Start: 2022-12-03 19:19:45 GMT [stretch] Package: smrtanalysis-dev Source: smrtanalysis Version: 0~20161126 Installed-Size: 9 Maintainer: Debian Med Packaging Team Architecture: all Depends: python-pbcore, python-pbcommand, python-pbconsensuscore | python3-pbconsensuscore, python-pbgenomicconsensus, python-pbh5tools, python-pbalign, python-kineticstools, libpbseq-dev, libpbbam-dev Description: develepment libraries for smrtanalysis Homepage: http://www.pacb.com/products-and-services/analytical-software/smrt-analysis/ Description-md5: 1a10b42e923f01861162fa9b4749811c Tag: devel::library, role::devel-lib Section: libdevel Priority: optional Filename: pool/main/s/smrtanalysis/smrtanalysis-dev_0~20161126_all.deb Size: 2546 MD5sum: eb18722733ed9307de4f2adce757384c SHA256: d2be1f45d6a20ba8427f576cb725a644394907f2c7253fce3cfb7d9e9554ff30 [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 --install-recommends --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-rcmd/reference-chroot-metadata.dat --apt smrtanalysis-dev=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 --install-recommends --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-rcmd/reference-chroot-metadata.dat --apt smrtanalysis-dev=None 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-19-amd64 #1 SMP Debian 5.10.149-2 (2022-10-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp2vg233f0 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp2vg233f0 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.6s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.6s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/proc'] 0m1.6s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/proc'] 0m1.6s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/dev/pts'] 0m1.6s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/dev/pts'] 0m1.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/dev/ptmx'] 0m1.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/dev/ptmx'] 0m1.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/dev/console'] 0m1.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/dev/console'] 0m1.6s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/dev/shm'] 0m1.6s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/dev/shm'] 0m1.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m1.6s DEBUG: Created policy-rc.d and chmodded it. 0m1.6s DEBUG: Created resolv.conf. 0m1.6s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp2vg233f0/tmp/scripts/ 0m1.6s INFO: Running scripts post_chroot_unpack 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-get', 'update'] 0m3.0s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-get', 'update'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-get', '-yf', 'dist-upgrade'] 0m3.6s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-get', '-yf', 'dist-upgrade'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.9s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.9s INFO: Running scripts post_setup 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_setup_dummy_users'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_setup_dummy_users'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_setup_forbid_home'] 0m4.8s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_setup_forbid_home'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.8s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_setup_minimize'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_setup_minimize'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_setup_zz_backports'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_setup_zz_backports'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.9s 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 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.9s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stretch2Xbuster-rcmd/reference-chroot-metadata.dat 0m4.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2vg233f0'] 0m5.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2vg233f0'] 0m5.2s INFO: Running scripts is_testable 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/is_testable_uninstallable'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/is_testable_uninstallable'] 0m5.2s INFO: Running scripts pre_test 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_test_exceptions'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_test_exceptions'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_test_root_password'] 0m5.2s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_test_root_password'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-cache', 'show', '--no-all-versions', 'smrtanalysis-dev'] 0m5.4s DUMP: Package: smrtanalysis-dev Source: smrtanalysis Version: 0~20161126 Installed-Size: 9 Maintainer: Debian Med Packaging Team Architecture: all Depends: python-pbcore, python-pbcommand, python-pbconsensuscore | python3-pbconsensuscore, python-pbgenomicconsensus, python-pbh5tools, python-pbalign, python-kineticstools, libpbseq-dev, libpbbam-dev Description-en: develepment libraries for smrtanalysis 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 SMRTAnalysis development tools. Description-md5: 1a10b42e923f01861162fa9b4749811c Homepage: http://www.pacb.com/products-and-services/analytical-software/smrt-analysis/ Tag: devel::library, role::devel-lib Section: libdevel Priority: optional Filename: pool/main/s/smrtanalysis/smrtanalysis-dev_0~20161126_all.deb Size: 2546 MD5sum: eb18722733ed9307de4f2adce757384c SHA256: d2be1f45d6a20ba8427f576cb725a644394907f2c7253fce3cfb7d9e9554ff30 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-cache', 'show', '--no-all-versions', 'smrtanalysis-dev'] 0m5.4s INFO: apt-cache knows about the following packages: smrtanalysis-dev 0m5.4s INFO: Running scripts pre_install 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_install_database-server'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_install_database-server'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_install_exceptions'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_install_exceptions'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_install_extras'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_install_extras'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-cache', 'policy'] 0m5.5s 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: 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-cache', 'policy'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-cache', 'policy', 'smrtanalysis-dev'] 0m5.6s DUMP: smrtanalysis-dev: Installed: (none) Candidate: 0~20161126 Version table: 0~20161126 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-cache', 'policy', 'smrtanalysis-dev'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-get', '-y', 'install', 'smrtanalysis-dev'] 0m44.1s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: binutils blasr bzip2 ca-certificates cpp cpp-6 file g++ g++-6 gcc gcc-6 hdf5-tools kineticstools-data krb5-locales libaec0 libasan3 libatomic1 libblas-common libblas3 libblasr libblasr-dev libc-dev-bin libc6-dev libcc1-0 libcilkrts5 libcurl3-gnutls libexpat1 libexpat1-dev libffi6 libfreetype6 libgcc-6-dev libgfortran3 libgmp10 libgnutls30 libgomp1 libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100 libhogweed4 libhts-dev libhts1 libidn11 libidn2-0 libisl15 libitm1 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common liblsan0 libmagic-mgc libmagic1 libmpc3 libmpfr4 libmpx2 libnettle6 libnghttp2-14 libp11-kit0 libpbbam libpbbam-dev libpbdata libpbdata-dev libpbihdf libpbihdf-dev libpbseq libpbseq-dev libpng16-16 libpsl5 libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules libsasl2-modules-db libsqlite3-0 libssh2-1 libssl-dev libssl-doc libssl1.1 libstdc++-6-dev libsz2 libtasn1-6 libtiff5 libtsan0 libubsan0 libunistring0 libwebp6 libwebpdemux2 libwebpmux2 linux-libc-dev manpages manpages-dev mime-support openssl publicsuffix python python-avro python-cffi-backend python-chardet python-cryptography python-decorator python-dev python-enum34 python-h5py python-idna python-imaging python-ipaddress python-iso8601 python-kineticstools python-minimal python-numpy python-openssl python-pbalign python-pbcommand python-pbconsensuscore python-pbcore python-pbgenomicconsensus python-pbh5tools python-pil python-pkg-resources python-pyasn1 python-pysam python-requests python-scipy python-setuptools python-six python-urllib3 python2.7 python2.7-dev python2.7-minimal readline-common xz-utils Suggested packages: binutils-doc bzip2-doc cpp-doc gcc-6-locales g++-multilib g++-6-multilib gcc-6-doc libstdc++6-6-dbg gcc-multilib make autoconf automake libtool flex bison gdb gcc-doc gcc-6-multilib libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg libasan3-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg libcilkrts5-dbg libmpx2-dbg libquadmath0-dbg glibc-doc gnutls-bin krb5-doc krb5-user liblcms2-utils libsasl2-modules-gssapi-mit | libsasl2-modules-gssapi-heimdal libsasl2-modules-ldap libsasl2-modules-otp libsasl2-modules-sql libstdc++-6-doc man-browser python-doc python-tk python-cryptography-doc python-cryptography-vectors python-enum34-doc python-h5py-doc python-pybigwig gfortran python-nose python-numpy-dbg python-numpy-doc python-openssl-doc python-openssl-dbg bowtie2 gmap pbalign-doc python-pbcore-doc python-consensuscore2 python-pil-doc python-pil-dbg doc-base python-socks python-scipy-doc python-setuptools-doc python-ntlm python2.7-doc binfmt-support readline-doc The following NEW packages will be installed: binutils blasr bzip2 ca-certificates cpp cpp-6 file g++ g++-6 gcc gcc-6 hdf5-tools kineticstools-data krb5-locales libaec0 libasan3 libatomic1 libblas-common libblas3 libblasr libblasr-dev libc-dev-bin libc6-dev libcc1-0 libcilkrts5 libcurl3-gnutls libexpat1 libexpat1-dev libffi6 libfreetype6 libgcc-6-dev libgfortran3 libgmp10 libgnutls30 libgomp1 libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100 libhogweed4 libhts-dev libhts1 libidn11 libidn2-0 libisl15 libitm1 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common liblsan0 libmagic-mgc libmagic1 libmpc3 libmpfr4 libmpx2 libnettle6 libnghttp2-14 libp11-kit0 libpbbam libpbbam-dev libpbdata libpbdata-dev libpbihdf libpbihdf-dev libpbseq libpbseq-dev libpng16-16 libpsl5 libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules libsasl2-modules-db libsqlite3-0 libssh2-1 libssl-dev libssl-doc libssl1.1 libstdc++-6-dev libsz2 libtasn1-6 libtiff5 libtsan0 libubsan0 libunistring0 libwebp6 libwebpdemux2 libwebpmux2 linux-libc-dev manpages manpages-dev mime-support openssl publicsuffix python python-avro python-cffi-backend python-chardet python-cryptography python-decorator python-dev python-enum34 python-h5py python-idna python-imaging python-ipaddress python-iso8601 python-kineticstools python-minimal python-numpy python-openssl python-pbalign python-pbcommand python-pbconsensuscore python-pbcore python-pbgenomicconsensus python-pbh5tools python-pil python-pkg-resources python-pyasn1 python-pysam python-requests python-scipy python-setuptools python-six python-urllib3 python2.7 python2.7-dev python2.7-minimal readline-common smrtanalysis-dev xz-utils 0 upgraded, 145 newly installed, 0 to remove and 0 not upgraded. Need to get 220 MB of archives. After this operation, 493 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian stretch/main amd64 libpython2.7-minimal amd64 2.7.13-2+deb9u3 [389 kB] Get:2 http://deb.debian.org/debian stretch/main amd64 python2.7-minimal amd64 2.7.13-2+deb9u3 [1382 kB] Get:3 http://deb.debian.org/debian stretch/main amd64 python-minimal amd64 2.7.13-2 [40.5 kB] Get:4 http://deb.debian.org/debian stretch/main amd64 mime-support all 3.60 [36.7 kB] Get:5 http://deb.debian.org/debian stretch/main amd64 libexpat1 amd64 2.2.0-2+deb9u3 [83.7 kB] Get:6 http://deb.debian.org/debian stretch/main amd64 libffi6 amd64 3.2.1-6 [20.4 kB] Get:7 http://deb.debian.org/debian stretch/main amd64 readline-common all 7.0-3 [70.4 kB] Get:8 http://deb.debian.org/debian stretch/main amd64 libreadline7 amd64 7.0-3 [151 kB] Get:9 http://deb.debian.org/debian stretch/main amd64 libsqlite3-0 amd64 3.16.2-5+deb9u1 [572 kB] Get:10 http://deb.debian.org/debian stretch/main amd64 libssl1.1 amd64 1.1.0l-1~deb9u1 [1358 kB] Get:11 http://deb.debian.org/debian stretch/main amd64 libpython2.7-stdlib amd64 2.7.13-2+deb9u3 [1897 kB] Get:12 http://deb.debian.org/debian stretch/main amd64 python2.7 amd64 2.7.13-2+deb9u3 [285 kB] Get:13 http://deb.debian.org/debian stretch/main amd64 libpython-stdlib amd64 2.7.13-2 [20.0 kB] Get:14 http://deb.debian.org/debian stretch/main amd64 python amd64 2.7.13-2 [154 kB] Get:15 http://deb.debian.org/debian stretch/main amd64 bzip2 amd64 1.0.6-8.1 [47.5 kB] Get:16 http://deb.debian.org/debian stretch/main amd64 libmagic-mgc amd64 1:5.30-1+deb9u3 [222 kB] Get:17 http://deb.debian.org/debian stretch/main amd64 libmagic1 amd64 1:5.30-1+deb9u3 [111 kB] Get:18 http://deb.debian.org/debian stretch/main amd64 file amd64 1:5.30-1+deb9u3 [64.2 kB] Get:19 http://deb.debian.org/debian stretch/main amd64 krb5-locales all 1.15-1+deb9u1 [93.8 kB] Get:20 http://deb.debian.org/debian stretch/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1 [253 kB] Get:21 http://deb.debian.org/debian stretch/main amd64 libnettle6 amd64 3.3-1+b2 [192 kB] Get:22 http://deb.debian.org/debian stretch/main amd64 libhogweed4 amd64 3.3-1+b2 [136 kB] Get:23 http://deb.debian.org/debian stretch/main amd64 libidn11 amd64 1.33-1+deb9u1 [115 kB] Get:24 http://deb.debian.org/debian stretch/main amd64 libp11-kit0 amd64 0.23.3-2 [111 kB] Get:25 http://deb.debian.org/debian stretch/main amd64 libtasn1-6 amd64 4.10-1.1+deb9u1 [50.6 kB] Get:26 http://deb.debian.org/debian stretch/main amd64 libgnutls30 amd64 3.5.8-5+deb9u5 [896 kB] Get:27 http://deb.debian.org/debian stretch/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:28 http://deb.debian.org/debian stretch/main amd64 libkrb5support0 amd64 1.15-1+deb9u1 [61.9 kB] Get:29 http://deb.debian.org/debian stretch/main amd64 libk5crypto3 amd64 1.15-1+deb9u1 [119 kB] Get:30 http://deb.debian.org/debian stretch/main amd64 libkrb5-3 amd64 1.15-1+deb9u1 [311 kB] Get:31 http://deb.debian.org/debian stretch/main amd64 libgssapi-krb5-2 amd64 1.15-1+deb9u1 [155 kB] Get:32 http://deb.debian.org/debian stretch/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [68.4 kB] Get:33 http://deb.debian.org/debian stretch/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [105 kB] Get:34 http://deb.debian.org/debian stretch/main amd64 libldap-common all 2.4.44+dfsg-5+deb9u4 [85.7 kB] Get:35 http://deb.debian.org/debian stretch/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-5+deb9u4 [219 kB] Get:36 http://deb.debian.org/debian stretch/main amd64 manpages all 4.10-2 [1222 kB] Get:37 http://deb.debian.org/debian stretch/main amd64 xz-utils amd64 5.2.2-1.2+b1 [266 kB] Get:38 http://deb.debian.org/debian stretch/main amd64 binutils amd64 2.28-5 [3770 kB] Get:39 http://deb.debian.org/debian stretch/main amd64 libquadmath0 amd64 6.3.0-18+deb9u1 [131 kB] Get:40 http://deb.debian.org/debian stretch/main amd64 libgfortran3 amd64 6.3.0-18+deb9u1 [265 kB] Get:41 http://deb.debian.org/debian stretch/main amd64 libaec0 amd64 0.3.2-1 [18.5 kB] Get:42 http://deb.debian.org/debian stretch/main amd64 libsz2 amd64 0.3.2-1 [5730 B] Get:43 http://deb.debian.org/debian stretch/main amd64 libhdf5-100 amd64 1.10.0-patch1+docs-3+deb9u1 [1282 kB] Get:44 http://deb.debian.org/debian stretch/main amd64 libhdf5-cpp-100 amd64 1.10.0-patch1+docs-3+deb9u1 [130 kB] Get:45 http://deb.debian.org/debian stretch/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:46 http://deb.debian.org/debian stretch/main amd64 libidn2-0 amd64 0.16-1+deb9u1 [60.7 kB] Get:47 http://deb.debian.org/debian stretch/main amd64 libnghttp2-14 amd64 1.18.1-1+deb9u1 [79.2 kB] Get:48 http://deb.debian.org/debian stretch/main amd64 libpsl5 amd64 0.17.0-3 [41.8 kB] Get:49 http://deb.debian.org/debian stretch/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:50 http://deb.debian.org/debian stretch/main amd64 libssh2-1 amd64 1.7.0-1+deb9u1 [139 kB] Get:51 http://deb.debian.org/debian stretch/main amd64 libcurl3-gnutls amd64 7.52.1-5+deb9u10 [290 kB] Get:52 http://deb.debian.org/debian stretch/main amd64 libhts1 amd64 1.3.2-2 [257 kB] Get:53 http://deb.debian.org/debian stretch/main amd64 libpbbam amd64 0.7.4+ds-1 [478 kB] Get:54 http://deb.debian.org/debian stretch/main amd64 libpbdata amd64 0~20161219-1 [129 kB] Get:55 http://deb.debian.org/debian stretch/main amd64 libpbihdf amd64 0~20161219-1 [167 kB] Get:56 http://deb.debian.org/debian stretch/main amd64 libblasr amd64 0~20161219-1 [867 kB] Get:57 http://deb.debian.org/debian stretch/main amd64 libpbseq all 0~20161219-1 [3876 B] Get:58 http://deb.debian.org/debian stretch/main amd64 blasr amd64 5.3+0-1 [691 kB] Get:59 http://deb.debian.org/debian stretch/main amd64 openssl amd64 1.1.0l-1~deb9u1 [749 kB] Get:60 http://deb.debian.org/debian stretch/main amd64 ca-certificates all 20200601~deb9u1 [160 kB] Get:61 http://deb.debian.org/debian stretch/main amd64 libisl15 amd64 0.18-1 [564 kB] Get:62 http://deb.debian.org/debian stretch/main amd64 libmpfr4 amd64 3.1.5-1 [556 kB] Get:63 http://deb.debian.org/debian stretch/main amd64 libmpc3 amd64 1.0.3-1+b2 [39.9 kB] Get:64 http://deb.debian.org/debian stretch/main amd64 cpp-6 amd64 6.3.0-18+deb9u1 [6584 kB] Get:65 http://deb.debian.org/debian stretch/main amd64 cpp amd64 4:6.3.0-4 [18.7 kB] Get:66 http://deb.debian.org/debian stretch/main amd64 libcc1-0 amd64 6.3.0-18+deb9u1 [30.6 kB] Get:67 http://deb.debian.org/debian stretch/main amd64 libgomp1 amd64 6.3.0-18+deb9u1 [73.3 kB] Get:68 http://deb.debian.org/debian stretch/main amd64 libitm1 amd64 6.3.0-18+deb9u1 [27.3 kB] Get:69 http://deb.debian.org/debian stretch/main amd64 libatomic1 amd64 6.3.0-18+deb9u1 [8966 B] Get:70 http://deb.debian.org/debian stretch/main amd64 libasan3 amd64 6.3.0-18+deb9u1 [311 kB] Get:71 http://deb.debian.org/debian stretch/main amd64 liblsan0 amd64 6.3.0-18+deb9u1 [115 kB] Get:72 http://deb.debian.org/debian stretch/main amd64 libtsan0 amd64 6.3.0-18+deb9u1 [257 kB] Get:73 http://deb.debian.org/debian stretch/main amd64 libubsan0 amd64 6.3.0-18+deb9u1 [107 kB] Get:74 http://deb.debian.org/debian stretch/main amd64 libcilkrts5 amd64 6.3.0-18+deb9u1 [40.5 kB] Get:75 http://deb.debian.org/debian stretch/main amd64 libmpx2 amd64 6.3.0-18+deb9u1 [11.2 kB] Get:76 http://deb.debian.org/debian stretch/main amd64 libgcc-6-dev amd64 6.3.0-18+deb9u1 [2296 kB] Get:77 http://deb.debian.org/debian stretch/main amd64 gcc-6 amd64 6.3.0-18+deb9u1 [6900 kB] Get:78 http://deb.debian.org/debian stretch/main amd64 gcc amd64 4:6.3.0-4 [5196 B] Get:79 http://deb.debian.org/debian stretch/main amd64 libc-dev-bin amd64 2.24-11+deb9u4 [259 kB] Get:80 http://deb.debian.org/debian stretch/main amd64 linux-libc-dev amd64 4.9.228-1 [1511 kB] Get:81 http://deb.debian.org/debian stretch/main amd64 libc6-dev amd64 2.24-11+deb9u4 [2364 kB] Get:82 http://deb.debian.org/debian stretch/main amd64 libstdc++-6-dev amd64 6.3.0-18+deb9u1 [1420 kB] Get:83 http://deb.debian.org/debian stretch/main amd64 g++-6 amd64 6.3.0-18+deb9u1 [7094 kB] Get:84 http://deb.debian.org/debian stretch/main amd64 g++ amd64 4:6.3.0-4 [1546 B] Get:85 http://deb.debian.org/debian stretch/main amd64 hdf5-tools amd64 1.10.0-patch1+docs-3+deb9u1 [405 kB] Get:86 http://deb.debian.org/debian stretch/main amd64 kineticstools-data all 0.6.1+20161222-1 [102 MB] Get:87 http://deb.debian.org/debian stretch/main amd64 libblas-common amd64 3.7.0-2 [14.2 kB] Get:88 http://deb.debian.org/debian stretch/main amd64 libblas3 amd64 3.7.0-2 [155 kB] Get:89 http://deb.debian.org/debian stretch/main amd64 libblasr-dev amd64 0~20161219-1 [1700 kB] Get:90 http://deb.debian.org/debian stretch/main amd64 libexpat1-dev amd64 2.2.0-2+deb9u3 [134 kB] Get:91 http://deb.debian.org/debian stretch/main amd64 libpng16-16 amd64 1.6.28-1+deb9u1 [280 kB] Get:92 http://deb.debian.org/debian stretch/main amd64 libfreetype6 amd64 2.6.3-3.2+deb9u1 [438 kB] Get:93 http://deb.debian.org/debian stretch/main amd64 libhts-dev amd64 1.3.2-2 [322 kB] Get:94 http://deb.debian.org/debian stretch/main amd64 libjpeg62-turbo amd64 1:1.5.1-2 [134 kB] Get:95 http://deb.debian.org/debian stretch/main amd64 liblapack3 amd64 3.7.0-2 [2141 kB] Get:96 http://deb.debian.org/debian stretch/main amd64 liblcms2-2 amd64 2.8-4+deb9u1 [143 kB] Get:97 http://deb.debian.org/debian stretch/main amd64 libssl-dev amd64 1.1.0l-1~deb9u1 [1594 kB] Get:98 http://deb.debian.org/debian stretch/main amd64 libpbbam-dev amd64 0.7.4+ds-1 [89.8 kB] Get:99 http://deb.debian.org/debian stretch/main amd64 libpbdata-dev amd64 0~20161219-1 [199 kB] Get:100 http://deb.debian.org/debian stretch/main amd64 libpbihdf-dev amd64 0~20161219-1 [259 kB] Get:101 http://deb.debian.org/debian stretch/main amd64 libpbseq-dev all 0~20161219-1 [3902 B] Get:102 http://deb.debian.org/debian stretch/main amd64 libpython2.7 amd64 2.7.13-2+deb9u3 [1071 kB] Get:103 http://deb.debian.org/debian stretch/main amd64 libpython2.7-dev amd64 2.7.13-2+deb9u3 [28.2 MB] Get:104 http://deb.debian.org/debian stretch/main amd64 libpython-dev amd64 2.7.13-2 [20.1 kB] Get:105 http://deb.debian.org/debian stretch/main amd64 libsasl2-modules amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [102 kB] Get:106 http://deb.debian.org/debian stretch/main amd64 libssl-doc all 1.1.0l-1~deb9u1 [1480 kB] Get:107 http://deb.debian.org/debian stretch/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:108 http://deb.debian.org/debian stretch/main amd64 libtiff5 amd64 4.0.8-2+deb9u5 [239 kB] Get:109 http://deb.debian.org/debian stretch/main amd64 libwebp6 amd64 0.5.2-1 [235 kB] Get:110 http://deb.debian.org/debian stretch/main amd64 libwebpdemux2 amd64 0.5.2-1 [73.7 kB] Get:111 http://deb.debian.org/debian stretch/main amd64 libwebpmux2 amd64 0.5.2-1 [83.9 kB] Get:112 http://deb.debian.org/debian stretch/main amd64 manpages-dev all 4.10-2 [2145 kB] Get:113 http://deb.debian.org/debian stretch/main amd64 python-avro all 1.8.1+dfsg-1 [58.1 kB] Get:114 http://deb.debian.org/debian stretch/main amd64 python-cffi-backend amd64 1.9.1-2 [69.0 kB] Get:115 http://deb.debian.org/debian stretch/main amd64 python-pkg-resources all 33.1.1-1 [166 kB] Get:116 http://deb.debian.org/debian stretch/main amd64 python-chardet all 2.3.0-2 [96.0 kB] Get:117 http://deb.debian.org/debian stretch/main amd64 python-enum34 all 1.1.6-1 [35.0 kB] Get:118 http://deb.debian.org/debian stretch/main amd64 python-idna all 2.2-1 [32.6 kB] Get:119 http://deb.debian.org/debian stretch/main amd64 python-ipaddress all 1.0.17-1 [18.1 kB] Get:120 http://deb.debian.org/debian stretch/main amd64 python-pyasn1 all 0.1.9-2 [51.8 kB] Get:121 http://deb.debian.org/debian stretch/main amd64 python-setuptools all 33.1.1-1 [297 kB] Get:122 http://deb.debian.org/debian stretch/main amd64 python-six all 1.10.0-3 [14.4 kB] Get:123 http://deb.debian.org/debian stretch/main amd64 python-cryptography amd64 1.7.1-3+deb9u2 [212 kB] Get:124 http://deb.debian.org/debian stretch/main amd64 python-decorator all 4.0.11-1 [13.3 kB] Get:125 http://deb.debian.org/debian stretch/main amd64 python2.7-dev amd64 2.7.13-2+deb9u3 [290 kB] Get:126 http://deb.debian.org/debian stretch/main amd64 python-dev amd64 2.7.13-2 [1126 B] Get:127 http://deb.debian.org/debian stretch/main amd64 python-numpy amd64 1:1.12.1-3 [1936 kB] Get:128 http://deb.debian.org/debian stretch/main amd64 python-h5py amd64 2.7.0-1 [634 kB] Get:129 http://deb.debian.org/debian stretch/main amd64 python-pil amd64 4.0.0-4+deb9u1 [376 kB] Get:130 http://deb.debian.org/debian stretch/main amd64 python-imaging all 4.0.0-4+deb9u1 [50.5 kB] Get:131 http://deb.debian.org/debian stretch/main amd64 python-iso8601 all 0.1.11-1 [12.7 kB] Get:132 http://deb.debian.org/debian stretch/main amd64 python-urllib3 all 1.19.1-1 [77.5 kB] Get:133 http://deb.debian.org/debian stretch/main amd64 python-requests all 2.12.4-1 [101 kB] Get:134 http://deb.debian.org/debian stretch/main amd64 python-pbcommand all 0.5.3-1 [79.6 kB] Get:135 http://deb.debian.org/debian stretch/main amd64 python-pysam amd64 0.10.0+ds-2 [1301 kB] Get:136 http://deb.debian.org/debian stretch/main amd64 python-pbcore all 1.2.11+dfsg-1 [9087 kB] Get:137 http://deb.debian.org/debian stretch/main amd64 python-scipy amd64 0.18.1-2 [8933 kB] Get:138 http://deb.debian.org/debian stretch/main amd64 python-kineticstools amd64 0.6.1+20161222-1 [49.3 kB] Get:139 http://deb.debian.org/debian stretch/main amd64 python-openssl all 16.2.0-1 [43.7 kB] Get:140 http://deb.debian.org/debian stretch/main amd64 python-pbalign all 0.3.0-1 [37.2 kB] Get:141 http://deb.debian.org/debian stretch/main amd64 python-pbconsensuscore amd64 1.0.2-2 [651 kB] Get:142 http://deb.debian.org/debian stretch/main amd64 python-pbgenomicconsensus all 2.1.0-1 [45.7 kB] Get:143 http://deb.debian.org/debian stretch/main amd64 python-pbh5tools amd64 0.8.0+dfsg-5 [29.0 kB] Get:144 http://deb.debian.org/debian stretch/main amd64 smrtanalysis-dev all 0~20161126 [2546 B] Get:145 http://deb.debian.org/debian stretch/main amd64 publicsuffix all 20190415.1030-0+deb9u1 [108 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 220 MB in 6s (34.3 MB/s) Selecting previously unselected package libpython2.7-minimal:amd64. 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Setting up libmagic-mgc (1:5.30-1+deb9u3) ... Setting up bzip2 (1.0.6-8.1) ... Setting up libmagic1:amd64 (1:5.30-1+deb9u3) ... Setting up liblsan0:amd64 (6.3.0-18+deb9u1) ... Setting up libmpx2:amd64 (6.3.0-18+deb9u1) ... 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) ... Setting up krb5-locales (1.15-1+deb9u1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up publicsuffix (20190415.1030-0+deb9u1) ... Setting up libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Setting up libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Setting up xz-utils (5.2.2-1.2+b1) ... update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode Setting up openssl (1.1.0l-1~deb9u1) ... Setting up libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Setting up libmpfr4:amd64 (3.1.5-1) ... Setting up libmpc3:amd64 (1.0.3-1+b2) ... Setting up binutils (2.28-5) ... Setting up libffi6:amd64 (3.2.1-6) ... Setting up libssl-doc (1.1.0l-1~deb9u1) ... Setting up libc-dev-bin (2.24-11+deb9u4) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up libsasl2-modules:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up ca-certificates (20200601~deb9u1) ... Updating certificates in /etc/ssl/certs... 126 added, 0 removed; done. Setting up manpages-dev (4.10-2) ... Setting up libc6-dev:amd64 (2.24-11+deb9u4) ... Setting up libitm1:amd64 (6.3.0-18+deb9u1) ... 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 libwebp6:amd64 (0.5.2-1) ... Setting up libidn2-0:amd64 (0.16-1+deb9u1) ... Setting up libgcc-6-dev:amd64 (6.3.0-18+deb9u1) ... Setting up libstdc++-6-dev:amd64 (6.3.0-18+deb9u1) ... Setting up libhdf5-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Setting up libpsl5:amd64 (0.17.0-3) ... Setting up libssl-dev:amd64 (1.1.0l-1~deb9u1) ... 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 libwebpmux2:amd64 (0.5.2-1) ... Setting up file (1:5.30-1+deb9u3) ... Setting up libkrb5support0:amd64 (1.15-1+deb9u1) ... Setting up hdf5-tools (1.10.0-patch1+docs-3+deb9u1) ... Setting up libhogweed4:amd64 (3.3-1+b2) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up libisl15:amd64 (0.18-1) ... Setting up libp11-kit0:amd64 (0.23.3-2) ... Setting up libpython2.7:amd64 (2.7.13-2+deb9u3) ... Setting up libwebpdemux2:amd64 (0.5.2-1) ... Setting up libexpat1-dev:amd64 (2.2.0-2+deb9u3) ... Setting up libpython2.7-dev:amd64 (2.7.13-2+deb9u3) ... Setting up cpp-6 (6.3.0-18+deb9u1) ... Setting up python2.7-dev (2.7.13-2+deb9u3) ... Setting up python (2.7.13-2) ... Setting up python-idna (2.2-1) ... Setting up cpp (4:6.3.0-4) ... Setting up libpython-dev:amd64 (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 python-dev (2.7.13-2) ... Setting up python-pyasn1 (0.1.9-2) ... 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 gcc-6 (6.3.0-18+deb9u1) ... Setting up g++-6 (6.3.0-18+deb9u1) ... Setting up python-cffi-backend (1.9.1-2) ... Setting up python-six (1.10.0-3) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Setting up python-enum34 (1.1.6-1) ... 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-ipaddress (1.0.17-1) ... Setting up python-pil:amd64 (4.0.0-4+deb9u1) ... Setting up python-pbconsensuscore (1.0.2-2) ... Setting up python-setuptools (33.1.1-1) ... Setting up python-urllib3 (1.19.1-1) ... Setting up python-h5py (2.7.0-1) ... Setting up python-chardet (2.3.0-2) ... Setting up python-scipy (0.18.1-2) ... Setting up gcc (4:6.3.0-4) ... Setting up libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Setting up python-imaging (4.0.0-4+deb9u1) ... Setting up python-cryptography (1.7.1-3+deb9u2) ... Setting up python-requests (2.12.4-1) ... Setting up g++ (4:6.3.0-4) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up python-pbcommand (0.5.3-1) ... Setting up python-openssl (16.2.0-1) ... Setting up libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Setting up libhts1:amd64 (1.3.2-2) ... Setting up libhts-dev: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 python-pbh5tools (0.8.0+dfsg-5) ... Setting up libpbbam-dev (0.7.4+ds-1) ... Setting up python-pbgenomicconsensus (2.1.0-1) ... Setting up libpbdata:amd64 (0~20161219-1) ... Setting up libpbihdf:amd64 (0~20161219-1) ... Setting up libblasr:amd64 (0~20161219-1) ... Setting up libpbihdf-dev:amd64 (0~20161219-1) ... Setting up libpbdata-dev:amd64 (0~20161219-1) ... Setting up libblasr-dev:amd64 (0~20161219-1) ... Setting up libpbseq-dev (0~20161219-1) ... Setting up libpbseq (0~20161219-1) ... Setting up blasr (5.3+0-1) ... Setting up python-pbalign (0.3.0-1) ... Setting up smrtanalysis-dev (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. 0m44.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-get', '-y', 'install', 'smrtanalysis-dev'] 0m44.1s INFO: Running scripts post_install 0m44.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_install_exceptions'] 0m44.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_install_exceptions'] 0m44.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2vg233f0'] 0m44.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2vg233f0'] 0m44.9s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp2vg233f0 to buster 0m44.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main 0m44.9s INFO: Running scripts pre_distupgrade 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_distupgrade_exceptions'] 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_distupgrade_exceptions'] 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m45.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m45.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m45.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m45.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-get', 'update'] 0m49.1s 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 3s (4477 kB/s) Reading package lists... 0m49.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-get', 'update'] 0m49.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-get', '-y', 'upgrade'] 1m13.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages have been kept back: apt bash binutils blasr ca-certificates coreutils cpp dash dpkg e2fslibs e2fsprogs g++ gcc gpgv hdf5-tools libapt-pkg5.0 libatomic1 libblas3 libblasr libblasr-dev libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcc1-0 libcilkrts5 libcomerr2 libcurl3-gnutls libexpat1 libexpat1-dev libfdisk1 libgcc1 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libhts-dev libidn2-0 libitm1 libk5crypto3 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 liblsan0 libmount1 libmpc3 libmpx2 libncursesw5 libp11-kit0 libpam-modules libpam-modules-bin libpbbam-dev libpbdata libpbdata-dev libpbihdf libpbihdf-dev libpbseq libpbseq-dev libpsl5 libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 libsmartcols1 libsqlite3-0 libss2 libssl-dev libssl1.1 libstdc++6 libsystemd0 libtiff5 libtinfo5 libtsan0 libubsan0 libudev1 libuuid1 login mount ncurses-base ncurses-bin openssl perl-base python python-cryptography python-dev python-h5py python-minimal python-numpy python-openssl python-pbcommand python-pbconsensuscore python-pil python-pysam python-requests python-scipy python-urllib3 python2.7 python2.7-dev python2.7-minimal util-linux The following packages will be upgraded: adduser base-files base-passwd bsdutils bzip2 debconf debian-archive-keyring debianutils diffutils file findutils grep gzip hostname init-system-helpers kineticstools-data krb5-locales libacl1 libaec0 libattr1 libaudit-common libaudit1 libbz2-1.0 libcap-ng0 libdb5.3 libdebconfclient0 libffi6 libfreetype6 libgcrypt20 libgmp10 libhogweed4 libidn11 libjpeg62-turbo libkeyutils1 liblcms2-2 libldap-common liblz4-1 liblzma5 libmagic-mgc libmagic1 libnettle6 libnghttp2-14 libpam-runtime libpam0g libpcre3 libpng16-16 librtmp1 libsasl2-2 libsasl2-modules libsasl2-modules-db libselinux1 libsemanage-common libsemanage1 libsepol1 libssh2-1 libssl-doc libsz2 libtasn1-6 libwebp6 libwebpdemux2 linux-libc-dev manpages manpages-dev mime-support multiarch-support passwd publicsuffix python-avro python-cffi-backend python-chardet python-decorator python-enum34 python-idna python-kineticstools python-pbalign python-pbcore python-pbgenomicconsensus python-pbh5tools python-pkg-resources python-pyasn1 python-setuptools python-six readline-common sed sensible-utils sysvinit-utils tar xz-utils zlib1g 89 upgraded, 0 newly installed, 0 to remove and 106 not upgraded. Need to get 132 MB of archives. After this operation, 12.3 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 debianutils amd64 4.8.6.1 [100 kB] Get:4 http://deb.debian.org/debian buster/main amd64 diffutils amd64 1:3.7-3 [371 kB] Get:5 http://deb.debian.org/debian buster/main amd64 findutils amd64 4.6.0+git+20190209-2 [684 kB] Get:6 http://deb.debian.org/debian buster/main amd64 grep amd64 3.3-1 [373 kB] Get:7 http://deb.debian.org/debian buster/main amd64 gzip amd64 1.9-3+deb10u1 [128 kB] Get:8 http://deb.debian.org/debian buster/main amd64 hostname amd64 3.21 [14.8 kB] Get:9 http://deb.debian.org/debian buster/main amd64 sed amd64 4.7-1 [310 kB] Get:10 http://deb.debian.org/debian buster/main amd64 tar amd64 1.30+dfsg-6 [780 kB] Get:11 http://deb.debian.org/debian buster/main amd64 libdebconfclient0 amd64 0.249 [49.1 kB] Get:12 http://deb.debian.org/debian buster/main amd64 base-passwd amd64 3.5.46 [56.7 kB] Get:13 http://deb.debian.org/debian buster/main amd64 init-system-helpers all 1.56+nmu1 [46.8 kB] Get:14 http://deb.debian.org/debian buster/main amd64 sysvinit-utils amd64 2.93-8 [78.4 kB] Get:15 http://deb.debian.org/debian buster/main amd64 debconf all 1.5.71+deb10u1 [145 kB] Get:16 http://deb.debian.org/debian buster/main amd64 libpam-runtime all 1.3.1-5 [211 kB] Get:17 http://deb.debian.org/debian buster/main amd64 libaudit-common all 1:2.8.4-3 [22.4 kB] Get:18 http://deb.debian.org/debian buster/main amd64 libcap-ng0 amd64 0.7.9-2 [14.3 kB] Get:19 http://deb.debian.org/debian buster/main amd64 libaudit1 amd64 1:2.8.4-3 [57.3 kB] Get:20 http://deb.debian.org/debian buster/main amd64 libpam0g amd64 1.3.1-5 [126 kB] Get:21 http://deb.debian.org/debian buster/main amd64 libpcre3 amd64 2:8.39-12 [341 kB] Get:22 http://deb.debian.org/debian buster/main amd64 libselinux1 amd64 2.8-1+b1 [86.9 kB] Get:23 http://deb.debian.org/debian buster/main amd64 libsepol1 amd64 2.8-1 [263 kB] Get:24 http://deb.debian.org/debian buster/main amd64 libsemanage-common all 2.8-2 [17.7 kB] Get:25 http://deb.debian.org/debian buster/main amd64 libsemanage1 amd64 2.8-2 [96.5 kB] Get:26 http://deb.debian.org/debian buster/main amd64 bzip2 amd64 1.0.6-9.2~deb10u1 [48.4 kB] Get:27 http://deb.debian.org/debian buster/main amd64 libbz2-1.0 amd64 1.0.6-9.2~deb10u1 [45.3 kB] Get:28 http://deb.debian.org/debian buster/main amd64 passwd amd64 1:4.5-1.1 [1005 kB] Get:29 http://deb.debian.org/debian buster/main amd64 adduser all 3.118 [240 kB] Get:30 http://deb.debian.org/debian buster/main amd64 debian-archive-keyring all 2019.1+deb10u1 [93.5 kB] Get:31 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:32 http://deb.debian.org/debian buster/main amd64 libattr1 amd64 1:2.4.48-4 [21.3 kB] Get:33 http://deb.debian.org/debian buster/main amd64 libacl1 amd64 2.2.53-4 [30.4 kB] Get:34 http://deb.debian.org/debian buster/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.5 [683 kB] Get:35 http://deb.debian.org/debian buster/main amd64 libgcrypt20 amd64 1.8.4-5+deb10u1 [556 kB] Get:36 http://deb.debian.org/debian buster/main amd64 liblz4-1 amd64 1.8.3-1+deb10u1 [53.3 kB] Get:37 http://deb.debian.org/debian buster/main amd64 liblzma5 amd64 5.2.4-1+deb10u1 [153 kB] Get:38 http://deb.debian.org/debian buster/main amd64 zlib1g amd64 1:1.2.11.dfsg-1+deb10u1 [90.8 kB] Get:39 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get:40 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get:41 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get:42 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get:43 http://deb.debian.org/debian buster/main amd64 krb5-locales all 1.17-3+deb10u4 [95.6 kB] Get:44 http://deb.debian.org/debian buster/main amd64 manpages-dev all 4.16-2 [2232 kB] Get:45 http://deb.debian.org/debian buster/main amd64 manpages all 4.16-2 [1295 kB] Get:46 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get:47 http://deb.debian.org/debian buster/main amd64 xz-utils amd64 5.2.4-1+deb10u1 [183 kB] Get:48 http://deb.debian.org/debian buster/main amd64 python-setuptools all 40.8.0-1 [382 kB] Get:49 http://deb.debian.org/debian buster/main amd64 python-pkg-resources all 40.8.0-1 [182 kB] Get:50 http://deb.debian.org/debian buster/main amd64 python-pbcore all 1.6.5+dfsg-1 [9100 kB] Get:51 http://deb.debian.org/debian buster/main amd64 python-kineticstools amd64 0.6.1+git20180425.27a1878-2 [49.5 kB] Get:52 http://deb.debian.org/debian buster/main amd64 kineticstools-data all 0.6.1+git20180425.27a1878-2 [103 MB] Get:53 http://deb.debian.org/debian buster/main amd64 libaec0 amd64 1.0.2-1 [20.1 kB] Get:54 http://deb.debian.org/debian buster/main amd64 libffi6 amd64 3.2.1-9 [20.8 kB] Get:55 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get:56 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u3 [380 kB] Get:57 http://deb.debian.org/debian buster/main amd64 libgmp10 amd64 2:6.1.2+dfsg-4+deb10u1 [251 kB] Get:58 http://deb.debian.org/debian buster/main amd64 libhogweed4 amd64 3.4.1-1+deb10u1 [141 kB] Get:59 http://deb.debian.org/debian buster/main amd64 libnettle6 amd64 3.4.1-1+deb10u1 [215 kB] Get:60 http://deb.debian.org/debian buster/main amd64 libidn11 amd64 1.33-2.2 [116 kB] Get:61 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get:62 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get:63 http://deb.debian.org/debian buster/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get:64 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u7 [90.1 kB] Get:65 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get:66 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get:67 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u2 [69.2 kB] Get:68 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u2 [106 kB] Get:69 http://deb.debian.org/debian buster/main amd64 libsasl2-modules amd64 2.1.27+dfsg-1+deb10u2 [104 kB] Get:70 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:71 http://deb.debian.org/debian buster/main amd64 libssl-doc all 1.1.1n-0+deb10u3 [1754 kB] Get:72 http://deb.debian.org/debian buster/main amd64 libsz2 amd64 1.0.2-1 [6676 B] Get:73 http://deb.debian.org/debian buster/main amd64 libtasn1-6 amd64 4.13-3 [51.9 kB] Get:74 http://deb.debian.org/debian buster/main amd64 libwebp6 amd64 0.6.1-2+deb10u1 [261 kB] Get:75 http://deb.debian.org/debian buster/main amd64 libwebpdemux2 amd64 0.6.1-2+deb10u1 [87.6 kB] Get:76 http://deb.debian.org/debian buster/main amd64 linux-libc-dev amd64 4.19.249-2 [1530 kB] Get:77 http://deb.debian.org/debian buster/main amd64 multiarch-support amd64 2.28-10+deb10u1 [216 kB] Get:78 http://deb.debian.org/debian buster/main amd64 publicsuffix all 20220811.1734-0+deb10u1 [127 kB] Get:79 http://deb.debian.org/debian buster/main amd64 python-avro all 1.8.2+dfsg-2 [59.4 kB] Get:80 http://deb.debian.org/debian buster/main amd64 python-cffi-backend amd64 1.12.2-1 [78.8 kB] Get:81 http://deb.debian.org/debian buster/main amd64 python-chardet all 3.0.4-3 [80.6 kB] Get:82 http://deb.debian.org/debian buster/main amd64 python-decorator all 4.3.0-1.1 [14.4 kB] Get:83 http://deb.debian.org/debian buster/main amd64 python-enum34 all 1.1.6-2 [35.3 kB] Get:84 http://deb.debian.org/debian buster/main amd64 python-idna all 2.6-1 [34.1 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 python-pbgenomicconsensus all 2.3.2-5 [47.2 kB] Get:87 http://deb.debian.org/debian buster/main amd64 python-pbh5tools amd64 0.8.0+git20170929.58d54ff+dfsg-1 [29.5 kB] Get:88 http://deb.debian.org/debian buster/main amd64 python-pyasn1 all 0.4.2-3 [57.6 kB] Get:89 http://deb.debian.org/debian buster/main amd64 python-six all 1.12.0-1 [15.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 MB in 8s (16.4 MB/s) (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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Setting up libtasn1-6:amd64 (4.13-3) ... Setting up libmagic-mgc (1:5.35-4+deb10u2) ... Setting up bzip2 (1.0.6-9.2~deb10u1) ... Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... 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) ... Setting up krb5-locales (1.17-3+deb10u4) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up publicsuffix (20220811.1734-0+deb10u1) ... Setting up xz-utils (5.2.4-1+deb10u1) ... Setting up python-pbcore (1.6.5+dfsg-1) ... Setting up python-enum34 (1.1.6-2) ... Setting up libffi6:amd64 (3.2.1-9) ... Setting up python-decorator (4.3.0-1.1) ... Setting up libssl-doc (1.1.1n-0+deb10u3) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up libsasl2-modules:amd64 (2.1.27+dfsg-1+deb10u2) ... Setting up manpages-dev (4.16-2) ... Setting up libidn11:amd64 (1.33-2.2) ... Setting up python-kineticstools (0.6.1+git20180425.27a1878-2) ... Setting up libsz2:amd64 (1.0.2-1) ... Setting up libwebp6:amd64 (0.6.1-2+deb10u1) ... Setting up python-setuptools (40.8.0-1) ... Setting up python-pbh5tools (0.8.0+git20170929.58d54ff+dfsg-1) ... Setting up python-chardet (3.0.4-3) ... Setting up python-pbgenomicconsensus (2.3.2-5) ... Setting up python-pbalign (0.3.2-1) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libhogweed4:amd64 (3.4.1-1+deb10u1) ... Setting up python-cffi-backend (1.12.2-1) ... Setting up libwebpdemux2:amd64 (0.6.1-2+deb10u1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 1m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-get', '-y', 'upgrade'] 1m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-get', '-yf', 'dist-upgrade'] 1m54.2s 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 libwebpmux2 python-imaging python-pyasn1 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: binutils-common binutils-x86-64-linux-gnu cpp-8 e2fsprogs-l10n fdisk g++-8 gcc-7-base gcc-8 gcc-8-base hdf5-helpers libaec-dev libasan5 libbinutils libcom-err2 libdeflate0 libext2fs2 libgcc-8-dev libgfortran5 libgpg-error-l10n libgpm2 libhdf5-103 libhdf5-cpp-103 libhdf5-dev libhts2 libimagequant0 libisl19 libjpeg-dev libjpeg62-turbo-dev liblzma-dev libmpfr6 libncursesw6 libpbbam0.19.0 libpython2-dev libpython2-stdlib libseccomp2 libstdc++-8-dev libtinfo6 libubsan1 libunistring2 libwebpmux3 libzstd1 python-asn1crypto python-certifi python-olefile python-tz python2 python2-dev python2-minimal tzdata zlib1g-dev The following packages will be upgraded: apt bash binutils blasr ca-certificates coreutils cpp dash dpkg e2fslibs e2fsprogs g++ gcc gpgv hdf5-tools libapt-pkg5.0 libatomic1 libblas3 libblasr libblasr-dev libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcc1-0 libcilkrts5 libcomerr2 libcurl3-gnutls libexpat1 libexpat1-dev libfdisk1 libgcc1 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libhts-dev libidn2-0 libitm1 libk5crypto3 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 liblsan0 libmount1 libmpc3 libmpx2 libncursesw5 libp11-kit0 libpam-modules libpam-modules-bin libpbbam-dev libpbdata libpbdata-dev libpbihdf libpbihdf-dev libpbseq libpbseq-dev libpsl5 libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 libsmartcols1 libsqlite3-0 libss2 libssl-dev libssl1.1 libstdc++6 libsystemd0 libtiff5 libtinfo5 libtsan0 libubsan0 libudev1 libuuid1 login mount ncurses-base ncurses-bin openssl perl-base python python-cryptography python-dev python-h5py python-minimal python-numpy python-openssl python-pbcommand python-pbconsensuscore python-pil python-pysam python-requests python-scipy python-urllib3 python2.7 python2.7-dev python2.7-minimal util-linux 106 upgraded, 50 newly installed, 3 to remove and 0 not upgraded. Need to get 145 MB of archives. After this operation, 190 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian buster/main amd64 libc6-dev amd64 2.28-10+deb10u1 [2692 kB] Get:2 http://deb.debian.org/debian buster/main amd64 libc-dev-bin amd64 2.28-10+deb10u1 [276 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 gcc-8-base amd64 8.3.0-6 [191 kB] Get:6 http://deb.debian.org/debian buster/main amd64 libgcc1 amd64 1:8.3.0-6 [40.6 kB] Get:7 http://deb.debian.org/debian buster/main amd64 libtinfo6 amd64 6.1+20181013-2+deb10u2 [325 kB] Get:8 http://deb.debian.org/debian buster/main amd64 bash amd64 5.0-4 [1378 kB] Get:9 http://deb.debian.org/debian buster/main amd64 coreutils amd64 8.30-3 [2708 kB] Get:10 http://deb.debian.org/debian buster/main amd64 libzstd1 amd64 1.3.8+dfsg-3+deb10u2 [237 kB] Get:11 http://deb.debian.org/debian buster/main amd64 libunistring2 amd64 0.9.10-1 [381 kB] Get:12 http://deb.debian.org/debian buster/main amd64 libidn2-0 amd64 2.0.5-1+deb10u1 [76.7 kB] Get:13 http://deb.debian.org/debian buster/main amd64 libp11-kit0 amd64 0.23.15-2+deb10u1 [316 kB] Get:14 http://deb.debian.org/debian buster/main amd64 libgnutls30 amd64 3.6.7-4+deb10u8 [1126 kB] Get:15 http://deb.debian.org/debian buster/main amd64 libseccomp2 amd64 2.3.3-4 [41.4 kB] Get:16 http://deb.debian.org/debian buster/main amd64 libgpg-error0 amd64 1.35-1 [71.1 kB] Get:17 http://deb.debian.org/debian buster/main amd64 gpgv amd64 2.2.12-1+deb10u2 [584 kB] Get:18 http://deb.debian.org/debian buster/main amd64 libstdc++6 amd64 8.3.0-6 [395 kB] Get:19 http://deb.debian.org/debian buster/main amd64 libapt-pkg5.0 amd64 1.8.2.3 [967 kB] Get:20 http://deb.debian.org/debian buster/main amd64 apt amd64 1.8.2.3 [1418 kB] Get:21 http://deb.debian.org/debian buster/main amd64 libsystemd0 amd64 241-7~deb10u8 [331 kB] Get:22 http://deb.debian.org/debian buster/main amd64 libudev1 amd64 241-7~deb10u8 [151 kB] Get:23 http://deb.debian.org/debian buster/main amd64 dpkg amd64 1.19.8 [2210 kB] Get:24 http://deb.debian.org/debian buster/main amd64 dash amd64 0.5.10.2-5 [112 kB] Get:25 http://deb.debian.org/debian buster/main amd64 libcom-err2 amd64 1.44.5-1+deb10u3 [68.4 kB] Get:26 http://deb.debian.org/debian buster/main amd64 libcomerr2 amd64 1.44.5-1+deb10u3 [64.2 kB] Get:27 http://deb.debian.org/debian buster/main amd64 libext2fs2 amd64 1.44.5-1+deb10u3 [221 kB] Get:28 http://deb.debian.org/debian buster/main amd64 e2fslibs amd64 1.44.5-1+deb10u3 [64.2 kB] Get:29 http://deb.debian.org/debian buster/main amd64 e2fsprogs amd64 1.44.5-1+deb10u3 [576 kB] Get:30 http://deb.debian.org/debian buster/main amd64 libuuid1 amd64 2.33.1-0.1 [78.3 kB] Get:31 http://deb.debian.org/debian buster/main amd64 libblkid1 amd64 2.33.1-0.1 [195 kB] Get:32 http://deb.debian.org/debian buster/main amd64 libsmartcols1 amd64 2.33.1-0.1 [150 kB] Get:33 http://deb.debian.org/debian buster/main amd64 libfdisk1 amd64 2.33.1-0.1 [234 kB] Get:34 http://deb.debian.org/debian buster/main amd64 libncursesw6 amd64 6.1+20181013-2+deb10u2 [132 kB] Get:35 http://deb.debian.org/debian buster/main amd64 libmount1 amd64 2.33.1-0.1 [207 kB] Get:36 http://deb.debian.org/debian buster/main amd64 fdisk amd64 2.33.1-0.1 [179 kB] Get:37 http://deb.debian.org/debian buster/main amd64 login amd64 1:4.5-1.1 [751 kB] Get:38 http://deb.debian.org/debian buster/main amd64 util-linux amd64 2.33.1-0.1 [1062 kB] Get:39 http://deb.debian.org/debian buster/main amd64 mount amd64 2.33.1-0.1 [174 kB] Get:40 http://deb.debian.org/debian buster/main amd64 ncurses-bin amd64 6.1+20181013-2+deb10u2 [406 kB] Get:41 http://deb.debian.org/debian buster/main amd64 perl-base amd64 5.28.1-6+deb10u1 [1514 kB] Get:42 http://deb.debian.org/debian buster/main amd64 libtinfo5 amd64 6.1+20181013-2+deb10u2 [321 kB] Get:43 http://deb.debian.org/debian buster/main amd64 libncursesw5 amd64 6.1+20181013-2+deb10u2 [118 kB] Get:44 http://deb.debian.org/debian buster/main amd64 ncurses-base all 6.1+20181013-2+deb10u2 [258 kB] Get:45 http://deb.debian.org/debian buster/main amd64 libquadmath0 amd64 8.3.0-6 [133 kB] Get:46 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get:47 http://deb.debian.org/debian buster/main amd64 libpbihdf-dev amd64 5.3.1+dfsg-2.1 [264 kB] Get:48 http://deb.debian.org/debian buster/main amd64 libblasr-dev amd64 5.3.1+dfsg-2.1 [1697 kB] Get:49 http://deb.debian.org/debian buster/main amd64 libblasr amd64 5.3.1+dfsg-2.1 [876 kB] Get:50 http://deb.debian.org/debian buster/main amd64 libpbihdf amd64 5.3.1+dfsg-2.1 [170 kB] Get:51 http://deb.debian.org/debian buster/main amd64 blasr amd64 5.3.2+dfsg-1.1 [212 kB] Get:52 http://deb.debian.org/debian buster/main amd64 hdf5-tools amd64 1.10.4+repack-10 [438 kB] Get:53 http://deb.debian.org/debian buster/main amd64 python-h5py amd64 2.8.0-3 [693 kB] Get:54 http://deb.debian.org/debian buster/main amd64 libhdf5-103 amd64 1.10.4+repack-10 [1325 kB] Get:55 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1+deb10u1 [210 kB] Get:56 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo-dev amd64 1:1.5.2-2+deb10u1 [208 kB] Get:57 http://deb.debian.org/debian buster/main amd64 libjpeg-dev all 1:1.5.2-2+deb10u1 [57.7 kB] Get:58 http://deb.debian.org/debian buster/main amd64 libaec-dev amd64 1.0.2-1 [18.4 kB] Get:59 http://deb.debian.org/debian buster/main amd64 hdf5-helpers amd64 1.10.4+repack-10 [35.2 kB] Get:60 http://deb.debian.org/debian buster/main amd64 libssl-dev amd64 1.1.1n-0+deb10u3 [1808 kB] Get:61 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1n-0+deb10u3 [1551 kB] Get:62 http://deb.debian.org/debian buster/main amd64 python2.7-dev amd64 2.7.16-2+deb10u1 [294 kB] Get:63 http://deb.debian.org/debian buster/main amd64 libpython2.7-dev amd64 2.7.16-2+deb10u1 [31.6 MB] Get:64 http://deb.debian.org/debian buster/main amd64 libpython2.7 amd64 2.7.16-2+deb10u1 [1036 kB] Get:65 http://deb.debian.org/debian buster/main amd64 libexpat1-dev amd64 2.2.6-2+deb10u4 [155 kB] Get:66 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u4 [108 kB] Get:67 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get:68 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get:69 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get:70 http://deb.debian.org/debian buster/main amd64 python-numpy amd64 1:1.16.2-1 [2101 kB] Get:71 http://deb.debian.org/debian buster/main amd64 python-scipy amd64 1.1.0-7 [10.1 MB] Get:72 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:73 http://deb.debian.org/debian buster/main amd64 libsqlite3-0 amd64 3.27.2-3+deb10u1 [641 kB] Get:74 http://deb.debian.org/debian buster/main amd64 python-pysam amd64 0.15.2+ds-2 [1629 kB] Get:75 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get:76 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get:77 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get:78 http://deb.debian.org/debian buster/main amd64 python-dev amd64 2.7.16-1 [1192 B] Get:79 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get:80 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get:81 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get:82 http://deb.debian.org/debian buster/main amd64 libpython-dev amd64 2.7.16-1 [20.9 kB] Get:83 http://deb.debian.org/debian buster/main amd64 libpython2-dev amd64 2.7.16-1 [20.9 kB] Get:84 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get:85 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get:86 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get:87 http://deb.debian.org/debian buster/main amd64 python2-dev amd64 2.7.16-1 [1212 B] Get:88 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u4 [158 kB] Get:89 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u4 [369 kB] Get:90 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u4 [122 kB] Get:91 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u4 [65.9 kB] Get:92 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u7 [224 kB] Get:93 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:94 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get:95 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get:96 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get:97 http://deb.debian.org/debian buster/main amd64 liblzma-dev amd64 5.2.4-1+deb10u1 [210 kB] Get:98 http://deb.debian.org/debian buster/main amd64 libhts-dev amd64 1.9-12~deb10u1 [4347 kB] Get:99 http://deb.debian.org/debian buster/main amd64 libpbdata-dev amd64 5.3.1+dfsg-2.1 [201 kB] Get:100 http://deb.debian.org/debian buster/main amd64 libpbdata amd64 5.3.1+dfsg-2.1 [130 kB] Get:101 http://deb.debian.org/debian buster/main amd64 libpbbam-dev amd64 0.19.0+dfsg-4 [93.3 kB] Get:102 http://deb.debian.org/debian buster/main amd64 libpbbam0.19.0 amd64 0.19.0+dfsg-4 [551 kB] Get:103 http://deb.debian.org/debian buster/main amd64 libpbseq all 5.3.1+dfsg-2.1 [4584 B] Get:104 http://deb.debian.org/debian buster/main amd64 libhdf5-cpp-103 amd64 1.10.4+repack-10 [146 kB] Get:105 http://deb.debian.org/debian buster/main amd64 libhdf5-dev amd64 1.10.4+repack-10 [2598 kB] Get:106 http://deb.debian.org/debian buster/main amd64 libpam-modules-bin amd64 1.3.1-5 [107 kB] Get:107 http://deb.debian.org/debian buster/main amd64 libpam-modules amd64 1.3.1-5 [309 kB] Get:108 http://deb.debian.org/debian buster/main amd64 libss2 amd64 1.44.5-1+deb10u3 [72.9 kB] Get:109 http://deb.debian.org/debian buster/main amd64 tzdata all 2021a-0+deb10u6 [265 kB] Get:110 http://deb.debian.org/debian buster/main amd64 binutils amd64 2.31.1-16 [56.8 kB] Get:111 http://deb.debian.org/debian buster/main amd64 binutils-common amd64 2.31.1-16 [2073 kB] Get:112 http://deb.debian.org/debian buster/main amd64 libbinutils amd64 2.31.1-16 [478 kB] Get:113 http://deb.debian.org/debian buster/main amd64 binutils-x86-64-linux-gnu amd64 2.31.1-16 [1823 kB] Get:114 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1n-0+deb10u3 [855 kB] Get:115 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get:116 http://deb.debian.org/debian buster/main amd64 libisl19 amd64 0.20-2 [587 kB] Get:117 http://deb.debian.org/debian buster/main amd64 libmpc3 amd64 1.1.0-1 [41.3 kB] Get:118 http://deb.debian.org/debian buster/main amd64 libmpfr6 amd64 4.0.2-1 [775 kB] Get:119 http://deb.debian.org/debian buster/main amd64 cpp-8 amd64 8.3.0-6 [8914 kB] Get:120 http://deb.debian.org/debian buster/main amd64 cpp amd64 4:8.3.0-1 [19.4 kB] Get:121 http://deb.debian.org/debian buster/main amd64 e2fsprogs-l10n all 1.44.5-1+deb10u3 [504 kB] Get:122 http://deb.debian.org/debian buster/main amd64 libcc1-0 amd64 8.3.0-6 [46.6 kB] Get:123 http://deb.debian.org/debian buster/main amd64 libgomp1 amd64 8.3.0-6 [75.8 kB] Get:124 http://deb.debian.org/debian buster/main amd64 libitm1 amd64 8.3.0-6 [27.7 kB] Get:125 http://deb.debian.org/debian buster/main amd64 libatomic1 amd64 8.3.0-6 [9032 B] Get:126 http://deb.debian.org/debian buster/main amd64 libasan5 amd64 8.3.0-6 [362 kB] Get:127 http://deb.debian.org/debian buster/main amd64 liblsan0 amd64 8.3.0-6 [131 kB] Get:128 http://deb.debian.org/debian buster/main amd64 libtsan0 amd64 8.3.0-6 [283 kB] Get:129 http://deb.debian.org/debian buster/main amd64 libubsan1 amd64 8.3.0-6 [120 kB] Get:130 http://deb.debian.org/debian buster/main amd64 libmpx2 amd64 8.3.0-6 [11.4 kB] Get:131 http://deb.debian.org/debian buster/main amd64 libgcc-8-dev amd64 8.3.0-6 [2298 kB] Get:132 http://deb.debian.org/debian buster/main amd64 gcc-8 amd64 8.3.0-6 [9452 kB] Get:133 http://deb.debian.org/debian buster/main amd64 gcc amd64 4:8.3.0-1 [5196 B] Get:134 http://deb.debian.org/debian buster/main amd64 libstdc++-8-dev amd64 8.3.0-6 [1532 kB] Get:135 http://deb.debian.org/debian buster/main amd64 g++-8 amd64 8.3.0-6 [9752 kB] Get:136 http://deb.debian.org/debian buster/main amd64 g++ amd64 4:8.3.0-1 [1644 B] Get:137 http://deb.debian.org/debian buster/main amd64 gcc-7-base amd64 7.4.0-6 [190 kB] Get:138 http://deb.debian.org/debian buster/main amd64 libcilkrts5 amd64 7.4.0-6 [42.2 kB] Get:139 http://deb.debian.org/debian buster/main amd64 libgpg-error-l10n all 1.35-1 [97.6 kB] Get:140 http://deb.debian.org/debian buster/main amd64 libgpm2 amd64 1.20.7-5 [35.1 kB] Get:141 http://deb.debian.org/debian buster/main amd64 libimagequant0 amd64 2.12.2-1.1 [32.5 kB] Get:142 http://deb.debian.org/debian buster/main amd64 libpbseq-dev all 5.3.1+dfsg-2.1 [4612 B] Get:143 http://deb.debian.org/debian buster/main amd64 libtiff5 amd64 4.1.0+git191117-2~deb10u4 [271 kB] Get:144 http://deb.debian.org/debian buster/main amd64 libubsan0 amd64 7.4.0-6 [124 kB] Get:145 http://deb.debian.org/debian buster/main amd64 libwebpmux3 amd64 0.6.1-2+deb10u1 [97.8 kB] Get:146 http://deb.debian.org/debian buster/main amd64 python-asn1crypto all 0.24.0-1 [78.1 kB] Get:147 http://deb.debian.org/debian buster/main amd64 python-certifi all 2018.8.24-1 [140 kB] Get:148 http://deb.debian.org/debian buster/main amd64 python-cryptography amd64 2.6.1-3+deb10u2 [218 kB] Get:149 http://deb.debian.org/debian buster/main amd64 python-olefile all 0.46-1 [35.9 kB] Get:150 http://deb.debian.org/debian buster/main amd64 python-openssl all 19.0.0-1 [52.0 kB] Get:151 http://deb.debian.org/debian buster/main amd64 python-requests all 2.21.0-1 [67.1 kB] Get:152 http://deb.debian.org/debian buster/main amd64 python-urllib3 all 1.24.1-1 [97.0 kB] Get:153 http://deb.debian.org/debian buster/main amd64 python-tz all 2019.1-1 [33.6 kB] Get:154 http://deb.debian.org/debian buster/main amd64 python-pbcommand all 1.1.1-1 [88.7 kB] Get:155 http://deb.debian.org/debian buster/main amd64 python-pbconsensuscore amd64 1.1.1+dfsg-1 [672 kB] Get:156 http://deb.debian.org/debian buster/main amd64 python-pil amd64 5.4.1-2+deb10u3 [395 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 145 MB in 4s (31.9 MB/s) (Reading database ... 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Setting up libc6:amd64 (2.28-10+deb10u1) ... Installing new version of config file /etc/ld.so.conf.d/x86_64-linux-gnu.conf ... (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 ... 18976 files and directories currently installed.) Preparing to unpack .../libc-bin_2.28-10+deb10u1_amd64.deb ... Unpacking libc-bin (2.28-10+deb10u1) over (2.24-11+deb9u4) ... Setting up libc-bin (2.28-10+deb10u1) ... Updating /etc/nsswitch.conf to current default. Selecting previously unselected package gcc-8-base: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 ... 18976 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 ... 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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 ... 19030 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 ... 19078 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-libpbihdf-dev_5.3.1+dfsg-2.1_amd64.deb ... 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Preparing to unpack .../44-python-tz_2019.1-1_all.deb ... Unpacking python-tz (2019.1-1) ... Preparing to unpack .../45-python-pbcommand_1.1.1-1_all.deb ... Unpacking python-pbcommand (1.1.1-1) over (0.5.3-1) ... Preparing to unpack .../46-python-pbconsensuscore_1.1.1+dfsg-1_amd64.deb ... Unpacking python-pbconsensuscore (1.1.1+dfsg-1) over (1.0.2-2) ... Preparing to unpack .../47-python-pil_5.4.1-2+deb10u3_amd64.deb ... Unpacking python-pil:amd64 (5.4.1-2+deb10u3) over (4.0.0-4+deb9u1) ... Setting up libexpat1:amd64 (2.2.6-2+deb10u4) ... 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 libgpm2:amd64 (1.20.7-5) ... Setting up hdf5-helpers (1.10.4+repack-10) ... Setting up e2fslibs:amd64 (1.44.5-1+deb10u3) ... Setting up e2fsprogs-l10n (1.44.5-1+deb10u3) ... Setting up libssl1.1:amd64 (1.1.1n-0+deb10u3) ... Setting up libsqlite3-0:amd64 (3.27.2-3+deb10u1) ... Setting up libaec-dev:amd64 (1.0.2-1) ... Setting up binutils-common:amd64 (2.31.1-16) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u7) ... Setting up libgomp1:amd64 (8.3.0-6) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u4) ... Setting up tzdata (2021a-0+deb10u6) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Dec 3 19:21:28 UTC 2022. Universal Time is now: Sat Dec 3 19:21:28 UTC 2022. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libasan5:amd64 (8.3.0-6) ... Setting up gcc-7-base:amd64 (7.4.0-6) ... Setting up libmpfr6:amd64 (4.0.2-1) ... Setting up libquadmath0:amd64 (8.3.0-6) ... Setting up libimagequant0:amd64 (2.12.2-1.1) ... Setting up libssl-dev:amd64 (1.1.1n-0+deb10u3) ... Setting up libmpc3:amd64 (1.1.0-1) ... Setting up libatomic1: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 libmpx2:amd64 (8.3.0-6) ... Setting up liblzma-dev:amd64 (5.2.4-1+deb10u1) ... Setting up libubsan1:amd64 (8.3.0-6) ... Setting up libisl19:amd64 (0.20-2) ... Setting up mount (2.33.1-0.1) ... Setting up libcomerr2:amd64 (1.44.5-1+deb10u3) ... Setting up libcilkrts5:amd64 (7.4.0-6) ... Setting up libubsan0:amd64 (7.4.0-6) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u4) ... Setting up libtiff5:amd64 (4.1.0+git191117-2~deb10u4) ... Setting up libbinutils:amd64 (2.31.1-16) ... Setting up cpp-8 (8.3.0-6) ... Setting up libc-dev-bin (2.28-10+deb10u1) ... Setting up openssl (1.1.1n-0+deb10u3) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up libwebpmux3:amd64 (0.6.1-2+deb10u1) ... Setting up libgpg-error-l10n (1.35-1) ... Setting up libcc1-0:amd64 (8.3.0-6) ... Setting up liblsan0:amd64 (8.3.0-6) ... Setting up libitm1:amd64 (8.3.0-6) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up binutils-x86-64-linux-gnu (2.31.1-16) ... Setting up libtsan0:amd64 (8.3.0-6) ... Setting up binutils (2.31.1-16) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 11 added, 0 removed; done. 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 libgcc-8-dev:amd64 (8.3.0-6) ... Setting up cpp (4:8.3.0-1) ... Setting up libc6-dev:amd64 (2.28-10+deb10u1) ... Setting up libstdc++-8-dev:amd64 (8.3.0-6) ... Setting up libpython2.7:amd64 (2.7.16-2+deb10u1) ... 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 gcc-8 (8.3.0-6) ... 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 gcc (4:8.3.0-1) ... Setting up hdf5-tools (1.10.4+repack-10) ... Setting up libpython-stdlib:amd64 (2.7.16-1) ... Setting up libexpat1-dev:amd64 (2.2.6-2+deb10u4) ... Setting up libjpeg62-turbo-dev:amd64 (1:1.5.2-2+deb10u1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-1+deb10u1) ... Setting up g++-8 (8.3.0-6) ... Setting up python (2.7.16-1) ... Setting up python-urllib3 (1.24.1-1) ... Setting up libpython2.7-dev:amd64 (2.7.16-2+deb10u1) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up python-numpy (1:1.16.2-1) ... Setting up libjpeg-dev (1:1.5.2-2+deb10u1) ... Setting up libhts-dev:amd64 (1.9-12~deb10u1) ... Setting up python-pil:amd64 (5.4.1-2+deb10u3) ... Setting up python-asn1crypto (0.24.0-1) ... Setting up python-certifi (2018.8.24-1) ... Setting up libhdf5-dev (1.10.4+repack-10) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up python-tz (2019.1-1) ... Setting up g++ (4:8.3.0-1) ... Setting up libpbbam0.19.0:amd64 (0.19.0+dfsg-4) ... Setting up libpython2-dev:amd64 (2.7.16-1) ... Setting up python-requests (2.21.0-1) ... Setting up libpbbam-dev (0.19.0+dfsg-4) ... Setting up python-scipy (1.1.0-7) ... Setting up python-olefile (0.46-1) ... Setting up python-h5py (2.8.0-3) ... Setting up python2.7-dev (2.7.16-2+deb10u1) ... Setting up python-pbconsensuscore (1.1.1+dfsg-1) ... Setting up python-pbcommand (1.1.1-1) ... Setting up python-pysam (0.15.2+ds-2) ... Setting up python2-dev (2.7.16-1) ... Setting up python-cryptography (2.6.1-3+deb10u2) ... Setting up libpbdata:amd64 (5.3.1+dfsg-2.1) ... Setting up libpython-dev:amd64 (2.7.16-1) ... Setting up python-openssl (19.0.0-1) ... Setting up python-dev (2.7.16-1) ... Setting up libpbihdf:amd64 (5.3.1+dfsg-2.1) ... Setting up libpbdata-dev:amd64 (5.3.1+dfsg-2.1) ... Setting up libblasr:amd64 (5.3.1+dfsg-2.1) ... Setting up libblasr-dev:amd64 (5.3.1+dfsg-2.1) ... Setting up libpbseq (5.3.1+dfsg-2.1) ... Setting up libpbihdf-dev:amd64 (5.3.1+dfsg-2.1) ... Setting up libpbseq-dev (5.3.1+dfsg-2.1) ... Setting up blasr (5.3.2+dfsg-1.1) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... Processing triggers for mime-support (3.62) ... 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. 1m54.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-get', '-yf', 'dist-upgrade'] 1m54.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m55.7s DUMP: f6fc0f2636004ef589309651dfd778f4 - 1m55.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m55.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-cache', 'show', '--no-all-versions', 'smrtanalysis-dev'] 1m55.9s DUMP: Package: smrtanalysis-dev Status: install ok installed Priority: optional Section: libdevel Installed-Size: 9 Maintainer: Debian Med Packaging Team Architecture: all Source: smrtanalysis Version: 0~20161126 Depends: python-pbcore, python-pbcommand, python-pbconsensuscore | python3-pbconsensuscore, python-pbgenomicconsensus, python-pbh5tools, python-pbalign, python-kineticstools, libpbseq-dev, libpbbam-dev Description: develepment libraries for smrtanalysis 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 SMRTAnalysis development tools. Description-md5: 1a10b42e923f01861162fa9b4749811c Homepage: http://www.pacb.com/products-and-services/analytical-software/smrt-analysis/ 1m55.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-cache', 'show', '--no-all-versions', 'smrtanalysis-dev'] 1m55.9s INFO: apt-cache does not know about any of the requested packages 1m55.9s INFO: Running scripts post_distupgrade 1m55.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m55.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m55.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_distupgrade_exceptions'] 1m56.1s DUMP: Normalized /etc/ca-certificates.conf Running pam-auth-update... 1m56.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_distupgrade_exceptions'] 1m56.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m56.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m56.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m56.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m56.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_distupgrade_zz_backports'] 1m56.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_distupgrade_zz_backports'] 1m56.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2vg233f0'] 1m57.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2vg233f0'] 1m57.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2vg233f0'] 1m58.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2vg233f0'] 1m58.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2vg233f0'] 1m59.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2vg233f0'] 2m0.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', '-ac', '--ignore-obsolete'] 2m4.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', '-ac', '--ignore-obsolete'] 2m4.1s INFO: Running scripts pre_remove 2m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_remove_exceptions'] 2m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/pre_remove_exceptions'] 2m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m9.9s 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 binutils binutils 2.31.1-16 install ok installed binutils-common:amd64 binutils-common 2.31.1-16 install ok installed binutils-x86-64-linux-gnu binutils-x86-64-linux-gnu 2.31.1-16 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 bzip2 bzip2 1.0.6-9.2~deb10u1 install ok installed ca-certificates ca-certificates 20200601~deb10u2 install ok installed coreutils coreutils 8.30-3 install ok installed cpp cpp 4:8.3.0-1 install ok installed cpp-6 cpp-6 6.3.0-18+deb9u1 install ok installed cpp-8 cpp-8 8.3.0-6 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 e2fsprogs-l10n e2fsprogs-l10n 1.44.5-1+deb10u3 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed file file 1:5.35-4+deb10u2 install ok installed findutils findutils 4.6.0+git+20190209-2 install ok installed g++ g++ 4:8.3.0-1 install ok installed g++-6 g++-6 6.3.0-18+deb9u1 install ok installed g++-8 g++-8 8.3.0-6 install ok installed gcc gcc 4:8.3.0-1 install ok installed gcc-6 gcc-6 6.3.0-18+deb9u1 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gcc-7-base:amd64 gcc-7-base 7.4.0-6 install ok installed gcc-8 gcc-8 8.3.0-6 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 hdf5-helpers hdf5-helpers 1.10.4+repack-10 install ok installed hdf5-tools hdf5-tools 1.10.4+repack-10 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed kineticstools-data kineticstools-data 0.6.1+git20180425.27a1878-2 install ok installed krb5-locales krb5-locales 1.17-3+deb10u4 install ok installed libacl1:amd64 libacl1 2.2.53-4 install ok installed libaec-dev:amd64 libaec-dev 1.0.2-1 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 libasan3:amd64 libasan3 6.3.0-18+deb9u1 install ok installed libasan5:amd64 libasan5 8.3.0-6 install ok installed libatomic1:amd64 libatomic1 8.3.0-6 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 libbinutils:amd64 libbinutils 2.31.1-16 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 libblasr-dev:amd64 libblasr-dev 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 libc-dev-bin libc-dev-bin 2.28-10+deb10u1 install ok installed libc6:amd64 libc6 2.28-10+deb10u1 install ok installed libc6-dev:amd64 libc6-dev 2.28-10+deb10u1 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcc1-0:amd64 libcc1-0 8.3.0-6 install ok installed libcilkrts5:amd64 libcilkrts5 7.4.0-6 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 libexpat1-dev:amd64 libexpat1-dev 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 libfreetype6:amd64 libfreetype6 2.9.1-3+deb10u3 install ok installed libgcc-6-dev:amd64 libgcc-6-dev 6.3.0-18+deb9u1 install ok installed libgcc-8-dev:amd64 libgcc-8-dev 8.3.0-6 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 libgomp1:amd64 libgomp1 8.3.0-6 install ok installed libgpg-error-l10n libgpg-error-l10n 1.35-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libgpm2:amd64 libgpm2 1.20.7-5 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 libhdf5-dev libhdf5-dev 1.10.4+repack-10 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libhts-dev:amd64 libhts-dev 1.9-12~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 libimagequant0:amd64 libimagequant0 2.12.2-1.1 install ok installed libisl15:amd64 libisl15 0.18-1 install ok installed libisl19:amd64 libisl19 0.20-2 install ok installed libitm1:amd64 libitm1 8.3.0-6 install ok installed libjbig0:amd64 libjbig0 2.1-3.1+b2 install ok installed libjpeg-dev libjpeg-dev 1:1.5.2-2+deb10u1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:1.5.2-2+deb10u1 install ok installed libjpeg62-turbo-dev:amd64 libjpeg62-turbo-dev 1:1.5.2-2+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 liblcms2-2:amd64 liblcms2-2 2.9-3 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 liblsan0:amd64 liblsan0 8.3.0-6 install ok installed liblz4-1:amd64 liblz4-1 1.8.3-1+deb10u1 install ok installed liblzma-dev:amd64 liblzma-dev 5.2.4-1+deb10u1 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+deb10u1 install ok installed libmagic-mgc libmagic-mgc 1:5.35-4+deb10u2 install ok installed libmagic1:amd64 libmagic1 1:5.35-4+deb10u2 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libmpc3:amd64 libmpc3 1.1.0-1 install ok installed libmpfr4:amd64 libmpfr4 3.1.5-1 install ok installed libmpfr6:amd64 libmpfr6 4.0.2-1 install ok installed libmpx2:amd64 libmpx2 8.3.0-6 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 libpbbam-dev libpbbam-dev 0.19.0+dfsg-4 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 libpbdata-dev:amd64 libpbdata-dev 5.3.1+dfsg-2.1 install ok installed libpbihdf:amd64 libpbihdf 5.3.1+dfsg-2.1 install ok installed libpbihdf-dev:amd64 libpbihdf-dev 5.3.1+dfsg-2.1 install ok installed libpbseq libpbseq 5.3.1+dfsg-2.1 install ok installed libpbseq-dev libpbseq-dev 5.3.1+dfsg-2.1 install ok installed libpcre3:amd64 libpcre3 2:8.39-12 install ok installed libpng16-16:amd64 libpng16-16 1.6.36-6 install ok installed libpsl5:amd64 libpsl5 0.20.2-2 install ok installed libpython-dev:amd64 libpython-dev 2.7.16-1 install ok installed libpython-stdlib:amd64 libpython-stdlib 2.7.16-1 install ok installed libpython2-dev:amd64 libpython2-dev 2.7.16-1 install ok installed libpython2-stdlib:amd64 libpython2-stdlib 2.7.16-1 install ok installed libpython2.7:amd64 libpython2.7 2.7.16-2+deb10u1 install ok installed libpython2.7-dev:amd64 libpython2.7-dev 2.7.16-2+deb10u1 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:amd64 libsasl2-modules 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 libssl-dev:amd64 libssl-dev 1.1.1n-0+deb10u3 install ok installed libssl-doc libssl-doc 1.1.1n-0+deb10u3 install ok installed libssl1.1:amd64 libssl1.1 1.1.1n-0+deb10u3 install ok installed libstdc++-6-dev:amd64 libstdc++-6-dev 6.3.0-18+deb9u1 install ok installed libstdc++-8-dev:amd64 libstdc++-8-dev 8.3.0-6 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 libtiff5:amd64 libtiff5 4.1.0+git191117-2~deb10u4 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 libtsan0:amd64 libtsan0 8.3.0-6 install ok installed libubsan0:amd64 libubsan0 7.4.0-6 install ok installed libubsan1:amd64 libubsan1 8.3.0-6 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 libwebp6:amd64 libwebp6 0.6.1-2+deb10u1 install ok installed libwebpdemux2:amd64 libwebpdemux2 0.6.1-2+deb10u1 install ok installed libwebpmux2:amd64 libwebpmux2 0.5.2-1 install ok installed libwebpmux3:amd64 libwebpmux3 0.6.1-2+deb10u1 install ok installed libzstd1:amd64 libzstd1 1.3.8+dfsg-3+deb10u2 install ok installed linux-libc-dev:amd64 linux-libc-dev 4.19.249-2 install ok installed login login 1:4.5-1.1 install ok installed manpages manpages 4.16-2 install ok installed manpages-dev manpages-dev 4.16-2 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 perl-base perl-base 5.28.1-6+deb10u1 install ok installed publicsuffix publicsuffix 20220811.1734-0+deb10u1 install ok installed python python 2.7.16-1 install ok installed python-asn1crypto python-asn1crypto 0.24.0-1 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-cffi-backend python-cffi-backend 1.12.2-1 install ok installed python-chardet python-chardet 3.0.4-3 install ok installed python-cryptography python-cryptography 2.6.1-3+deb10u2 install ok installed python-decorator python-decorator 4.3.0-1.1 install ok installed python-dev python-dev 2.7.16-1 install ok installed python-enum34 python-enum34 1.1.6-2 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-imaging python-imaging 4.0.0-4+deb9u1 install ok installed python-ipaddress python-ipaddress 1.0.17-1 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-numpy python-numpy 1:1.16.2-1 install ok installed python-olefile python-olefile 0.46-1 install ok installed python-openssl python-openssl 19.0.0-1 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-pil:amd64 python-pil 5.4.1-2+deb10u3 install ok installed python-pkg-resources python-pkg-resources 40.8.0-1 install ok installed python-pyasn1 python-pyasn1 0.4.2-3 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-setuptools python-setuptools 40.8.0-1 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-dev python2-dev 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-dev python2.7-dev 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 sed sed 4.7-1 install ok installed sensible-utils sensible-utils 0.0.12 install ok installed smrtanalysis-dev smrtanalysis-dev 0~20161126 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed tzdata tzdata 2021a-0+deb10u6 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed xz-utils xz-utils 5.2.4-1+deb10u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u1 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.2.11.dfsg-1+deb10u1 2m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-get', 'remove', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blasr', 'bzip2', 'cpp', 'cpp-6', 'cpp-8', 'file', 'g++-', 'g++-6', 'g++-8', 'gcc', 'gcc-6', 'gcc-7-base:amd64', 'gcc-8', 'hdf5-helpers', 'hdf5-tools', 'kineticstools-data', 'krb5-locales', 'libaec-dev:amd64', 'libaec0:amd64', 'libasan3:amd64', 'libasan5:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas-common', 'libblas3:amd64', 'libblasr:amd64', 'libblasr-dev:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcc1-0:amd64', 'libcilkrts5:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfreetype6:amd64', 'libgcc-6-dev:amd64', 'libgcc-8-dev:amd64', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103:amd64', 'libhdf5-cpp-103:amd64', 'libhdf5-dev', 'libhts-dev:amd64', 'libhts1:amd64', 'libhts2:amd64', 'libidn11:amd64', 'libimagequant0:amd64', 'libisl15:amd64', 'libisl19:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg-dev', 'libjpeg62-turbo:amd64', 'libjpeg62-turbo-dev:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'liblsan0:amd64', 'liblzma-dev:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmpc3:amd64', 'libmpfr4:amd64', 'libmpfr6:amd64', 'libmpx2:amd64', 'libnghttp2-14:amd64', 'libpbbam-dev', 'libpbbam0.19.0:amd64', 'libpbdata:amd64', 'libpbdata-dev:amd64', 'libpbihdf:amd64', 'libpbihdf-dev:amd64', 'libpbseq', 'libpbseq-dev', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython-dev:amd64', 'libpython-stdlib:amd64', 'libpython2-dev:amd64', 'libpython2-stdlib:amd64', 'libpython2.7:amd64', 'libpython2.7-dev:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl-dev:amd64', 'libssl-doc', 'libstdc++-6-dev:amd64', 'libstdc++-8-dev:amd64', 'libsz2:amd64', 'libtiff5:amd64', 'libtsan0:amd64', 'libubsan0:amd64', 'libubsan1:amd64', 'libunistring0:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux2:amd64', 'libwebpmux3:amd64', 'linux-libc-dev:amd64', 'manpages', 'manpages-dev', 'mime-support', 'publicsuffix', 'python', 'python-asn1crypto', 'python-avro', 'python-certifi', 'python-cffi-backend', 'python-chardet', 'python-cryptography', 'python-decorator', 'python-dev', 'python-enum34', 'python-h5py', 'python-idna', 'python-imaging', 'python-ipaddress', 'python-iso8601', 'python-kineticstools', 'python-minimal', 'python-numpy', 'python-olefile', 'python-openssl', 'python-pbalign', 'python-pbcommand', 'python-pbconsensuscore', 'python-pbcore', 'python-pbgenomicconsensus', 'python-pbh5tools', 'python-pil:amd64', 'python-pkg-resources', 'python-pyasn1', 'python-pysam', 'python-requests', 'python-scipy', 'python-setuptools', 'python-six', 'python-tz', 'python-urllib3', 'python2', 'python2-dev', 'python2-minimal', 'python2.7', 'python2.7-dev', 'python2.7-minimal', 'readline-common', 'tzdata', 'xz-utils', 'zlib1g-dev:amd64', 'smrtanalysis-dev'] 2m15.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: binutils binutils-common binutils-x86-64-linux-gnu blasr bzip2 cpp cpp-6 cpp-8 file g++ g++-6 g++-8 gcc gcc-6 gcc-7-base gcc-8 hdf5-helpers hdf5-tools kineticstools-data krb5-locales libaec-dev libaec0 libasan3 libasan5 libatomic1 libbinutils libblas-common libblas3 libblasr libblasr-dev libc-dev-bin libc6-dev libcc1-0 libcilkrts5 libcurl3-gnutls libdeflate0 libexpat1 libexpat1-dev libfreetype6 libgcc-6-dev libgcc-8-dev libgfortran3 libgfortran5 libgomp1 libgssapi-krb5-2 libhdf5-103 libhdf5-cpp-103 libhdf5-dev libhts-dev libhts1 libhts2 libidn11 libimagequant0 libisl15 libisl19 libitm1 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common liblsan0 liblzma-dev libmagic-mgc libmagic1 libmpc3 libmpfr4 libmpfr6 libmpx2 libnghttp2-14 libpbbam-dev libpbbam0.19.0 libpbdata libpbdata-dev libpbihdf libpbihdf-dev libpbseq libpbseq-dev libpng16-16 libpsl5 libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules libsasl2-modules-db libsqlite3-0 libssh2-1 libssl-dev libssl-doc libstdc++-6-dev libstdc++-8-dev libsz2 libtiff5 libtsan0 libubsan0 libubsan1 libunistring0 libwebp6 libwebpdemux2 libwebpmux2 libwebpmux3 linux-libc-dev manpages manpages-dev mime-support publicsuffix python python-asn1crypto python-avro python-certifi python-cffi-backend python-chardet python-cryptography python-decorator python-dev python-enum34 python-h5py python-idna python-imaging python-ipaddress python-iso8601 python-kineticstools python-minimal python-numpy python-olefile python-openssl python-pbalign python-pbcommand python-pbconsensuscore python-pbcore python-pbgenomicconsensus python-pbh5tools python-pil python-pkg-resources python-pyasn1 python-pysam python-requests python-scipy python-setuptools python-six python-tz python-urllib3 python2 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal readline-common smrtanalysis-dev tzdata xz-utils zlib1g-dev 0 upgraded, 0 newly installed, 169 to remove and 0 not upgraded. After this operation, 670 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 ... 22568 files and directories currently installed.) Removing g++-6 (6.3.0-18+deb9u1) ... Removing gcc-6 (6.3.0-18+deb9u1) ... Removing g++ (4:8.3.0-1) ... Removing smrtanalysis-dev (0~20161126) ... Removing python-pbalign (0.3.2-1) ... Removing blasr (5.3.2+dfsg-1.1) ... Removing bzip2 (1.0.6-9.2~deb10u1) ... Removing gcc (4:8.3.0-1) ... Removing cpp (4:8.3.0-1) ... Removing cpp-6 (6.3.0-18+deb9u1) ... Removing file (1:5.35-4+deb10u2) ... Removing g++-8 (8.3.0-6) ... Removing libstdc++-6-dev:amd64 (6.3.0-18+deb9u1) ... Removing libgcc-6-dev:amd64 (6.3.0-18+deb9u1) ... Removing libubsan0:amd64 (7.4.0-6) ... Removing libcilkrts5:amd64 (7.4.0-6) ... Removing gcc-7-base:amd64 (7.4.0-6) ... Removing libpbseq-dev (5.3.1+dfsg-2.1) ... Removing libpbihdf-dev:amd64 (5.3.1+dfsg-2.1) ... Removing libhdf5-dev (1.10.4+repack-10) ... Removing hdf5-helpers (1.10.4+repack-10) ... Removing hdf5-tools (1.10.4+repack-10) ... Removing python-kineticstools (0.6.1+git20180425.27a1878-2) ... Removing kineticstools-data (0.6.1+git20180425.27a1878-2) ... Removing krb5-locales (1.17-3+deb10u4) ... Removing libaec-dev:amd64 (1.0.2-1) ... Removing libblasr-dev:amd64 (5.3.1+dfsg-2.1) ... 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 python-pbh5tools (0.8.0+git20170929.58d54ff+dfsg-1) ... Removing libasan3:amd64 (6.3.0-18+deb9u1) ... Removing libstdc++-8-dev:amd64 (8.3.0-6) ... Removing libblas-common (3.7.0-2) ... Removing python-scipy (1.1.0-7) ... Removing python-pbgenomicconsensus (2.3.2-5) ... Removing python-pbcore (1.6.5+dfsg-1) ... Removing python-pbcommand (1.1.1-1) ... Removing python-pbconsensuscore (1.1.1+dfsg-1) ... Removing libpbbam-dev (0.19.0+dfsg-4) ... Removing libhts-dev:amd64 (1.9-12~deb10u1) ... Removing zlib1g-dev:amd64 (1:1.2.11.dfsg-1+deb10u1) ... Removing libjpeg-dev (1:1.5.2-2+deb10u1) ... Removing libjpeg62-turbo-dev:amd64 (1:1.5.2-2+deb10u1) ... Removing python-dev (2.7.16-1) ... Removing libhts1:amd64 (1.3.2-2) ... Removing python-pysam (0.15.2+ds-2) ... Removing python-openssl (19.0.0-1) ... Removing python-cryptography (2.6.1-3+deb10u2) ... Removing python-imaging (4.0.0-4+deb9u1) ... Removing libpython-dev:amd64 (2.7.16-1) ... Removing python-pil:amd64 (5.4.1-2+deb10u3) ... Removing libfreetype6:amd64 (2.9.1-3+deb10u3) ... Removing libgfortran3:amd64 (6.3.0-18+deb9u1) ... Removing libidn11:amd64 (1.33-2.2) ... Removing libimagequant0:amd64 (2.12.2-1.1) ... Removing libisl15:amd64 (0.18-1) ... Removing libtiff5:amd64 (4.1.0+git191117-2~deb10u4) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Removing liblcms2-2:amd64 (2.9-3) ... Removing liblzma-dev:amd64 (5.2.4-1+deb10u1) ... Removing libmagic1:amd64 (1:5.35-4+deb10u2) ... Removing libmagic-mgc (1:5.35-4+deb10u2) ... Removing libmpfr4:amd64 (3.1.5-1) ... Removing libpbdata-dev:amd64 (5.3.1+dfsg-2.1) ... Removing libpbdata:amd64 (5.3.1+dfsg-2.1) ... Removing libpbbam0.19.0:amd64 (0.19.0+dfsg-4) ... Removing libpng16-16:amd64 (1.6.36-6) ... Removing python-requests (2.21.0-1) ... Removing python-urllib3 (1.24.1-1) ... Removing python2-dev (2.7.16-1) ... Removing libpython2-dev:amd64 (2.7.16-1) ... Removing libsasl2-modules:amd64 (2.1.27+dfsg-1+deb10u2) ... Removing libssl-dev:amd64 (1.1.1n-0+deb10u3) ... Removing libssl-doc (1.1.1n-0+deb10u3) ... Removing libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Removing libwebpmux2:amd64 (0.5.2-1) ... Removing libwebpmux3:amd64 (0.6.1-2+deb10u1) ... Removing libwebpdemux2:amd64 (0.6.1-2+deb10u1) ... Removing manpages-dev (4.16-2) ... Removing manpages (4.16-2) ... Removing publicsuffix (20220811.1734-0+deb10u1) ... Removing python-asn1crypto (0.24.0-1) ... Removing python-avro (1.8.2+dfsg-2) ... Removing python-certifi (2018.8.24-1) ... Removing python-cffi-backend (1.12.2-1) ... Removing python-chardet (3.0.4-3) ... Removing python-decorator (4.3.0-1.1) ... Removing python-enum34 (1.1.6-2) ... Removing python-idna (2.6-1) ... Removing python-ipaddress (1.0.17-1) ... Removing python-iso8601 (0.1.11-1) ... Removing python-olefile (0.46-1) ... Removing python-setuptools (40.8.0-1) ... Removing python-pyasn1 (0.4.2-3) ... Removing python-tz (2019.1-1) ... Removing tzdata (2021a-0+deb10u6) ... Removing xz-utils (5.2.4-1+deb10u1) ... Removing gcc-8 (8.3.0-6) ... Removing binutils (2.31.1-16) ... Removing binutils-x86-64-linux-gnu (2.31.1-16) ... Removing libbinutils:amd64 (2.31.1-16) ... Removing binutils-common:amd64 (2.31.1-16) ... Removing cpp-8 (8.3.0-6) ... 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 libgcc-8-dev:amd64 (8.3.0-6) ... Removing libasan5:amd64 (8.3.0-6) ... Removing libatomic1:amd64 (8.3.0-6) ... Removing python-numpy (1:1.16.2-1) ... Removing liblapack3:amd64 (3.8.0-2) ... Removing libblas3:amd64 (3.8.0-2) ... Removing python2.7-dev (2.7.16-2+deb10u1) ... Removing libcc1-0:amd64 (8.3.0-6) ... Removing libhts2:amd64 (1.9-12~deb10u1) ... Removing libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Removing libdeflate0:amd64 (1.2-1) ... Removing libpython2.7-dev:amd64 (2.7.16-2+deb10u1) ... Removing libpython2.7:amd64 (2.7.16-2+deb10u1) ... Removing libgfortran5:amd64 (8.3.0-6) ... Removing libgomp1:amd64 (8.3.0-6) ... Removing libgssapi-krb5-2:amd64 (1.17-3+deb10u4) ... Removing libisl19:amd64 (0.20-2) ... Removing libitm1:amd64 (8.3.0-6) ... 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 liblsan0:amd64 (8.3.0-6) ... Removing libmpc3:amd64 (1.1.0-1) ... Removing libmpfr6:amd64 (4.0.2-1) ... Removing libmpx2:amd64 (8.3.0-6) ... Removing libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Removing libpsl5:amd64 (0.20.2-2) ... Removing python-six (1.12.0-1) ... 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 libtsan0:amd64 (8.3.0-6) ... Removing libubsan1:amd64 (8.3.0-6) ... Removing libwebp6:amd64 (0.6.1-2+deb10u1) ... Removing python-pkg-resources (40.8.0-1) ... Removing libexpat1-dev:amd64 (2.2.6-2+deb10u4) ... Removing libc6-dev:amd64 (2.28-10+deb10u1) ... Removing libc-dev-bin (2.28-10+deb10u1) ... Removing python (2.7.16-1) ... Removing libpython-stdlib:amd64 (2.7.16-1) ... Removing python2 (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 linux-libc-dev:amd64 (4.19.249-2) ... Removing python2.7 (2.7.16-2+deb10u1) ... Removing libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Removing libexpat1:amd64 (2.2.6-2+deb10u4) ... Removing python2.7-minimal (2.7.16-2+deb10u1) ... 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 mime-support (3.62) ... Removing readline-common (7.0-5) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... 2m15.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-get', 'remove', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blasr', 'bzip2', 'cpp', 'cpp-6', 'cpp-8', 'file', 'g++-', 'g++-6', 'g++-8', 'gcc', 'gcc-6', 'gcc-7-base:amd64', 'gcc-8', 'hdf5-helpers', 'hdf5-tools', 'kineticstools-data', 'krb5-locales', 'libaec-dev:amd64', 'libaec0:amd64', 'libasan3:amd64', 'libasan5:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas-common', 'libblas3:amd64', 'libblasr:amd64', 'libblasr-dev:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcc1-0:amd64', 'libcilkrts5:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfreetype6:amd64', 'libgcc-6-dev:amd64', 'libgcc-8-dev:amd64', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103:amd64', 'libhdf5-cpp-103:amd64', 'libhdf5-dev', 'libhts-dev:amd64', 'libhts1:amd64', 'libhts2:amd64', 'libidn11:amd64', 'libimagequant0:amd64', 'libisl15:amd64', 'libisl19:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg-dev', 'libjpeg62-turbo:amd64', 'libjpeg62-turbo-dev:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'liblsan0:amd64', 'liblzma-dev:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmpc3:amd64', 'libmpfr4:amd64', 'libmpfr6:amd64', 'libmpx2:amd64', 'libnghttp2-14:amd64', 'libpbbam-dev', 'libpbbam0.19.0:amd64', 'libpbdata:amd64', 'libpbdata-dev:amd64', 'libpbihdf:amd64', 'libpbihdf-dev:amd64', 'libpbseq', 'libpbseq-dev', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython-dev:amd64', 'libpython-stdlib:amd64', 'libpython2-dev:amd64', 'libpython2-stdlib:amd64', 'libpython2.7:amd64', 'libpython2.7-dev:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl-dev:amd64', 'libssl-doc', 'libstdc++-6-dev:amd64', 'libstdc++-8-dev:amd64', 'libsz2:amd64', 'libtiff5:amd64', 'libtsan0:amd64', 'libubsan0:amd64', 'libubsan1:amd64', 'libunistring0:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux2:amd64', 'libwebpmux3:amd64', 'linux-libc-dev:amd64', 'manpages', 'manpages-dev', 'mime-support', 'publicsuffix', 'python', 'python-asn1crypto', 'python-avro', 'python-certifi', 'python-cffi-backend', 'python-chardet', 'python-cryptography', 'python-decorator', 'python-dev', 'python-enum34', 'python-h5py', 'python-idna', 'python-imaging', 'python-ipaddress', 'python-iso8601', 'python-kineticstools', 'python-minimal', 'python-numpy', 'python-olefile', 'python-openssl', 'python-pbalign', 'python-pbcommand', 'python-pbconsensuscore', 'python-pbcore', 'python-pbgenomicconsensus', 'python-pbh5tools', 'python-pil:amd64', 'python-pkg-resources', 'python-pyasn1', 'python-pysam', 'python-requests', 'python-scipy', 'python-setuptools', 'python-six', 'python-tz', 'python-urllib3', 'python2', 'python2-dev', 'python2-minimal', 'python2.7', 'python2.7-dev', 'python2.7-minimal', 'readline-common', 'tzdata', 'xz-utils', 'zlib1g-dev:amd64', 'smrtanalysis-dev'] 2m15.3s INFO: Running scripts post_remove 2m15.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_remove_exceptions'] 2m15.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_remove_exceptions'] 2m15.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'dpkg', '--purge', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blasr', 'bzip2', 'cpp', 'cpp-6', 'cpp-8', 'file', 'g++', 'g++-6', 'g++-8', 'gcc', 'gcc-6', 'gcc-7-base:amd64', 'gcc-8', 'hdf5-helpers', 'hdf5-tools', 'kineticstools-data', 'krb5-locales', 'libaec-dev:amd64', 'libaec0:amd64', 'libasan3:amd64', 'libasan5:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas-common', 'libblas3:amd64', 'libblasr:amd64', 'libblasr-dev:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcc1-0:amd64', 'libcilkrts5:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfreetype6:amd64', 'libgcc-6-dev:amd64', 'libgcc-8-dev:amd64', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103:amd64', 'libhdf5-cpp-103:amd64', 'libhdf5-dev', 'libhts-dev:amd64', 'libhts1:amd64', 'libhts2:amd64', 'libidn11:amd64', 'libimagequant0:amd64', 'libisl15:amd64', 'libisl19:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg-dev', 'libjpeg62-turbo:amd64', 'libjpeg62-turbo-dev:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'liblsan0:amd64', 'liblzma-dev:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmpc3:amd64', 'libmpfr4:amd64', 'libmpfr6:amd64', 'libmpx2:amd64', 'libnghttp2-14:amd64', 'libpbbam-dev', 'libpbbam0.19.0:amd64', 'libpbdata:amd64', 'libpbdata-dev:amd64', 'libpbihdf:amd64', 'libpbihdf-dev:amd64', 'libpbseq', 'libpbseq-dev', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython-dev:amd64', 'libpython-stdlib:amd64', 'libpython2-dev:amd64', 'libpython2-stdlib:amd64', 'libpython2.7:amd64', 'libpython2.7-dev:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl-dev:amd64', 'libssl-doc', 'libstdc++-6-dev:amd64', 'libstdc++-8-dev:amd64', 'libsz2:amd64', 'libtiff5:amd64', 'libtsan0:amd64', 'libubsan0:amd64', 'libubsan1:amd64', 'libunistring0:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux2:amd64', 'libwebpmux3:amd64', 'linux-libc-dev:amd64', 'manpages', 'manpages-dev', 'mime-support', 'publicsuffix', 'python', 'python-asn1crypto', 'python-avro', 'python-certifi', 'python-cffi-backend', 'python-chardet', 'python-cryptography', 'python-decorator', 'python-dev', 'python-enum34', 'python-h5py', 'python-idna', 'python-imaging', 'python-ipaddress', 'python-iso8601', 'python-kineticstools', 'python-minimal', 'python-numpy', 'python-olefile', 'python-openssl', 'python-pbalign', 'python-pbcommand', 'python-pbconsensuscore', 'python-pbcore', 'python-pbgenomicconsensus', 'python-pbh5tools', 'python-pil:amd64', 'python-pkg-resources', 'python-pyasn1', 'python-pysam', 'python-requests', 'python-scipy', 'python-setuptools', 'python-six', 'python-tz', 'python-urllib3', 'python2', 'python2-dev', 'python2-minimal', 'python2.7', 'python2.7-dev', 'python2.7-minimal', 'readline-common', 'tzdata', 'xz-utils', 'zlib1g-dev:amd64'] 2m15.7s DUMP: dpkg: warning: ignoring request to remove binutils which isn't installed dpkg: warning: ignoring request to remove binutils-common which isn't installed dpkg: warning: ignoring request to remove binutils-x86-64-linux-gnu which isn't installed dpkg: warning: ignoring request to remove blasr which isn't installed dpkg: warning: ignoring request to remove bzip2 which isn't installed dpkg: warning: ignoring request to remove cpp which isn't installed dpkg: warning: ignoring request to remove cpp-6 which isn't installed dpkg: warning: ignoring request to remove cpp-8 which isn't installed dpkg: warning: ignoring request to remove file which isn't installed dpkg: warning: ignoring request to remove g++ which isn't installed dpkg: warning: ignoring request to remove g++-6 which isn't installed dpkg: warning: ignoring request to remove g++-8 which isn't installed dpkg: warning: ignoring request to remove gcc which isn't installed dpkg: warning: ignoring request to remove gcc-6 which isn't installed dpkg: warning: ignoring request to remove gcc-7-base which isn't installed dpkg: warning: ignoring request to remove gcc-8 which isn't installed dpkg: warning: ignoring request to remove hdf5-helpers which isn't installed dpkg: warning: ignoring request to remove hdf5-tools which isn't installed dpkg: warning: ignoring request to remove kineticstools-data which isn't installed dpkg: warning: ignoring request to remove krb5-locales which isn't installed dpkg: warning: ignoring request to remove libaec-dev which isn't installed dpkg: warning: ignoring request to remove libaec0 which isn't installed dpkg: warning: ignoring request to remove libasan3 which isn't installed dpkg: warning: ignoring request to remove libasan5 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libbinutils 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 libblasr-dev which isn't installed dpkg: warning: ignoring request to remove libc-dev-bin which isn't installed dpkg: warning: ignoring request to remove libc6-dev which isn't installed dpkg: warning: ignoring request to remove libcc1-0 which isn't installed dpkg: warning: ignoring request to remove libcilkrts5 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 libexpat1-dev which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libgcc-6-dev which isn't installed dpkg: warning: ignoring request to remove libgcc-8-dev 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 dpkg: warning: ignoring request to remove libgomp1 which isn't installed (Reading database ... 5018 files and directories currently 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 libhdf5-dev which isn't installed dpkg: warning: ignoring request to remove libhts-dev 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 libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libisl15 which isn't installed dpkg: warning: ignoring request to remove libisl19 which isn't installed dpkg: warning: ignoring request to remove libitm1 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg-dev which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo-dev 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 liblcms2-2 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 liblsan0 which isn't installed dpkg: warning: ignoring request to remove liblzma-dev which isn't installed dpkg: warning: ignoring request to remove libmagic-mgc which isn't installed Purging configuration files for libmagic1:amd64 (1:5.35-4+deb10u2) ... dpkg: warning: ignoring request to remove libmpc3 which isn't installed dpkg: warning: ignoring request to remove libmpfr4 which isn't installed dpkg: warning: ignoring request to remove libmpfr6 which isn't installed dpkg: warning: ignoring request to remove libmpx2 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libpbbam-dev 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 libpbdata-dev which isn't installed dpkg: warning: ignoring request to remove libpbihdf which isn't installed dpkg: warning: ignoring request to remove libpbihdf-dev which isn't installed dpkg: warning: ignoring request to remove libpbseq which isn't installed dpkg: warning: ignoring request to remove libpbseq-dev which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython-dev which isn't installed dpkg: warning: ignoring request to remove libpython-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython2-dev which isn't installed dpkg: warning: ignoring request to remove libpython2-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython2.7 which isn't installed dpkg: warning: ignoring request to remove libpython2.7-dev 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 Purging configuration files for libsasl2-modules:amd64 (2.1.27+dfsg-1+deb10u2) ... 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 dpkg: warning: ignoring request to remove libssl-dev which isn't installed dpkg: warning: ignoring request to remove libssl-doc which isn't installed dpkg: warning: ignoring request to remove libstdc++-6-dev which isn't installed dpkg: warning: ignoring request to remove libstdc++-8-dev which isn't installed dpkg: warning: ignoring request to remove libsz2 which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed dpkg: warning: ignoring request to remove libtsan0 which isn't installed dpkg: warning: ignoring request to remove libubsan0 which isn't installed dpkg: warning: ignoring request to remove libubsan1 which isn't installed dpkg: warning: ignoring request to remove libunistring0 which isn't installed dpkg: warning: ignoring request to remove libwebp6 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove linux-libc-dev which isn't installed dpkg: warning: ignoring request to remove manpages which isn't installed dpkg: warning: ignoring request to remove manpages-dev which isn't installed Purging configuration files for mime-support (3.62) ... dpkg: warning: ignoring request to remove publicsuffix which isn't installed Purging configuration files for python (2.7.16-1) ... dpkg: warning: ignoring request to remove python-asn1crypto which isn't installed 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-cffi-backend which isn't installed dpkg: warning: ignoring request to remove python-chardet which isn't installed dpkg: warning: ignoring request to remove python-cryptography which isn't installed dpkg: warning: ignoring request to remove python-decorator which isn't installed dpkg: warning: ignoring request to remove python-dev which isn't installed dpkg: warning: ignoring request to remove python-enum34 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-imaging which isn't installed dpkg: warning: ignoring request to remove python-ipaddress 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-numpy which isn't installed dpkg: warning: ignoring request to remove python-olefile which isn't installed dpkg: warning: ignoring request to remove python-openssl 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-pil which isn't installed dpkg: warning: ignoring request to remove python-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python-pyasn1 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-setuptools 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-dev 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 dpkg: warning: ignoring request to remove python2.7-dev 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 tzdata (2021a-0+deb10u6) ... dpkg: warning: ignoring request to remove xz-utils which isn't installed dpkg: warning: ignoring request to remove zlib1g-dev which isn't installed 2m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'dpkg', '--purge', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blasr', 'bzip2', 'cpp', 'cpp-6', 'cpp-8', 'file', 'g++', 'g++-6', 'g++-8', 'gcc', 'gcc-6', 'gcc-7-base:amd64', 'gcc-8', 'hdf5-helpers', 'hdf5-tools', 'kineticstools-data', 'krb5-locales', 'libaec-dev:amd64', 'libaec0:amd64', 'libasan3:amd64', 'libasan5:amd64', 'libatomic1:amd64', 'libbinutils:amd64', 'libblas-common', 'libblas3:amd64', 'libblasr:amd64', 'libblasr-dev:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcc1-0:amd64', 'libcilkrts5:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfreetype6:amd64', 'libgcc-6-dev:amd64', 'libgcc-8-dev:amd64', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103:amd64', 'libhdf5-cpp-103:amd64', 'libhdf5-dev', 'libhts-dev:amd64', 'libhts1:amd64', 'libhts2:amd64', 'libidn11:amd64', 'libimagequant0:amd64', 'libisl15:amd64', 'libisl19:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg-dev', 'libjpeg62-turbo:amd64', 'libjpeg62-turbo-dev:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'liblsan0:amd64', 'liblzma-dev:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmpc3:amd64', 'libmpfr4:amd64', 'libmpfr6:amd64', 'libmpx2:amd64', 'libnghttp2-14:amd64', 'libpbbam-dev', 'libpbbam0.19.0:amd64', 'libpbdata:amd64', 'libpbdata-dev:amd64', 'libpbihdf:amd64', 'libpbihdf-dev:amd64', 'libpbseq', 'libpbseq-dev', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython-dev:amd64', 'libpython-stdlib:amd64', 'libpython2-dev:amd64', 'libpython2-stdlib:amd64', 'libpython2.7:amd64', 'libpython2.7-dev:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl-dev:amd64', 'libssl-doc', 'libstdc++-6-dev:amd64', 'libstdc++-8-dev:amd64', 'libsz2:amd64', 'libtiff5:amd64', 'libtsan0:amd64', 'libubsan0:amd64', 'libubsan1:amd64', 'libunistring0:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux2:amd64', 'libwebpmux3:amd64', 'linux-libc-dev:amd64', 'manpages', 'manpages-dev', 'mime-support', 'publicsuffix', 'python', 'python-asn1crypto', 'python-avro', 'python-certifi', 'python-cffi-backend', 'python-chardet', 'python-cryptography', 'python-decorator', 'python-dev', 'python-enum34', 'python-h5py', 'python-idna', 'python-imaging', 'python-ipaddress', 'python-iso8601', 'python-kineticstools', 'python-minimal', 'python-numpy', 'python-olefile', 'python-openssl', 'python-pbalign', 'python-pbcommand', 'python-pbconsensuscore', 'python-pbcore', 'python-pbgenomicconsensus', 'python-pbh5tools', 'python-pil:amd64', 'python-pkg-resources', 'python-pyasn1', 'python-pysam', 'python-requests', 'python-scipy', 'python-setuptools', 'python-six', 'python-tz', 'python-urllib3', 'python2', 'python2-dev', 'python2-minimal', 'python2.7', 'python2.7-dev', 'python2.7-minimal', 'readline-common', 'tzdata', 'xz-utils', 'zlib1g-dev:amd64'] 2m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'dpkg', '--purge', 'smrtanalysis-dev'] 2m15.7s DUMP: dpkg: warning: ignoring request to remove smrtanalysis-dev which isn't installed 2m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'dpkg', '--purge', 'smrtanalysis-dev'] 2m15.7s INFO: Running scripts post_purge 2m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_purge_exceptions'] 2m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_purge_exceptions'] 2m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'dpkg', '--purge', '--pending'] 2m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'dpkg', '--purge', '--pending'] 2m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'dpkg', '--remove', '--pending'] 2m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'dpkg', '--remove', '--pending'] 2m15.8s INFO: Running scripts post_test 2m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_test_exceptions'] 2m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'tmp/scripts/post_test_exceptions'] 2m15.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2vg233f0'] 2m16.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2vg233f0'] 2m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'dpkg-divert', '--list'] 2m16.3s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 2m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'dpkg-divert', '--list'] 2m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-get', 'clean'] 2m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2vg233f0', 'apt-get', 'clean'] 2m16.4s DEBUG: Recording chroot state 2m17.1s INFO: Warning: Package purging left files on system: /etc/ca-certificates.conf.dpkg-old not owned 2m17.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/dev/shm'] 2m17.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/dev/shm'] 2m17.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/dev/console'] 2m17.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/dev/console'] 2m17.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/dev/ptmx'] 2m17.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/dev/ptmx'] 2m17.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/dev/pts'] 2m17.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/dev/pts'] 2m17.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/proc'] 2m17.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp2vg233f0/proc'] 2m17.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp2vg233f0'] 2m17.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp2vg233f0'] 2m17.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp2vg233f0 2m17.6s INFO: PASS: Upgrading between Debian distributions. 2m17.6s INFO: PASS: All tests. 2m17.6s INFO: piuparts run ends. ret=0 End: 2022-12-03 19:22:03 GMT