u3 [855 kB] Get:57 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get:58 http://deb.debian.org/debian buster/main amd64 python-pkg-resources all 40.8.0-1 [182 kB] Get:59 http://deb.debian.org/debian buster/main amd64 python-pbcore all 1.6.5+dfsg-1 [9100 kB] Get:60 http://deb.debian.org/debian buster/main amd64 python-numpy amd64 1:1.16.2-1 [2101 kB] Get:61 http://deb.debian.org/debian buster/main amd64 python-kineticstools amd64 0.6.1+git20180425.27a1878-2 [49.5 kB] Get:62 http://deb.debian.org/debian buster/main amd64 kineticstools-data all 0.6.1+git20180425.27a1878-2 [103 MB] Get:63 http://deb.debian.org/debian buster/main amd64 kineticstools all 0.6.1+git20180425.27a1878-2 [14.3 kB] Get:64 http://deb.debian.org/debian buster/main amd64 libaec0 amd64 1.0.2-1 [20.1 kB] Get:65 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u4 [108 kB] Get:66 http://deb.debian.org/debian buster/main amd64 libffi6 amd64 3.2.1-9 [20.8 kB] Get:67 http://deb.debian.org/debian buster/main amd64 libgmp10 amd64 2:6.1.2+dfsg-4+deb10u1 [251 kB] Get:68 http://deb.debian.org/debian buster/main amd64 libhogweed4 amd64 3.4.1-1+deb10u1 [141 kB] Get:69 http://deb.debian.org/debian buster/main amd64 libnettle6 amd64 3.4.1-1+deb10u1 [215 kB] Get:70 http://deb.debian.org/debian buster/main amd64 libidn11 amd64 1.33-2.2 [116 kB] Get:71 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get:72 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u7 [90.1 kB] Get:73 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get:74 http://deb.debian.org/debian buster/main amd64 libp11-kit0 amd64 0.23.15-2+deb10u1 [316 kB] Get:75 http://deb.debian.org/debian buster/main amd64 libpopt0 amd64 1.16-12 [49.4 kB] Get:76 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get:77 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u2 [69.2 kB] Get:78 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u2 [106 kB] Get:79 http://deb.debian.org/debian buster/main amd64 libsqlite3-0 amd64 3.27.2-3+deb10u1 [641 kB] Get:80 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:81 http://deb.debian.org/debian buster/main amd64 libsz2 amd64 1.0.2-1 [6676 B] Get:82 http://deb.debian.org/debian buster/main amd64 libtasn1-6 amd64 4.13-3 [51.9 kB] Get:83 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get:84 http://deb.debian.org/debian buster/main amd64 multiarch-support amd64 2.28-10+deb10u1 [216 kB] Get:85 http://deb.debian.org/debian buster/main amd64 python-pbalign all 0.3.2-1 [37.4 kB] Get:86 http://deb.debian.org/debian buster/main amd64 pbalign all 0.3.2-1 [9512 B] Get:87 http://deb.debian.org/debian buster/main amd64 pbbarcode amd64 0.8.0-5 [26.8 kB] Get:88 http://deb.debian.org/debian buster/main amd64 python-pbconsensuscore amd64 1.1.1+dfsg-1 [672 kB] Get:89 http://deb.debian.org/debian buster/main amd64 pbgenomicconsensus all 2.3.2-5 [34.3 kB] Get:90 http://deb.debian.org/debian buster/main amd64 python-pbgenomicconsensus all 2.3.2-5 [47.2 kB] Get:91 http://deb.debian.org/debian buster/main amd64 python-pbh5tools amd64 0.8.0+git20170929.58d54ff+dfsg-1 [29.5 kB] Get:92 http://deb.debian.org/debian buster/main amd64 pbh5tools all 0.8.0+git20170929.58d54ff+dfsg-1 [8796 B] Get:93 http://deb.debian.org/debian buster/main amd64 python-avro all 1.8.2+dfsg-2 [59.4 kB] Get:94 http://deb.debian.org/debian buster/main amd64 python-chardet all 3.0.4-3 [80.6 kB] Get:95 http://deb.debian.org/debian buster/main amd64 python-decorator all 4.3.0-1.1 [14.4 kB] Get:96 http://deb.debian.org/debian buster/main amd64 python-networkx all 2.2-1 [1020 kB] Get:97 http://deb.debian.org/debian buster/main amd64 python-six all 1.12.0-1 [15.7 kB] Get:98 http://deb.debian.org/debian buster/main amd64 rsync amd64 3.1.3-6 [397 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 140 MB in 1s (129 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 ... 9177 files and directories currently installed.) Preparing to unpack .../base-files_10.3+deb10u13_amd64.deb ... Unpacking base-files (10.3+deb10u13) over (9.9+deb9u13) ... Setting up base-files (10.3+deb10u13) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... (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 ... 9178 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.33.1-0.1_amd64.deb ... Unpacking bsdutils (1:2.33.1-0.1) over (1:2.29.2-1+deb9u1) ... Setting up bsdutils (1:2.33.1-0.1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9176 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.6.1_amd64.deb ... Unpacking debianutils (4.8.6.1) over (4.8.1.1) ... Setting up debianutils (4.8.6.1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9178 files and directories currently installed.) Preparing to unpack .../findutils_4.6.0+git+20190209-2_amd64.deb ... Unpacking findutils (4.6.0+git+20190209-2) over (4.6.0+git+20161106-2) ... Setting up findutils (4.6.0+git+20190209-2) ... (Reading database ... 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Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-buster-security-automatic.gpg ... Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-buster-stable.gpg ... Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-stretch-automatic.gpg ... Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-stretch-security-automatic.gpg ... Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-stretch-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-jessie-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-jessie-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-jessie-stable.gpg ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9224 files and directories currently installed.) Preparing to unpack .../libuuid1_2.33.1-0.1_amd64.deb ... Unpacking libuuid1:amd64 (2.33.1-0.1) over (2.29.2-1+deb9u1) ... Setting up libuuid1:amd64 (2.33.1-0.1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9224 files and directories currently installed.) Preparing to unpack .../libfdisk1_2.33.1-0.1_amd64.deb ... Unpacking libfdisk1:amd64 (2.33.1-0.1) over (2.29.2-1+deb9u1) ... Setting up libfdisk1:amd64 (2.33.1-0.1) ... (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 ... 9224 files and directories currently installed.) Preparing to unpack .../liblz4-1_1.8.3-1+deb10u1_amd64.deb ... Unpacking liblz4-1:amd64 (1.8.3-1+deb10u1) over (0.0~r131-2+b1) ... Setting up liblz4-1:amd64 (1.8.3-1+deb10u1) ... (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 ... 9223 files and directories currently installed.) Preparing to unpack .../liblzma5_5.2.4-1+deb10u1_amd64.deb ... Unpacking liblzma5:amd64 (5.2.4-1+deb10u1) over (5.2.2-1.2+b1) ... Setting up liblzma5:amd64 (5.2.4-1+deb10u1) ... (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 ... 9222 files and directories currently installed.) Preparing to unpack .../libmount1_2.33.1-0.1_amd64.deb ... Unpacking libmount1:amd64 (2.33.1-0.1) over (2.29.2-1+deb9u1) ... Setting up libmount1:amd64 (2.33.1-0.1) ... (Reading database ... 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Unpacking rsync (3.1.3-6) over (3.1.2-1+deb9u2) ... Setting up readline-common (7.0-5) ... Setting up libnettle6:amd64 (3.4.1-1+deb10u1) ... Setting up libpopt0:amd64 (1.16-12) ... Setting up libaec0:amd64 (1.0.2-1) ... Setting up libexpat1:amd64 (2.2.6-2+deb10u4) ... Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up mime-support (3.62) ... Installing new version of config file /etc/mime.types ... Setting up libldap-common (2.4.47+dfsg-3+deb10u7) ... Setting up kineticstools-data (0.6.1+git20180425.27a1878-2) ... Setting up multiarch-support (2.28-10+deb10u1) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u2) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u2) ... Setting up python-avro (1.8.2+dfsg-2) ... Setting up python-pkg-resources (40.8.0-1) ... Setting up python-numpy (1:1.16.2-1) ... Setting up libtasn1-6:amd64 (4.13-3) ... Setting up lsb-base (10.2019051400) ... Setting up rsync (3.1.3-6) ... Installing new version of config file /etc/init.d/rsync ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up libgmp10:amd64 (2:6.1.2+dfsg-4+deb10u1) ... Setting up python-six (1.12.0-1) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... Setting up libssl1.1:amd64 (1.1.1n-0+deb10u3) ... Setting up python-pbcore (1.6.5+dfsg-1) ... Setting up openssl (1.1.1n-0+deb10u3) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up libsqlite3-0:amd64 (3.27.2-3+deb10u1) ... Setting up libffi6:amd64 (3.2.1-9) ... Setting up python-decorator (4.3.0-1.1) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 11 added, 0 removed; done. Setting up libidn11:amd64 (1.33-2.2) ... Setting up python-pbconsensuscore (1.1.1+dfsg-1) ... Setting up python-kineticstools (0.6.1+git20180425.27a1878-2) ... Setting up libsz2:amd64 (1.0.2-1) ... Setting up kineticstools (0.6.1+git20180425.27a1878-2) ... Setting up python-pbh5tools (0.8.0+git20170929.58d54ff+dfsg-1) ... Setting up python-networkx (2.2-1) ... Setting up pbbarcode (0.8.0-5) ... Setting up python-chardet (3.0.4-3) ... Setting up pbh5tools (0.8.0+git20170929.58d54ff+dfsg-1) ... Setting up python-pbgenomicconsensus (2.3.2-5) ... Setting up python-pbalign (0.3.2-1) ... Setting up libhogweed4:amd64 (3.4.1-1+deb10u1) ... Setting up pbalign (0.3.2-1) ... Setting up libp11-kit0:amd64 (0.23.15-2+deb10u1) ... Setting up pbgenomicconsensus (2.3.2-5) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... Processing triggers for ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m43.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-get', '-y', 'upgrade'] 0m43.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-get', '-yf', 'dist-upgrade'] 0m53.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libblas-common libgfortran3 libhts1 libidn11 libunistring0 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libhdf5-100 libhdf5-cpp-100 libpbbam The following NEW packages will be installed: fdisk gcc-8-base libcom-err2 libdeflate0 libext2fs2 libgfortran5 libhdf5-103 libhdf5-cpp-103 libhts2 libncursesw6 libpbbam0.19.0 libpython2-stdlib libseccomp2 libtinfo6 libunistring2 libzstd1 python-certifi python-idna python-tz python2 python2-minimal tzdata The following packages will be upgraded: apt bash blasr dash dpkg e2fslibs e2fsprogs libapt-pkg5.0 libblas3 libblasr libcomerr2 libcurl3-gnutls libgcc1 libgnutls30 libgssapi-krb5-2 libidn2-0 libk5crypto3 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libncursesw5 libpbdata libpbihdf libpbseq libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 libss2 libstdc++6 libtinfo5 login mount ncurses-base ncurses-bin pbbamtools pbdagcon python python-h5py python-minimal python-pbcommand python-pysam python-requests python-scipy python-urllib3 python2.7 python2.7-minimal util-linux 51 upgraded, 22 newly installed, 3 to remove and 0 not upgraded. Need to get 39.3 MB of archives. After this operation, 16.0 MB of additional disk space will be used. 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amd64 2.7.16-2+deb10u1 [1912 kB] Get:44 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get:45 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get:46 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get:47 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get:48 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get:49 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get:50 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get:51 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get:52 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u4 [158 kB] Get:53 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u4 [369 kB] Get:54 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u4 [122 kB] Get:55 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u4 [65.9 kB] Get:56 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u7 [224 kB] Get:57 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:58 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get:59 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get:60 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get:61 http://deb.debian.org/debian buster/main amd64 pbbamtools amd64 0.19.0+dfsg-4 [150 kB] Get:62 http://deb.debian.org/debian buster/main amd64 libpbdata amd64 5.3.1+dfsg-2.1 [130 kB] Get:63 http://deb.debian.org/debian buster/main amd64 libpbseq all 5.3.1+dfsg-2.1 [4584 B] Get:64 http://deb.debian.org/debian buster/main amd64 libhdf5-cpp-103 amd64 1.10.4+repack-10 [146 kB] Get:65 http://deb.debian.org/debian buster/main amd64 libpbbam0.19.0 amd64 0.19.0+dfsg-4 [551 kB] Get:66 http://deb.debian.org/debian buster/main amd64 libss2 amd64 1.44.5-1+deb10u3 [72.9 kB] Get:67 http://deb.debian.org/debian buster/main amd64 tzdata all 2021a-0+deb10u6 [265 kB] Get:68 http://deb.debian.org/debian buster/main amd64 python-certifi all 2018.8.24-1 [140 kB] Get:69 http://deb.debian.org/debian buster/main amd64 python-idna all 2.6-1 [34.1 kB] Get:70 http://deb.debian.org/debian buster/main amd64 python-requests all 2.21.0-1 [67.1 kB] Get:71 http://deb.debian.org/debian buster/main amd64 python-urllib3 all 1.24.1-1 [97.0 kB] Get:72 http://deb.debian.org/debian buster/main amd64 python-tz all 2019.1-1 [33.6 kB] Get:73 http://deb.debian.org/debian buster/main amd64 python-pbcommand all 1.1.1-1 [88.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 39.3 MB in 0s (125 MB/s) Selecting previously unselected package libtinfo6: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 ... 9444 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libtinfo6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libtinfo6:amd64 (6.1+20181013-2+deb10u2) ... (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 ... 9454 files and directories currently installed.) Preparing to unpack .../archives/bash_5.0-4_amd64.deb ... Unpacking bash (5.0-4) over (4.4-5) ... Setting up bash (5.0-4) ... Installing new version of config file /etc/bash.bashrc ... Installing new version of config file /etc/skel/.profile ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode Selecting previously unselected package libzstd1: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 ... 9455 files and directories currently installed.) Preparing to unpack .../libzstd1_1.3.8+dfsg-3+deb10u2_amd64.deb ... Unpacking libzstd1:amd64 (1.3.8+dfsg-3+deb10u2) ... Setting up libzstd1:amd64 (1.3.8+dfsg-3+deb10u2) ... Selecting previously unselected package libunistring2: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 ... 9461 files and directories currently installed.) Preparing to unpack .../libunistring2_0.9.10-1_amd64.deb ... Unpacking libunistring2:amd64 (0.9.10-1) ... Setting up libunistring2:amd64 (0.9.10-1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9492 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.6.7-4+deb10u8_amd64.deb ... Unpacking libgnutls30:amd64 (3.6.7-4+deb10u8) over (3.5.8-5+deb9u5) ... Setting up libgnutls30:amd64 (3.6.7-4+deb10u8) ... Selecting previously unselected package libseccomp2:amd64. (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9499 files and directories currently installed.) Preparing to unpack .../gcc-8-base_8.3.0-6_amd64.deb ... Unpacking gcc-8-base:amd64 (8.3.0-6) ... Setting up gcc-8-base:amd64 (8.3.0-6) ... (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 ... 9505 files and directories currently installed.) Preparing to unpack .../libgcc1_1%3a8.3.0-6_amd64.deb ... Unpacking libgcc1:amd64 (1:8.3.0-6) over (1:6.3.0-18+deb9u1) ... Setting up libgcc1:amd64 (1:8.3.0-6) ... (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 ... 9505 files and directories currently installed.) Preparing to unpack .../libstdc++6_8.3.0-6_amd64.deb ... Unpacking libstdc++6:amd64 (8.3.0-6) over (6.3.0-18+deb9u1) ... Setting up libstdc++6:amd64 (8.3.0-6) ... (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 ... 9505 files and directories currently installed.) Preparing to unpack .../archives/apt_1.8.2.3_amd64.deb ... Unpacking apt (1.8.2.3) over (1.4.10) ... Preparing to unpack .../libapt-pkg5.0_1.8.2.3_amd64.deb ... Unpacking libapt-pkg5.0:amd64 (1.8.2.3) over (1.4.10) ... Setting up libapt-pkg5.0:amd64 (1.8.2.3) ... (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 ... 9533 files and directories currently installed.) Preparing to unpack .../archives/dpkg_1.19.8_amd64.deb ... Unpacking dpkg (1.19.8) over (1.18.25) ... Setting up dpkg (1.19.8) ... Installing new version of config file /etc/alternatives/README ... Installing new version of config file /etc/cron.daily/dpkg ... Installing new version of config file /etc/logrotate.d/dpkg ... (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 ... 9531 files and directories currently installed.) Preparing to unpack .../dash_0.5.10.2-5_amd64.deb ... Unpacking dash (0.5.10.2-5) over (0.5.8-2.4) ... Setting up dash (0.5.10.2-5) ... (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 ... 9532 files and directories currently installed.) Preparing to unpack .../libcomerr2_1.44.5-1+deb10u3_amd64.deb ... Unpacking libcomerr2:amd64 (1.44.5-1+deb10u3) over (1.43.4-2+deb9u1) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../libcom-err2_1.44.5-1+deb10u3_amd64.deb ... Unpacking libcom-err2:amd64 (1.44.5-1+deb10u3) ... Setting up libcom-err2:amd64 (1.44.5-1+deb10u3) ... (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 ... 9535 files and directories currently installed.) Preparing to unpack .../e2fslibs_1.44.5-1+deb10u3_amd64.deb ... Unpacking e2fslibs:amd64 (1.44.5-1+deb10u3) over (1.43.4-2+deb9u1) ... Selecting previously unselected package libext2fs2:amd64. Preparing to unpack .../libext2fs2_1.44.5-1+deb10u3_amd64.deb ... Unpacking libext2fs2:amd64 (1.44.5-1+deb10u3) ... Setting up libext2fs2:amd64 (1.44.5-1+deb10u3) ... (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 ... 9538 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.44.5-1+deb10u3_amd64.deb ... Unpacking e2fsprogs (1.44.5-1+deb10u3) over (1.43.4-2+deb9u1) ... Setting up e2fsprogs (1.44.5-1+deb10u3) ... Installing new version of config file /etc/mke2fs.conf ... Selecting previously unselected package libncursesw6: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 ... 9521 files and directories currently installed.) Preparing to unpack .../libncursesw6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncursesw6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libncursesw6:amd64 (6.1+20181013-2+deb10u2) ... (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 ... 9530 files and directories currently installed.) Preparing to unpack .../mount_2.33.1-0.1_amd64.deb ... Unpacking mount (2.33.1-0.1) over (2.29.2-1+deb9u1) ... Preparing to unpack .../util-linux_2.33.1-0.1_amd64.deb ... Unpacking util-linux (2.33.1-0.1) over (2.29.2-1+deb9u1) ... Replacing files in old package login (1:4.4-4.1) ... Selecting previously unselected package fdisk. Preparing to unpack .../fdisk_2.33.1-0.1_amd64.deb ... Unpacking fdisk (2.33.1-0.1) ... Setting up fdisk (2.33.1-0.1) ... (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 ... 9547 files and directories currently installed.) Preparing to unpack .../login_1%3a4.5-1.1_amd64.deb ... Unpacking login (1:4.5-1.1) over (1:4.4-4.1) ... Setting up login (1:4.5-1.1) ... Installing new version of config file /etc/securetty ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9537 files and directories currently installed.) Preparing to unpack .../libtinfo5_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libtinfo5:amd64 (6.1+20181013-2+deb10u2) over (6.0+20161126-1+deb9u2) ... Setting up libtinfo5:amd64 (6.1+20181013-2+deb10u2) ... (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 ... 9535 files and directories currently installed.) Preparing to unpack .../libncursesw5_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncursesw5:amd64 (6.1+20181013-2+deb10u2) over (6.0+20161126-1+deb9u2) ... Setting up libncursesw5:amd64 (6.1+20181013-2+deb10u2) ... (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 ... 9535 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.1+20181013-2+deb10u2_all.deb ... Unpacking ncurses-base (6.1+20181013-2+deb10u2) over (6.0+20161126-1+deb9u2) ... Setting up ncurses-base (6.1+20181013-2+deb10u2) ... (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 ... 9537 files and directories currently installed.) Preparing to unpack .../0-libquadmath0_8.3.0-6_amd64.deb ... Unpacking libquadmath0:amd64 (8.3.0-6) over (6.3.0-18+deb9u1) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../1-libgfortran5_8.3.0-6_amd64.deb ... Unpacking libgfortran5:amd64 (8.3.0-6) ... Preparing to unpack .../2-libblasr_5.3.1+dfsg-2.1_amd64.deb ... Unpacking libblasr:amd64 (5.3.1+dfsg-2.1) over (0~20161219-1) ... Preparing to unpack .../3-libpbihdf_5.3.1+dfsg-2.1_amd64.deb ... Unpacking libpbihdf:amd64 (5.3.1+dfsg-2.1) over (0~20161219-1) ... Preparing to unpack .../4-blasr_5.3.2+dfsg-1.1_amd64.deb ... Unpacking blasr (5.3.2+dfsg-1.1) over (5.3+0-1) ... Preparing to unpack .../5-pbdagcon_0.3+git20161121.0000000+ds-1.1_amd64.deb ... Unpacking pbdagcon (0.3+git20161121.0000000+ds-1.1) over (0.3+20161121+ds-1) ... Preparing to unpack .../6-python-h5py_2.8.0-3_amd64.deb ... Unpacking python-h5py (2.8.0-3) over (2.7.0-1) ... (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 ... 9523 files and directories currently installed.) Removing libhdf5-cpp-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Removing libhdf5-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Selecting previously unselected package libhdf5-103: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 ... 9499 files and directories currently installed.) Preparing to unpack .../00-libhdf5-103_1.10.4+repack-10_amd64.deb ... Unpacking libhdf5-103:amd64 (1.10.4+repack-10) ... Preparing to unpack .../01-libblas3_3.8.0-2_amd64.deb ... Unpacking libblas3:amd64 (3.8.0-2) over (3.7.0-2) ... Preparing to unpack .../02-liblapack3_3.8.0-2_amd64.deb ... Unpacking liblapack3:amd64 (3.8.0-2) over (3.7.0-2) ... Preparing to unpack .../03-python-scipy_1.1.0-7_amd64.deb ... Unpacking python-scipy (1.1.0-7) over (0.18.1-2) ... Preparing to unpack .../04-python2.7_2.7.16-2+deb10u1_amd64.deb ... Unpacking python2.7 (2.7.16-2+deb10u1) over (2.7.13-2+deb9u3) ... Preparing to unpack .../05-libreadline7_7.0-5_amd64.deb ... Unpacking libreadline7:amd64 (7.0-5) over (7.0-3) ... Preparing to unpack .../06-python-pysam_0.15.2+ds-2_amd64.deb ... Unpacking python-pysam (0.15.2+ds-2) over (0.10.0+ds-2) ... Preparing to unpack .../07-libpython2.7-stdlib_2.7.16-2+deb10u1_amd64.deb ... Unpacking libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) over (2.7.13-2+deb9u3) ... Preparing to unpack .../08-python2.7-minimal_2.7.16-2+deb10u1_amd64.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) over (2.7.13-2+deb9u3) ... Preparing to unpack .../09-libpython2.7-minimal_2.7.16-2+deb10u1_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) over (2.7.13-2+deb9u3) ... Preparing to unpack .../10-python-minimal_2.7.16-1_amd64.deb ... Unpacking python-minimal (2.7.16-1) over (2.7.13-2) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../11-python2-minimal_2.7.16-1_amd64.deb ... Unpacking python2-minimal (2.7.16-1) ... Setting up libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... (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 ... 9451 files and directories currently installed.) Preparing to unpack .../00-python_2.7.16-1_amd64.deb ... Unpacking python (2.7.16-1) over (2.7.13-2) ... Preparing to unpack .../01-libpython-stdlib_2.7.16-1_amd64.deb ... Unpacking libpython-stdlib:amd64 (2.7.16-1) over (2.7.13-2) ... Selecting previously unselected package libpython2-stdlib:amd64. Preparing to unpack .../02-libpython2-stdlib_2.7.16-1_amd64.deb ... Unpacking libpython2-stdlib:amd64 (2.7.16-1) ... Selecting previously unselected package python2. Preparing to unpack .../03-python2_2.7.16-1_amd64.deb ... Unpacking python2 (2.7.16-1) ... Preparing to unpack .../04-libgssapi-krb5-2_1.17-3+deb10u4_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.17-3+deb10u4) over (1.15-1+deb9u1) ... Preparing to unpack .../05-libkrb5-3_1.17-3+deb10u4_amd64.deb ... Unpacking libkrb5-3:amd64 (1.17-3+deb10u4) over (1.15-1+deb9u1) ... Preparing to unpack .../06-libk5crypto3_1.17-3+deb10u4_amd64.deb ... Unpacking libk5crypto3:amd64 (1.17-3+deb10u4) over (1.15-1+deb9u1) ... Preparing to unpack .../07-libkrb5support0_1.17-3+deb10u4_amd64.deb ... Unpacking libkrb5support0:amd64 (1.17-3+deb10u4) over (1.15-1+deb9u1) ... Preparing to unpack .../08-libldap-2.4-2_2.4.47+dfsg-3+deb10u7_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u7) over (2.4.44+dfsg-5+deb9u4) ... Preparing to unpack .../09-libpsl5_0.20.2-2_amd64.deb ... Unpacking libpsl5:amd64 (0.20.2-2) over (0.17.0-3) ... Preparing to unpack .../10-libcurl3-gnutls_7.64.0-4+deb10u2_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) over (7.52.1-5+deb9u10) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../11-libdeflate0_1.2-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.2-1) ... Selecting previously unselected package libhts2:amd64. Preparing to unpack .../12-libhts2_1.9-12~deb10u1_amd64.deb ... Unpacking libhts2:amd64 (1.9-12~deb10u1) ... Preparing to unpack .../13-pbbamtools_0.19.0+dfsg-4_amd64.deb ... Unpacking pbbamtools (0.19.0+dfsg-4) over (0.7.4+ds-1) ... Preparing to unpack .../14-libpbdata_5.3.1+dfsg-2.1_amd64.deb ... Unpacking libpbdata:amd64 (5.3.1+dfsg-2.1) over (0~20161219-1) ... Preparing to unpack .../15-libpbseq_5.3.1+dfsg-2.1_all.deb ... Unpacking libpbseq (5.3.1+dfsg-2.1) over (0~20161219-1) ... Selecting previously unselected package libhdf5-cpp-103:amd64. Preparing to unpack .../16-libhdf5-cpp-103_1.10.4+repack-10_amd64.deb ... Unpacking libhdf5-cpp-103:amd64 (1.10.4+repack-10) ... (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 ... 9464 files and directories currently installed.) Removing libpbbam:amd64 (0.7.4+ds-1) ... Selecting previously unselected package libpbbam0.19.0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9458 files and directories currently installed.) Preparing to unpack .../libpbbam0.19.0_0.19.0+dfsg-4_amd64.deb ... Unpacking libpbbam0.19.0:amd64 (0.19.0+dfsg-4) ... Preparing to unpack .../libss2_1.44.5-1+deb10u3_amd64.deb ... Unpacking libss2:amd64 (1.44.5-1+deb10u3) over (1.43.4-2+deb9u1) ... Setting up libss2:amd64 (1.44.5-1+deb10u3) ... Selecting previously unselected package tzdata. (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 ... 9463 files and directories currently installed.) Preparing to unpack .../0-tzdata_2021a-0+deb10u6_all.deb ... Unpacking tzdata (2021a-0+deb10u6) ... Selecting previously unselected package python-certifi. Preparing to unpack .../1-python-certifi_2018.8.24-1_all.deb ... Unpacking python-certifi (2018.8.24-1) ... Selecting previously unselected package python-idna. Preparing to unpack .../2-python-idna_2.6-1_all.deb ... Unpacking python-idna (2.6-1) ... Preparing to unpack .../3-python-requests_2.21.0-1_all.deb ... Unpacking python-requests (2.21.0-1) over (2.12.4-1) ... Preparing to unpack .../4-python-urllib3_1.24.1-1_all.deb ... Unpacking python-urllib3 (1.24.1-1) over (1.19.1-1) ... Selecting previously unselected package python-tz. Preparing to unpack .../5-python-tz_2019.1-1_all.deb ... Unpacking python-tz (2019.1-1) ... Preparing to unpack .../6-python-pbcommand_1.1.1-1_all.deb ... Unpacking python-pbcommand (1.1.1-1) over (0.5.3-1) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up apt (1.8.2.3) ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... Installing new version of config file /etc/cron.daily/apt-compat ... Setting up e2fslibs:amd64 (1.44.5-1+deb10u3) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u7) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u4) ... Setting up tzdata (2021a-0+deb10u6) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Jan 30 07:53:45 UTC 2023. Universal Time is now: Mon Jan 30 07:53:45 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libquadmath0:amd64 (8.3.0-6) ... Setting up util-linux (2.33.1-0.1) ... update-alternatives: warning: alternative /usr/bin/pg (part of link group pager) doesn't exist; removing from list of alternatives Setting up libk5crypto3:amd64 (1.17-3+deb10u4) ... Setting up libgfortran5:amd64 (8.3.0-6) ... Setting up mount (2.33.1-0.1) ... Setting up libcomerr2:amd64 (1.44.5-1+deb10u3) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u4) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up libblas3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libhdf5-103:amd64 (1.10.4+repack-10) ... Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u4) ... Setting up liblapack3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... Setting up libhdf5-cpp-103:amd64 (1.10.4+repack-10) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up python2 (2.7.16-1) ... Setting up libpython-stdlib:amd64 (2.7.16-1) ... Setting up python (2.7.16-1) ... Setting up python-h5py (2.8.0-3) ... Setting up python-urllib3 (1.24.1-1) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up python-certifi (2018.8.24-1) ... Setting up python-idna (2.6-1) ... Setting up python-tz (2019.1-1) ... Setting up libpbbam0.19.0:amd64 (0.19.0+dfsg-4) ... Setting up python-requests (2.21.0-1) ... Setting up pbbamtools (0.19.0+dfsg-4) ... Setting up python-scipy (1.1.0-7) ... Setting up python-pbcommand (1.1.1-1) ... Setting up python-pysam (0.15.2+ds-2) ... Setting up libpbdata:amd64 (5.3.1+dfsg-2.1) ... Setting up libpbihdf:amd64 (5.3.1+dfsg-2.1) ... Setting up libblasr:amd64 (5.3.1+dfsg-2.1) ... Setting up libpbseq (5.3.1+dfsg-2.1) ... Setting up blasr (5.3.2+dfsg-1.1) ... Setting up pbdagcon (0.3+git20161121.0000000+ds-1.1) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... Processing triggers for mime-support (3.62) ... 0m53.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-get', '-yf', 'dist-upgrade'] 0m53.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m54.8s DUMP: f6fc0f2636004ef589309651dfd778f4 - 0m54.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m54.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-cache', 'show', '--no-all-versions', 'smrtanalysis'] 0m55.0s DUMP: Package: smrtanalysis Status: install ok installed Priority: optional Section: science Installed-Size: 9 Maintainer: Debian Med Packaging Team Architecture: all Version: 0~20161126 Depends: pbbamtools, pbh5tools, pbbarcode, pbalign, blasr, pbdagcon, pbgenomicconsensus, kineticstools, falcon Description: software suite for single molecule, real-time sequencing SMRT® Analysis is a powerful, open-source bioinformatics software suite available for analysis of DNA sequencing data from Pacific Biosciences’ SMRT technology. Users can choose from a variety of analysis protocols that utilize PacBio® and third-party tools. Analysis protocols include de novo genome assembly, cDNA mapping, DNA base-modification detection, and long-amplicon analysis to determine phased consensus sequences. . This is a metapackage that depends on the components of SMRT Analysis. Description-md5: 07f41ceb2de8cc7b1a670a30f40ef08a Homepage: http://www.pacb.com/products-and-services/analytical-software/smrt-analysis/ 0m55.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-cache', 'show', '--no-all-versions', 'smrtanalysis'] 0m55.0s INFO: apt-cache does not know about any of the requested packages 0m55.0s INFO: Running scripts post_distupgrade 0m55.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m55.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m55.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_distupgrade_exceptions'] 0m55.0s DUMP: Normalized /etc/ca-certificates.conf 0m55.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_distupgrade_exceptions'] 0m55.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m55.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m55.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m55.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m55.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_distupgrade_zz_backports'] 0m55.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_distupgrade_zz_backports'] 0m55.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0'] 0m56.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0'] 0m56.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0'] 0m56.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0'] 0m56.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0'] 0m57.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0'] 0m57.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', '-ac', '--ignore-obsolete'] 0m58.9s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', '-ac', '--ignore-obsolete'] 0m58.9s INFO: Running scripts pre_remove 0m58.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m58.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m58.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m58.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m58.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_remove_exceptions'] 1m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/pre_remove_exceptions'] 1m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m0.6s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.2.3 install ok installed base-files base-files 10.3+deb10u13 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-4 install ok installed blasr blasr 5.3.2+dfsg-1.1 install ok installed bsdutils bsdutils 1:2.33.1-0.1 install ok installed ca-certificates ca-certificates 20200601~deb10u2 install ok installed coreutils coreutils 8.30-3 install ok installed dash dash 0.5.10.2-5 install ok installed debconf debconf 1.5.71+deb10u1 install ok installed debian-archive-keyring debian-archive-keyring 2019.1+deb10u1 install ok installed debianutils debianutils 4.8.6.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.8 install ok installed e2fslibs:amd64 e2fslibs 1.44.5-1+deb10u3 install ok installed e2fsprogs e2fsprogs 1.44.5-1+deb10u3 install ok installed falcon falcon 1.8.6-1.1 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed findutils findutils 4.6.0+git+20190209-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gcc-8-base:amd64 gcc-8-base 8.3.0-6 install ok installed gpgv gpgv 2.2.12-1+deb10u2 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+deb10u1 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed kineticstools kineticstools 0.6.1+git20180425.27a1878-2 install ok installed kineticstools-data kineticstools-data 0.6.1+git20180425.27a1878-2 install ok installed libacl1:amd64 libacl1 2.2.53-4 install ok installed libaec0:amd64 libaec0 1.0.2-1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.2.3 install ok installed libattr1:amd64 libattr1 1:2.4.48-4 install ok installed libaudit-common libaudit-common 1:2.8.4-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-3 install ok installed libblas-common libblas-common 3.7.0-2 install ok installed libblas3:amd64 libblas3 3.8.0-2 install ok installed libblasr:amd64 libblasr 5.3.1+dfsg-2.1 install ok installed libblkid1:amd64 libblkid1 2.33.1-0.1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-9.2~deb10u1 install ok installed libc-bin libc-bin 2.28-10+deb10u1 install ok installed libc6:amd64 libc6 2.28-10+deb10u1 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcom-err2:amd64 libcom-err2 1.44.5-1+deb10u3 install ok installed libcomerr2:amd64 libcomerr2 1.44.5-1+deb10u3 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.64.0-4+deb10u2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.249 install ok installed libdeflate0:amd64 libdeflate0 1.2-1 install ok installed libexpat1:amd64 libexpat1 2.2.6-2+deb10u4 install ok installed libext2fs2:amd64 libext2fs2 1.44.5-1+deb10u3 install ok installed libfdisk1:amd64 libfdisk1 2.33.1-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libgcc1:amd64 libgcc1 1:8.3.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-5+deb10u1 install ok installed libgfortran3:amd64 libgfortran3 6.3.0-18+deb9u1 install ok installed libgfortran5:amd64 libgfortran5 8.3.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4+deb10u1 install ok installed libgnutls30:amd64 libgnutls30 3.6.7-4+deb10u8 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.17-3+deb10u4 install ok installed libhdf5-103:amd64 libhdf5-103 1.10.4+repack-10 install ok installed libhdf5-cpp-103:amd64 libhdf5-cpp-103 1.10.4+repack-10 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libhts1:amd64 libhts1 1.3.2-2 install ok installed libhts2:amd64 libhts2 1.9-12~deb10u1 install ok installed libidn11:amd64 libidn11 1.33-2.2 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1+deb10u1 install ok installed libk5crypto3:amd64 libk5crypto3 1.17-3+deb10u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6-6 install ok installed libkrb5-3:amd64 libkrb5-3 1.17-3+deb10u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.17-3+deb10u4 install ok installed liblapack3:amd64 liblapack3 3.8.0-2 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.47+dfsg-3+deb10u7 install ok installed libldap-common libldap-common 2.4.47+dfsg-3+deb10u7 install ok installed liblz4-1:amd64 liblz4-1 1.8.3-1+deb10u1 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+deb10u1 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libncursesw5:amd64 libncursesw5 6.1+20181013-2+deb10u2 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-2+deb10u2 install ok installed libnettle6:amd64 libnettle6 3.4.1-1+deb10u1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.36.0-2+deb10u1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.15-2+deb10u1 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 libpbbam0.19.0:amd64 libpbbam0.19.0 0.19.0+dfsg-4 install ok installed libpbdata:amd64 libpbdata 5.3.1+dfsg-2.1 install ok installed libpbihdf:amd64 libpbihdf 5.3.1+dfsg-2.1 install ok installed libpbseq libpbseq 5.3.1+dfsg-2.1 install ok installed libpcre3:amd64 libpcre3 2:8.39-12 install ok installed libpopt0:amd64 libpopt0 1.16-12 install ok installed libpsl5:amd64 libpsl5 0.20.2-2 install ok installed libpython-stdlib:amd64 libpython-stdlib 2.7.16-1 install ok installed libpython2-stdlib:amd64 libpython2-stdlib 2.7.16-1 install ok installed libpython2.7-minimal:amd64 libpython2.7-minimal 2.7.16-2+deb10u1 install ok installed libpython2.7-stdlib:amd64 libpython2.7-stdlib 2.7.16-2+deb10u1 install ok installed libquadmath0:amd64 libquadmath0 8.3.0-6 install ok installed libreadline7:amd64 libreadline7 7.0-5 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27+dfsg-1+deb10u2 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27+dfsg-1+deb10u2 install ok installed libseccomp2:amd64 libseccomp2 2.3.3-4 install ok installed libselinux1:amd64 libselinux1 2.8-1+b1 install ok installed libsemanage-common libsemanage-common 2.8-2 install ok installed libsemanage1:amd64 libsemanage1 2.8-2 install ok installed libsepol1:amd64 libsepol1 2.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.27.2-3+deb10u1 install ok installed libss2:amd64 libss2 1.44.5-1+deb10u3 install ok installed libssh2-1:amd64 libssh2-1 1.8.0-2.1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1n-0+deb10u3 install ok installed libstdc++6:amd64 libstdc++6 8.3.0-6 install ok installed libsystemd0:amd64 libsystemd0 241-7~deb10u8 install ok installed libsz2:amd64 libsz2 1.0.2-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3 install ok installed libtinfo5:amd64 libtinfo5 6.1+20181013-2+deb10u2 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-2+deb10u2 install ok installed libudev1:amd64 libudev1 241-7~deb10u8 install ok installed libunistring0:amd64 libunistring0 0.9.6+really0.9.3-0.1 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libzstd1:amd64 libzstd1 1.3.8+dfsg-3+deb10u2 install ok installed login login 1:4.5-1.1 install ok installed lsb-base lsb-base 10.2019051400 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mime-support mime-support 3.62 install ok installed mount mount 2.33.1-0.1 install ok installed multiarch-support multiarch-support 2.28-10+deb10u1 install ok installed ncurses-base ncurses-base 6.1+20181013-2+deb10u2 install ok installed ncurses-bin ncurses-bin 6.1+20181013-2+deb10u2 install ok installed openssl openssl 1.1.1n-0+deb10u3 install ok installed passwd passwd 1:4.5-1.1 install ok installed pbalign pbalign 0.3.2-1 install ok installed pbbamtools pbbamtools 0.19.0+dfsg-4 install ok installed pbbarcode pbbarcode 0.8.0-5 install ok installed pbdagcon pbdagcon 0.3+git20161121.0000000+ds-1.1 install ok installed pbgenomicconsensus pbgenomicconsensus 2.3.2-5 install ok installed pbh5tools pbh5tools 0.8.0+git20170929.58d54ff+dfsg-1 install ok installed perl-base perl-base 5.28.1-6+deb10u1 install ok installed python python 2.7.16-1 install ok installed python-avro python-avro 1.8.2+dfsg-2 install ok installed python-certifi python-certifi 2018.8.24-1 install ok installed python-chardet python-chardet 3.0.4-3 install ok installed python-decorator python-decorator 4.3.0-1.1 install ok installed python-h5py python-h5py 2.8.0-3 install ok installed python-idna python-idna 2.6-1 install ok installed python-iso8601 python-iso8601 0.1.11-1 install ok installed python-kineticstools python-kineticstools 0.6.1+git20180425.27a1878-2 install ok installed python-minimal python-minimal 2.7.16-1 install ok installed python-networkx python-networkx 2.2-1 install ok installed python-numpy python-numpy 1:1.16.2-1 install ok installed python-pbalign python-pbalign 0.3.2-1 install ok installed python-pbcommand python-pbcommand 1.1.1-1 install ok installed python-pbconsensuscore python-pbconsensuscore 1.1.1+dfsg-1 install ok installed python-pbcore python-pbcore 1.6.5+dfsg-1 install ok installed python-pbgenomicconsensus python-pbgenomicconsensus 2.3.2-5 install ok installed python-pbh5tools python-pbh5tools 0.8.0+git20170929.58d54ff+dfsg-1 install ok installed python-pkg-resources python-pkg-resources 40.8.0-1 install ok installed python-pysam python-pysam 0.15.2+ds-2 install ok installed python-requests python-requests 2.21.0-1 install ok installed python-scipy python-scipy 1.1.0-7 install ok installed python-six python-six 1.12.0-1 install ok installed python-tz python-tz 2019.1-1 install ok installed python-urllib3 python-urllib3 1.24.1-1 install ok installed python2 python2 2.7.16-1 install ok installed python2-minimal python2-minimal 2.7.16-1 install ok installed python2.7 python2.7 2.7.16-2+deb10u1 install ok installed python2.7-minimal python2.7-minimal 2.7.16-2+deb10u1 install ok installed readline-common readline-common 7.0-5 install ok installed rsync rsync 3.1.3-6 install ok installed sed sed 4.7-1 install ok installed sensible-utils sensible-utils 0.0.12 install ok installed smrtanalysis smrtanalysis 0~20161126 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed time time 1.7-25.1+b1 install ok installed tzdata tzdata 2021a-0+deb10u6 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u1 1m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-get', 'remove', 'blasr', 'ca-certificates', 'falcon', 'kineticstools', 'kineticstools-data', 'libaec0:amd64', 'libblas-common', 'libblas3:amd64', 'libblasr:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103:amd64', 'libhdf5-cpp-103:amd64', 'libhts1:amd64', 'libhts2:amd64', 'libidn11:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libnghttp2-14:amd64', 'libpbbam0.19.0:amd64', 'libpbdata:amd64', 'libpbihdf:amd64', 'libpbseq', 'libpopt0:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libsz2:amd64', 'libunistring0:amd64', 'lsb-base', 'mime-support', 'openssl', 'pbalign', 'pbbamtools', 'pbbarcode', 'pbdagcon', 'pbgenomicconsensus', 'pbh5tools', 'python', 'python-avro', 'python-certifi', 'python-chardet', 'python-decorator', 'python-h5py', 'python-idna', 'python-iso8601', 'python-kineticstools', 'python-minimal', 'python-networkx', 'python-numpy', 'python-pbalign', 'python-pbcommand', 'python-pbconsensuscore', 'python-pbcore', 'python-pbgenomicconsensus', 'python-pbh5tools', 'python-pkg-resources', 'python-pysam', 'python-requests', 'python-scipy', 'python-six', 'python-tz', 'python-urllib3', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'rsync', 'time', 'tzdata', 'smrtanalysis'] 1m3.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: blasr ca-certificates falcon kineticstools kineticstools-data libaec0 libblas-common libblas3 libblasr libcurl3-gnutls libdeflate0 libexpat1 libgfortran3 libgfortran5 libgssapi-krb5-2 libhdf5-103 libhdf5-cpp-103 libhts1 libhts2 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common libnghttp2-14 libpbbam0.19.0 libpbdata libpbihdf libpbseq libpopt0 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libsz2 libunistring0 lsb-base mime-support openssl pbalign pbbamtools pbbarcode pbdagcon pbgenomicconsensus pbh5tools python python-avro python-certifi python-chardet python-decorator python-h5py python-idna python-iso8601 python-kineticstools python-minimal python-networkx python-numpy python-pbalign python-pbcommand python-pbconsensuscore python-pbcore python-pbgenomicconsensus python-pbh5tools python-pkg-resources python-pysam python-requests python-scipy python-six python-tz python-urllib3 python2 python2-minimal python2.7 python2.7-minimal readline-common rsync smrtanalysis time tzdata 0 upgraded, 0 newly installed, 91 to remove and 0 not upgraded. After this operation, 276 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 ... 11416 files and directories currently installed.) Removing smrtanalysis (0~20161126) ... Removing pbalign (0.3.2-1) ... Removing python-pbalign (0.3.2-1) ... Removing blasr (5.3.2+dfsg-1.1) ... Removing pbgenomicconsensus (2.3.2-5) ... Removing python-pbgenomicconsensus (2.3.2-5) ... Removing kineticstools (0.6.1+git20180425.27a1878-2) ... Removing python-kineticstools (0.6.1+git20180425.27a1878-2) ... Removing python-pbcommand (1.1.1-1) ... Removing python-requests (2.21.0-1) ... Removing python-certifi (2018.8.24-1) ... Removing ca-certificates (20200601~deb10u2) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing falcon (1.8.6-1.1) ... Removing kineticstools-data (0.6.1+git20180425.27a1878-2) ... Removing pbdagcon (0.3+git20161121.0000000+ds-1.1) ... Removing libpbseq (5.3.1+dfsg-2.1) ... Removing libblasr:amd64 (5.3.1+dfsg-2.1) ... Removing libpbihdf:amd64 (5.3.1+dfsg-2.1) ... Removing libhdf5-cpp-103:amd64 (1.10.4+repack-10) ... Removing pbh5tools (0.8.0+git20170929.58d54ff+dfsg-1) ... Removing python-pbh5tools (0.8.0+git20170929.58d54ff+dfsg-1) ... Removing libblas-common (3.7.0-2) ... Removing python-scipy (1.1.0-7) ... Removing pbbarcode (0.8.0-5) ... Removing python-pbcore (1.6.5+dfsg-1) ... Removing python-pbconsensuscore (1.1.1+dfsg-1) ... Removing libhts1:amd64 (1.3.2-2) ... Removing python-pysam (0.15.2+ds-2) ... Removing python-urllib3 (1.24.1-1) ... Removing python-tz (2019.1-1) ... Removing libgfortran3:amd64 (6.3.0-18+deb9u1) ... Removing libidn11:amd64 (1.33-2.2) ... Removing libpbdata:amd64 (5.3.1+dfsg-2.1) ... Removing pbbamtools (0.19.0+dfsg-4) ... Removing libpbbam0.19.0:amd64 (0.19.0+dfsg-4) ... Removing rsync (3.1.3-6) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing libpopt0:amd64 (1.16-12) ... Removing openssl (1.1.1n-0+deb10u3) ... Removing libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Removing lsb-base (10.2019051400) ... Removing python-avro (1.8.2+dfsg-2) ... Removing python-chardet (3.0.4-3) ... Removing python-networkx (2.2-1) ... Removing python-decorator (4.3.0-1.1) ... Removing python-idna (2.6-1) ... Removing python-iso8601 (0.1.11-1) ... Removing time (1.7-25.1+b1) ... Removing tzdata (2021a-0+deb10u6) ... Removing python-h5py (2.8.0-3) ... Removing libhdf5-103:amd64 (1.10.4+repack-10) ... Removing libsz2:amd64 (1.0.2-1) ... Removing libaec0:amd64 (1.0.2-1) ... Removing python-numpy (1:1.16.2-1) ... Removing liblapack3:amd64 (3.8.0-2) ... Removing libblas3:amd64 (3.8.0-2) ... Removing libhts2:amd64 (1.9-12~deb10u1) ... Removing libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Removing libdeflate0:amd64 (1.2-1) ... Removing python-six (1.12.0-1) ... Removing libgfortran5:amd64 (8.3.0-6) ... Removing libgssapi-krb5-2:amd64 (1.17-3+deb10u4) ... Removing libkrb5-3:amd64 (1.17-3+deb10u4) ... Removing libk5crypto3:amd64 (1.17-3+deb10u4) ... Removing libkrb5support0:amd64 (1.17-3+deb10u4) ... Removing libkeyutils1:amd64 (1.6-6) ... Removing libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u7) ... Removing libldap-common (2.4.47+dfsg-3+deb10u7) ... Removing libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Removing libpsl5:amd64 (0.20.2-2) ... Removing libquadmath0:amd64 (8.3.0-6) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Removing libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u2) ... Removing libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u2) ... Removing libssh2-1:amd64 (1.8.0-2.1) ... Removing python-pkg-resources (40.8.0-1) ... Removing python (2.7.16-1) ... Removing python2 (2.7.16-1) ... Removing python2.7 (2.7.16-2+deb10u1) ... Removing libpython-stdlib:amd64 (2.7.16-1) ... Removing libpython2-stdlib:amd64 (2.7.16-1) ... Removing python-minimal (2.7.16-1) ... Removing python2-minimal (2.7.16-1) ... Removing python2.7-minimal (2.7.16-2+deb10u1) ... Removing libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Removing libexpat1:amd64 (2.2.6-2+deb10u4) ... Removing libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... find: '/usr/lib/python2.7': No such file or directory Removing libreadline7:amd64 (7.0-5) ... Removing libsqlite3-0:amd64 (3.27.2-3+deb10u1) ... Removing libssl1.1:amd64 (1.1.1n-0+deb10u3) ... Removing mime-support (3.62) ... Removing readline-common (7.0-5) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... 1m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-get', 'remove', 'blasr', 'ca-certificates', 'falcon', 'kineticstools', 'kineticstools-data', 'libaec0:amd64', 'libblas-common', 'libblas3:amd64', 'libblasr:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103:amd64', 'libhdf5-cpp-103:amd64', 'libhts1:amd64', 'libhts2:amd64', 'libidn11:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libnghttp2-14:amd64', 'libpbbam0.19.0:amd64', 'libpbdata:amd64', 'libpbihdf:amd64', 'libpbseq', 'libpopt0:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libsz2:amd64', 'libunistring0:amd64', 'lsb-base', 'mime-support', 'openssl', 'pbalign', 'pbbamtools', 'pbbarcode', 'pbdagcon', 'pbgenomicconsensus', 'pbh5tools', 'python', 'python-avro', 'python-certifi', 'python-chardet', 'python-decorator', 'python-h5py', 'python-idna', 'python-iso8601', 'python-kineticstools', 'python-minimal', 'python-networkx', 'python-numpy', 'python-pbalign', 'python-pbcommand', 'python-pbconsensuscore', 'python-pbcore', 'python-pbgenomicconsensus', 'python-pbh5tools', 'python-pkg-resources', 'python-pysam', 'python-requests', 'python-scipy', 'python-six', 'python-tz', 'python-urllib3', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'rsync', 'time', 'tzdata', 'smrtanalysis'] 1m3.8s INFO: Running scripts post_remove 1m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_remove_exceptions'] 1m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_remove_exceptions'] 1m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'dpkg', '--purge', 'blasr', 'ca-certificates', 'falcon', 'kineticstools', 'kineticstools-data', 'libaec0:amd64', 'libblas-common', 'libblas3:amd64', 'libblasr:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103:amd64', 'libhdf5-cpp-103:amd64', 'libhts1:amd64', 'libhts2:amd64', 'libidn11:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libnghttp2-14:amd64', 'libpbbam0.19.0:amd64', 'libpbdata:amd64', 'libpbihdf:amd64', 'libpbseq', 'libpopt0:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libsz2:amd64', 'libunistring0:amd64', 'lsb-base', 'mime-support', 'openssl', 'pbalign', 'pbbamtools', 'pbbarcode', 'pbdagcon', 'pbgenomicconsensus', 'pbh5tools', 'python', 'python-avro', 'python-certifi', 'python-chardet', 'python-decorator', 'python-h5py', 'python-idna', 'python-iso8601', 'python-kineticstools', 'python-minimal', 'python-networkx', 'python-numpy', 'python-pbalign', 'python-pbcommand', 'python-pbconsensuscore', 'python-pbcore', 'python-pbgenomicconsensus', 'python-pbh5tools', 'python-pkg-resources', 'python-pysam', 'python-requests', 'python-scipy', 'python-six', 'python-tz', 'python-urllib3', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'rsync', 'time', 'tzdata'] 1m4.2s DUMP: dpkg: warning: ignoring request to remove blasr which isn't installed (Reading database ... 4638 files and directories currently installed.) Purging configuration files for ca-certificates (20200601~deb10u2) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove falcon which isn't installed dpkg: warning: ignoring request to remove kineticstools which isn't installed dpkg: warning: ignoring request to remove kineticstools-data which isn't installed dpkg: warning: ignoring request to remove libaec0 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 libblasr which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libgfortran3 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.17-3+deb10u4) ... dpkg: warning: ignoring request to remove libhdf5-103 which isn't installed dpkg: warning: ignoring request to remove libhdf5-cpp-103 which isn't installed dpkg: warning: ignoring request to remove libhts1 which isn't installed dpkg: warning: ignoring request to remove libhts2 which isn't installed dpkg: warning: ignoring request to remove libidn11 which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed Purging configuration files for libldap-common (2.4.47+dfsg-3+deb10u7) ... dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libpbbam0.19.0 which isn't installed dpkg: warning: ignoring request to remove libpbdata which isn't installed dpkg: warning: ignoring request to remove libpbihdf which isn't installed dpkg: warning: ignoring request to remove libpbseq which isn't installed dpkg: warning: ignoring request to remove libpopt0 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython2-stdlib which isn't installed Purging configuration files for libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... 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 librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed Purging configuration files for libssl1.1:amd64 (1.1.1n-0+deb10u3) ... dpkg: warning: ignoring request to remove libsz2 which isn't installed dpkg: warning: ignoring request to remove libunistring0 which isn't installed dpkg: warning: ignoring request to remove lsb-base which isn't installed Purging configuration files for mime-support (3.62) ... Purging configuration files for openssl (1.1.1n-0+deb10u3) ... dpkg: warning: ignoring request to remove pbalign which isn't installed dpkg: warning: ignoring request to remove pbbamtools which isn't installed dpkg: warning: ignoring request to remove pbbarcode which isn't installed dpkg: warning: ignoring request to remove pbdagcon which isn't installed dpkg: warning: ignoring request to remove pbgenomicconsensus which isn't installed dpkg: warning: ignoring request to remove pbh5tools which isn't installed Purging configuration files for python (2.7.16-1) ... dpkg: warning: ignoring request to remove python-avro which isn't installed dpkg: warning: ignoring request to remove python-certifi which isn't installed dpkg: warning: ignoring request to remove python-chardet which isn't installed dpkg: warning: ignoring request to remove python-decorator which isn't installed dpkg: warning: ignoring request to remove python-h5py which isn't installed dpkg: warning: ignoring request to remove python-idna which isn't installed dpkg: warning: ignoring request to remove python-iso8601 which isn't installed dpkg: warning: ignoring request to remove python-kineticstools which isn't installed dpkg: warning: ignoring request to remove python-minimal which isn't installed dpkg: warning: ignoring request to remove python-networkx which isn't installed dpkg: warning: ignoring request to remove python-numpy which isn't installed dpkg: warning: ignoring request to remove python-pbalign which isn't installed dpkg: warning: ignoring request to remove python-pbcommand which isn't installed dpkg: warning: ignoring request to remove python-pbconsensuscore which isn't installed dpkg: warning: ignoring request to remove python-pbcore which isn't installed dpkg: warning: ignoring request to remove python-pbgenomicconsensus which isn't installed dpkg: warning: ignoring request to remove python-pbh5tools which isn't installed dpkg: warning: ignoring request to remove python-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python-pysam which isn't installed dpkg: warning: ignoring request to remove python-requests 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 python-urllib3 which isn't installed dpkg: warning: ignoring request to remove python2 which isn't installed dpkg: warning: ignoring request to remove python2-minimal which isn't installed dpkg: warning: ignoring request to remove python2.7 which isn't installed Purging configuration files for python2.7-minimal (2.7.16-2+deb10u1) ... Purging configuration files for readline-common (7.0-5) ... Purging configuration files for rsync (3.1.3-6) ... dpkg: warning: ignoring request to remove time which isn't installed Purging configuration files for tzdata (2021a-0+deb10u6) ... 1m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'dpkg', '--purge', 'blasr', 'ca-certificates', 'falcon', 'kineticstools', 'kineticstools-data', 'libaec0:amd64', 'libblas-common', 'libblas3:amd64', 'libblasr:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103:amd64', 'libhdf5-cpp-103:amd64', 'libhts1:amd64', 'libhts2:amd64', 'libidn11:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libnghttp2-14:amd64', 'libpbbam0.19.0:amd64', 'libpbdata:amd64', 'libpbihdf:amd64', 'libpbseq', 'libpopt0:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libsz2:amd64', 'libunistring0:amd64', 'lsb-base', 'mime-support', 'openssl', 'pbalign', 'pbbamtools', 'pbbarcode', 'pbdagcon', 'pbgenomicconsensus', 'pbh5tools', 'python', 'python-avro', 'python-certifi', 'python-chardet', 'python-decorator', 'python-h5py', 'python-idna', 'python-iso8601', 'python-kineticstools', 'python-minimal', 'python-networkx', 'python-numpy', 'python-pbalign', 'python-pbcommand', 'python-pbconsensuscore', 'python-pbcore', 'python-pbgenomicconsensus', 'python-pbh5tools', 'python-pkg-resources', 'python-pysam', 'python-requests', 'python-scipy', 'python-six', 'python-tz', 'python-urllib3', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'rsync', 'time', 'tzdata'] 1m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'dpkg', '--purge', 'smrtanalysis'] 1m4.2s DUMP: dpkg: warning: ignoring request to remove smrtanalysis which isn't installed 1m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'dpkg', '--purge', 'smrtanalysis'] 1m4.2s INFO: Running scripts post_purge 1m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_purge_exceptions'] 1m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_purge_exceptions'] 1m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'dpkg', '--purge', '--pending'] 1m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'dpkg', '--purge', '--pending'] 1m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'dpkg', '--remove', '--pending'] 1m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'dpkg', '--remove', '--pending'] 1m4.3s INFO: Running scripts post_test 1m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_test_exceptions'] 1m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'tmp/scripts/post_test_exceptions'] 1m4.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0'] 1m4.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0'] 1m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'dpkg-divert', '--list'] 1m4.7s 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 1m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'dpkg-divert', '--list'] 1m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-get', 'clean'] 1m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0', 'apt-get', 'clean'] 1m4.8s DEBUG: Recording chroot state 1m5.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/dev/shm'] 1m5.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/dev/shm'] 1m5.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/dev/console'] 1m5.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/dev/console'] 1m5.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/dev/ptmx'] 1m5.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/dev/ptmx'] 1m5.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/dev/pts'] 1m5.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/dev/pts'] 1m5.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/proc'] 1m5.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0/proc'] 1m5.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0'] 1m5.7s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmptp7cv_q0'] 1m5.7s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmptp7cv_q0 1m5.7s INFO: PASS: Upgrading between Debian distributions. 1m5.7s INFO: PASS: All tests. 1m5.7s INFO: piuparts run ends. ret=0 End: 2023-01-30 07:54:01 GMT