Start: 2023-02-10 20:49:27 GMT Package: pbalign Version: 0.3.0-1 Installed-Size: 33 Maintainer: Debian Med Packaging Team Architecture: all Depends: python:any, python-pbalign, python-pkg-resources, blasr (>= 5.3+0) Recommends: python-pbh5tools, hdf5-tools Suggests: bowtie2, gmap, pbalign-doc Description: map Pacific Biosciences reads to reference DNA sequences Homepage: https://github.com/PacificBiosciences/pbalign Description-md5: 24cf008f794715d775f6d8960513670a Section: python Priority: optional Filename: pool/main/p/pbalign/pbalign_0.3.0-1_all.deb Size: 7482 MD5sum: ba118c2ab0277ec4f417c60415fc1954 SHA256: 3ba173f9e1f4b7115ca5c7d1be6fa25a61d23844ced92e694f3b0aefd3a5674a 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 --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch --no-upgrade-test --apt pbalign=0.3.0-1 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 --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch --no-upgrade-test --apt pbalign=0.3.0-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpy_7qufqd 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpy_7qufqd 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/proc'] 0m1.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/proc'] 0m1.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/dev/pts'] 0m1.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/dev/pts'] 0m1.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/dev/ptmx'] 0m1.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/dev/ptmx'] 0m1.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/dev/console'] 0m1.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/dev/console'] 0m1.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/dev/shm'] 0m1.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/dev/shm'] 0m1.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m1.2s DEBUG: Created policy-rc.d and chmodded it. 0m1.2s DEBUG: Created resolv.conf. 0m1.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpy_7qufqd/tmp/scripts/ 0m1.2s INFO: Running scripts post_chroot_unpack 0m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'apt-get', 'update'] 0m2.0s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'apt-get', 'update'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.7s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.7s INFO: Running scripts post_setup 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_setup_dummy_users'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_setup_dummy_users'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_setup_forbid_home'] 0m3.7s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_setup_forbid_home'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.7s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_setup_minimize'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_setup_minimize'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_setup_zz_backports'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_setup_zz_backports'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'apt-get', 'clean'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'apt-get', 'clean'] 0m3.7s DEBUG: Recording chroot state 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.2s 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 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'dpkg-divert', '--list'] 0m4.2s 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 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'dpkg-divert', '--list'] 0m4.2s INFO: Running scripts is_testable 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/is_testable_uninstallable'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/is_testable_uninstallable'] 0m4.2s INFO: apt-cache does not know about any of the requested packages 0m4.2s INFO: Running scripts pre_test 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_test_exceptions'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_test_exceptions'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_test_root_password'] 0m4.2s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_test_root_password'] 0m4.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd'] 0m4.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd'] 0m4.8s DEBUG: No broken symlinks as far as we can find. 0m4.8s INFO: Running scripts pre_install 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_install_database-server'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_install_database-server'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_install_exceptions'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_install_exceptions'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_install_extras'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_install_extras'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd'] 0m5.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd'] 0m5.5s DEBUG: No broken symlinks as far as we can find. 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'apt-cache', 'policy'] 0m6.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian stretch/main amd64 Packages release v=9.13,o=Debian,a=oldoldstable,n=stretch,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'apt-cache', 'policy'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'apt-cache', 'policy', 'pbalign'] 0m6.3s DUMP: pbalign: Installed: (none) Candidate: 0.3.0-1 Version table: 0.3.0-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'apt-cache', 'policy', 'pbalign'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'apt-get', '-y', 'install', 'pbalign=0.3.0-1'] 0m23.6s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: blasr bzip2 ca-certificates file hdf5-tools krb5-locales libaec0 libblas-common libblas3 libblasr libcurl3-gnutls libexpat1 libffi6 libgfortran3 libgmp10 libgnutls30 libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100 libhogweed4 libhts1 libidn11 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libnettle6 libnghttp2-14 libp11-kit0 libpbbam libpbdata libpbihdf libpbseq libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libsz2 libtasn1-6 libunistring0 mime-support openssl publicsuffix python python-avro python-cffi-backend python-chardet python-cryptography python-enum34 python-h5py python-idna python-ipaddress python-iso8601 python-minimal python-numpy python-openssl python-pbalign python-pbcommand python-pbcore python-pbh5tools python-pkg-resources python-pyasn1 python-pysam python-requests python-setuptools python-six python-urllib3 python2.7 python2.7-minimal readline-common xz-utils Suggested packages: bzip2-doc gnutls-bin krb5-doc krb5-user libsasl2-modules-gssapi-mit | libsasl2-modules-gssapi-heimdal libsasl2-modules-ldap libsasl2-modules-otp libsasl2-modules-sql bowtie2 gmap pbalign-doc python-doc python-tk python-cryptography-doc python-cryptography-vectors python-enum34-doc python-h5py-doc gcc gfortran python-dev python-nose python-numpy-dbg python-numpy-doc python-openssl-doc python-openssl-dbg python-pbcore-doc doc-base python-socks python-setuptools-doc python-ntlm python2.7-doc binutils binfmt-support readline-doc The following NEW packages will be installed: blasr bzip2 ca-certificates file hdf5-tools krb5-locales libaec0 libblas-common libblas3 libblasr libcurl3-gnutls libexpat1 libffi6 libgfortran3 libgmp10 libgnutls30 libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100 libhogweed4 libhts1 libidn11 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libnettle6 libnghttp2-14 libp11-kit0 libpbbam libpbdata libpbihdf libpbseq libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libsz2 libtasn1-6 libunistring0 mime-support openssl pbalign publicsuffix python python-avro python-cffi-backend python-chardet python-cryptography python-enum34 python-h5py python-idna python-ipaddress python-iso8601 python-minimal python-numpy python-openssl python-pbalign python-pbcommand python-pbcore python-pbh5tools python-pkg-resources python-pyasn1 python-pysam python-requests python-setuptools python-six python-urllib3 python2.7 python2.7-minimal readline-common xz-utils 0 upgraded, 87 newly installed, 0 to remove and 0 not upgraded. Need to get 33.8 MB of archives. After this operation, 109 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 xz-utils amd64 5.2.2-1.2+b1 [266 kB] Get:37 http://deb.debian.org/debian stretch/main amd64 libquadmath0 amd64 6.3.0-18+deb9u1 [131 kB] Get:38 http://deb.debian.org/debian stretch/main amd64 libgfortran3 amd64 6.3.0-18+deb9u1 [265 kB] Get:39 http://deb.debian.org/debian stretch/main amd64 libaec0 amd64 0.3.2-1 [18.5 kB] Get:40 http://deb.debian.org/debian stretch/main amd64 libsz2 amd64 0.3.2-1 [5730 B] Get:41 http://deb.debian.org/debian stretch/main amd64 libhdf5-100 amd64 1.10.0-patch1+docs-3+deb9u1 [1282 kB] Get:42 http://deb.debian.org/debian stretch/main amd64 libhdf5-cpp-100 amd64 1.10.0-patch1+docs-3+deb9u1 [130 kB] Get:43 http://deb.debian.org/debian stretch/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:44 http://deb.debian.org/debian stretch/main amd64 libidn2-0 amd64 0.16-1+deb9u1 [60.7 kB] Get:45 http://deb.debian.org/debian stretch/main amd64 libnghttp2-14 amd64 1.18.1-1+deb9u1 [79.2 kB] Get:46 http://deb.debian.org/debian stretch/main amd64 libpsl5 amd64 0.17.0-3 [41.8 kB] Get:47 http://deb.debian.org/debian stretch/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:48 http://deb.debian.org/debian stretch/main amd64 libssh2-1 amd64 1.7.0-1+deb9u1 [139 kB] Get:49 http://deb.debian.org/debian stretch/main amd64 libcurl3-gnutls amd64 7.52.1-5+deb9u10 [290 kB] Get:50 http://deb.debian.org/debian stretch/main amd64 libhts1 amd64 1.3.2-2 [257 kB] Get:51 http://deb.debian.org/debian stretch/main amd64 libpbbam amd64 0.7.4+ds-1 [478 kB] Get:52 http://deb.debian.org/debian stretch/main amd64 libpbdata amd64 0~20161219-1 [129 kB] Get:53 http://deb.debian.org/debian stretch/main amd64 libpbihdf amd64 0~20161219-1 [167 kB] Get:54 http://deb.debian.org/debian stretch/main amd64 libblasr amd64 0~20161219-1 [867 kB] Get:55 http://deb.debian.org/debian stretch/main amd64 libpbseq all 0~20161219-1 [3876 B] Get:56 http://deb.debian.org/debian stretch/main amd64 blasr amd64 5.3+0-1 [691 kB] Get:57 http://deb.debian.org/debian stretch/main amd64 openssl amd64 1.1.0l-1~deb9u1 [749 kB] Get:58 http://deb.debian.org/debian stretch/main amd64 ca-certificates all 20200601~deb9u1 [160 kB] Get:59 http://deb.debian.org/debian stretch/main amd64 hdf5-tools amd64 1.10.0-patch1+docs-3+deb9u1 [405 kB] Get:60 http://deb.debian.org/debian stretch/main amd64 libblas-common amd64 3.7.0-2 [14.2 kB] Get:61 http://deb.debian.org/debian stretch/main amd64 libblas3 amd64 3.7.0-2 [155 kB] Get:62 http://deb.debian.org/debian stretch/main amd64 liblapack3 amd64 3.7.0-2 [2141 kB] Get:63 http://deb.debian.org/debian stretch/main amd64 libsasl2-modules amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [102 kB] Get:64 http://deb.debian.org/debian stretch/main amd64 python-avro all 1.8.1+dfsg-1 [58.1 kB] Get:65 http://deb.debian.org/debian stretch/main amd64 python-iso8601 all 0.1.11-1 [12.7 kB] Get:66 http://deb.debian.org/debian stretch/main amd64 python-six all 1.10.0-3 [14.4 kB] Get:67 http://deb.debian.org/debian stretch/main amd64 python-urllib3 all 1.19.1-1 [77.5 kB] Get:68 http://deb.debian.org/debian stretch/main amd64 python-pkg-resources all 33.1.1-1 [166 kB] Get:69 http://deb.debian.org/debian stretch/main amd64 python-chardet all 2.3.0-2 [96.0 kB] Get:70 http://deb.debian.org/debian stretch/main amd64 python-requests all 2.12.4-1 [101 kB] Get:71 http://deb.debian.org/debian stretch/main amd64 python-numpy amd64 1:1.12.1-3 [1936 kB] Get:72 http://deb.debian.org/debian stretch/main amd64 python-pbcommand all 0.5.3-1 [79.6 kB] Get:73 http://deb.debian.org/debian stretch/main amd64 python-h5py amd64 2.7.0-1 [634 kB] Get:74 http://deb.debian.org/debian stretch/main amd64 python-pysam amd64 0.10.0+ds-2 [1301 kB] Get:75 http://deb.debian.org/debian stretch/main amd64 python-pbcore all 1.2.11+dfsg-1 [9087 kB] Get:76 http://deb.debian.org/debian stretch/main amd64 python-pbalign all 0.3.0-1 [37.2 kB] Get:77 http://deb.debian.org/debian stretch/main amd64 pbalign all 0.3.0-1 [7482 B] Get:78 http://deb.debian.org/debian stretch/main amd64 python-cffi-backend amd64 1.9.1-2 [69.0 kB] Get:79 http://deb.debian.org/debian stretch/main amd64 python-enum34 all 1.1.6-1 [35.0 kB] Get:80 http://deb.debian.org/debian stretch/main amd64 python-idna all 2.2-1 [32.6 kB] Get:81 http://deb.debian.org/debian stretch/main amd64 python-ipaddress all 1.0.17-1 [18.1 kB] Get:82 http://deb.debian.org/debian stretch/main amd64 python-pyasn1 all 0.1.9-2 [51.8 kB] Get:83 http://deb.debian.org/debian stretch/main amd64 python-setuptools all 33.1.1-1 [297 kB] Get:84 http://deb.debian.org/debian stretch/main amd64 python-cryptography amd64 1.7.1-3+deb9u2 [212 kB] Get:85 http://deb.debian.org/debian stretch/main amd64 python-openssl all 16.2.0-1 [43.7 kB] Get:86 http://deb.debian.org/debian stretch/main amd64 python-pbh5tools amd64 0.8.0+dfsg-5 [29.0 kB] Get:87 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 33.8 MB in 0s (112 MB/s) Selecting previously unselected package libpython2.7-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4411 files and directories currently installed.) Preparing to unpack .../00-libpython2.7-minimal_2.7.13-2+deb9u3_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../01-python2.7-minimal_2.7.13-2+deb9u3_amd64.deb ... Unpacking python2.7-minimal (2.7.13-2+deb9u3) ... Selecting previously unselected package python-minimal. Preparing to unpack .../02-python-minimal_2.7.13-2_amd64.deb ... Unpacking python-minimal (2.7.13-2) ... Selecting previously unselected package mime-support. Preparing to unpack .../03-mime-support_3.60_all.deb ... Unpacking mime-support (3.60) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../04-libexpat1_2.2.0-2+deb9u3_amd64.deb ... Unpacking libexpat1:amd64 (2.2.0-2+deb9u3) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../05-libffi6_3.2.1-6_amd64.deb ... Unpacking libffi6:amd64 (3.2.1-6) ... Selecting previously unselected package readline-common. Preparing to unpack .../06-readline-common_7.0-3_all.deb ... Unpacking readline-common (7.0-3) ... Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../07-libreadline7_7.0-3_amd64.deb ... Unpacking libreadline7:amd64 (7.0-3) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../08-libsqlite3-0_3.16.2-5+deb9u1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../09-libssl1.1_1.1.0l-1~deb9u1_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Selecting previously unselected package libpython2.7-stdlib:amd64. Preparing to unpack .../10-libpython2.7-stdlib_2.7.13-2+deb9u3_amd64.deb ... Unpacking libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ... Selecting previously unselected package python2.7. Preparing to unpack .../11-python2.7_2.7.13-2+deb9u3_amd64.deb ... Unpacking python2.7 (2.7.13-2+deb9u3) ... Selecting previously unselected package libpython-stdlib:amd64. Preparing to unpack .../12-libpython-stdlib_2.7.13-2_amd64.deb ... Unpacking libpython-stdlib:amd64 (2.7.13-2) ... Setting up libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) ... Setting up python2.7-minimal (2.7.13-2+deb9u3) ... Setting up python-minimal (2.7.13-2) ... Selecting previously unselected package python. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5237 files and directories currently installed.) Preparing to unpack .../00-python_2.7.13-2_amd64.deb ... Unpacking python (2.7.13-2) ... Selecting previously unselected package bzip2. Preparing to unpack .../01-bzip2_1.0.6-8.1_amd64.deb ... Unpacking bzip2 (1.0.6-8.1) ... Selecting previously unselected package libmagic-mgc. 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Unpacking libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../30-libidn2-0_0.16-1+deb9u1_amd64.deb ... Unpacking libidn2-0:amd64 (0.16-1+deb9u1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../31-libnghttp2-14_1.18.1-1+deb9u1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.18.1-1+deb9u1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../32-libpsl5_0.17.0-3_amd64.deb ... Unpacking libpsl5:amd64 (0.17.0-3) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../33-librtmp1_2.4+20151223.gitfa8646d.1-1+b1_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../34-libssh2-1_1.7.0-1+deb9u1_amd64.deb ... Unpacking libssh2-1:amd64 (1.7.0-1+deb9u1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../35-libcurl3-gnutls_7.52.1-5+deb9u10_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Selecting previously unselected package libhts1:amd64. Preparing to unpack .../36-libhts1_1.3.2-2_amd64.deb ... Unpacking libhts1:amd64 (1.3.2-2) ... Selecting previously unselected package libpbbam:amd64. Preparing to unpack .../37-libpbbam_0.7.4+ds-1_amd64.deb ... Unpacking libpbbam:amd64 (0.7.4+ds-1) ... Selecting previously unselected package libpbdata:amd64. Preparing to unpack .../38-libpbdata_0~20161219-1_amd64.deb ... Unpacking libpbdata:amd64 (0~20161219-1) ... Selecting previously unselected package libpbihdf:amd64. Preparing to unpack .../39-libpbihdf_0~20161219-1_amd64.deb ... Unpacking libpbihdf:amd64 (0~20161219-1) ... Selecting previously unselected package libblasr:amd64. Preparing to unpack .../40-libblasr_0~20161219-1_amd64.deb ... Unpacking libblasr:amd64 (0~20161219-1) ... Selecting previously unselected package libpbseq. 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Preparing to unpack .../71-python-openssl_16.2.0-1_all.deb ... Unpacking python-openssl (16.2.0-1) ... Selecting previously unselected package python-pbh5tools. Preparing to unpack .../72-python-pbh5tools_0.8.0+dfsg-5_amd64.deb ... Unpacking python-pbh5tools (0.8.0+dfsg-5) ... Selecting previously unselected package publicsuffix. Preparing to unpack .../73-publicsuffix_20190415.1030-0+deb9u1_all.deb ... Unpacking publicsuffix (20190415.1030-0+deb9u1) ... Setting up libquadmath0:amd64 (6.3.0-18+deb9u1) ... Setting up readline-common (7.0-3) ... Setting up libnettle6:amd64 (3.3-1+b2) ... Setting up libaec0:amd64 (0.3.2-1) ... Setting up libexpat1:amd64 (2.2.0-2+deb9u3) ... Setting up libnghttp2-14:amd64 (1.18.1-1+deb9u1) ... Setting up mime-support (3.60) ... Setting up libldap-common (2.4.44+dfsg-5+deb9u4) ... Setting up libreadline7:amd64 (7.0-3) ... Setting up libblas-common (3.7.0-2) ... Setting up libgfortran3:amd64 (6.3.0-18+deb9u1) ... Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Setting up 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 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 libffi6:amd64 (3.2.1-6) ... 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 libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ... Setting up libidn11:amd64 (1.33-1+deb9u1) ... Setting up libsz2:amd64 (0.3.2-1) ... Setting up libidn2-0:amd64 (0.16-1+deb9u1) ... Setting up libhdf5-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Setting up libpsl5:amd64 (0.17.0-3) ... Setting up liblapack3 (3.7.0-2) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up python2.7 (2.7.13-2+deb9u3) ... Setting up 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 libp11-kit0:amd64 (0.23.3-2) ... Setting up python (2.7.13-2) ... Setting up python-idna (2.2-1) ... Setting up libk5crypto3:amd64 (1.15-1+deb9u1) ... Setting up libhdf5-cpp-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... 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 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-ipaddress (1.0.17-1) ... 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 libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Setting up python-cryptography (1.7.1-3+deb9u2) ... Setting up python-requests (2.12.4-1) ... 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 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-pbh5tools (0.8.0+dfsg-5) ... Setting up libpbdata:amd64 (0~20161219-1) ... Setting up libpbihdf:amd64 (0~20161219-1) ... Setting up libblasr:amd64 (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 pbalign (0.3.0-1) ... 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. 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'apt-get', '-y', 'install', 'pbalign=0.3.0-1'] 0m23.6s INFO: Running scripts post_install 0m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_install_exceptions'] 0m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_install_exceptions'] 0m23.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd'] 0m24.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd'] 0m24.9s DEBUG: No broken symlinks as far as we can find. 0m25.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', '-ac', '--ignore-obsolete'] 0m26.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', '-ac', '--ignore-obsolete'] 0m26.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m26.1s DUMP: 0.15.6 0m26.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m26.1s INFO: Running adequate version 0.15.6 now. 0m26.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'pbalign'] 0m26.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'pbalign'] 0m26.1s INFO: Running scripts pre_remove 0m26.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_remove_exceptions'] 0m27.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/pre_remove_exceptions'] 0m27.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m27.4s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.10 install ok installed base-files base-files 9.9+deb9u13 install ok installed base-passwd base-passwd 3.5.43 install ok installed bash bash 4.4-5 install ok installed blasr blasr 5.3+0-1 install ok installed bsdutils bsdutils 1:2.29.2-1+deb9u1 install ok installed bzip2 bzip2 1.0.6-8.1 install ok installed ca-certificates ca-certificates 20200601~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 file file 1:5.30-1+deb9u3 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 hdf5-tools hdf5-tools 1.10.0-patch1+docs-3+deb9u1 install ok installed hostname hostname 3.18+b1 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed krb5-locales krb5-locales 1.15-1+deb9u1 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libaec0:amd64 libaec0 0.3.2-1 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 libblas-common libblas-common 3.7.0-2 install ok installed libblas3 libblas3 3.7.0-2 install ok installed libblasr:amd64 libblasr 0~20161219-1 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 libcurl3-gnutls:amd64 libcurl3-gnutls 7.52.1-5+deb9u10 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libexpat1:amd64 libexpat1 2.2.0-2+deb9u3 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libffi6:amd64 libffi6 3.2.1-6 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u3 install ok installed libgfortran3:amd64 libgfortran3 6.3.0-18+deb9u1 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-1 install ok installed libgnutls30:amd64 libgnutls30 3.5.8-5+deb9u5 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.15-1+deb9u1 install ok installed libhdf5-100:amd64 libhdf5-100 1.10.0-patch1+docs-3+deb9u1 install ok installed libhdf5-cpp-100:amd64 libhdf5-cpp-100 1.10.0-patch1+docs-3+deb9u1 install ok installed libhogweed4:amd64 libhogweed4 3.3-1+b2 install ok installed libhts1:amd64 libhts1 1.3.2-2 install ok installed libidn11:amd64 libidn11 1.33-1+deb9u1 install ok installed libidn2-0:amd64 libidn2-0 0.16-1+deb9u1 install ok installed libk5crypto3:amd64 libk5crypto3 1.15-1+deb9u1 install ok installed libkeyutils1:amd64 libkeyutils1 1.5.9-9 install ok installed libkrb5-3:amd64 libkrb5-3 1.15-1+deb9u1 install ok installed libkrb5support0:amd64 libkrb5support0 1.15-1+deb9u1 install ok installed liblapack3 liblapack3 3.7.0-2 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.44+dfsg-5+deb9u4 install ok installed libldap-common libldap-common 2.4.44+dfsg-5+deb9u4 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 libmagic-mgc libmagic-mgc 1:5.30-1+deb9u3 install ok installed libmagic1:amd64 libmagic1 1:5.30-1+deb9u3 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 libnettle6:amd64 libnettle6 3.3-1+b2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.18.1-1+deb9u1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.3-2 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 libpbbam:amd64 libpbbam 0.7.4+ds-1 install ok installed libpbdata:amd64 libpbdata 0~20161219-1 install ok installed libpbihdf:amd64 libpbihdf 0~20161219-1 install ok installed libpbseq libpbseq 0~20161219-1 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libpsl5:amd64 libpsl5 0.17.0-3 install ok installed libpython-stdlib:amd64 libpython-stdlib 2.7.13-2 install ok installed libpython2.7-minimal:amd64 libpython2.7-minimal 2.7.13-2+deb9u3 install ok installed libpython2.7-stdlib:amd64 libpython2.7-stdlib 2.7.13-2+deb9u3 install ok installed libquadmath0:amd64 libquadmath0 6.3.0-18+deb9u1 install ok installed libreadline7:amd64 libreadline7 7.0-3 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-1+b1 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27~101-g0780600+dfsg-3+deb9u1 install ok installed libsasl2-modules:amd64 libsasl2-modules 2.1.27~101-g0780600+dfsg-3+deb9u1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27~101-g0780600+dfsg-3+deb9u1 install ok installed libselinux1:amd64 libselinux1 2.6-3+b3 install ok installed libsemanage-common libsemanage-common 2.6-2 install ok installed libsemanage1:amd64 libsemanage1 2.6-2 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.16.2-5+deb9u1 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u1 install ok installed libssh2-1:amd64 libssh2-1 1.7.0-1+deb9u1 install ok installed libssl1.1:amd64 libssl1.1 1.1.0l-1~deb9u1 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u12 install ok installed libsz2:amd64 libsz2 0.3.2-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.10-1.1+deb9u1 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u12 install ok installed libunistring0:amd64 libunistring0 0.9.6+really0.9.3-0.1 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 mime-support mime-support 3.60 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed ncurses-base ncurses-base 6.0+20161126-1+deb9u2 install ok installed ncurses-bin ncurses-bin 6.0+20161126-1+deb9u2 install ok installed openssl openssl 1.1.0l-1~deb9u1 install ok installed passwd passwd 1:4.4-4.1 install ok installed pbalign pbalign 0.3.0-1 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed publicsuffix publicsuffix 20190415.1030-0+deb9u1 install ok installed python python 2.7.13-2 install ok installed python-avro python-avro 1.8.1+dfsg-1 install ok installed python-cffi-backend python-cffi-backend 1.9.1-2 install ok installed python-chardet python-chardet 2.3.0-2 install ok installed python-cryptography python-cryptography 1.7.1-3+deb9u2 install ok installed python-enum34 python-enum34 1.1.6-1 install ok installed python-h5py python-h5py 2.7.0-1 install ok installed python-idna python-idna 2.2-1 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-minimal python-minimal 2.7.13-2 install ok installed python-numpy python-numpy 1:1.12.1-3 install ok installed python-openssl python-openssl 16.2.0-1 install ok installed python-pbalign python-pbalign 0.3.0-1 install ok installed python-pbcommand python-pbcommand 0.5.3-1 install ok installed python-pbcore python-pbcore 1.2.11+dfsg-1 install ok installed python-pbh5tools python-pbh5tools 0.8.0+dfsg-5 install ok installed python-pkg-resources python-pkg-resources 33.1.1-1 install ok installed python-pyasn1 python-pyasn1 0.1.9-2 install ok installed python-pysam python-pysam 0.10.0+ds-2 install ok installed python-requests python-requests 2.12.4-1 install ok installed python-setuptools python-setuptools 33.1.1-1 install ok installed python-six python-six 1.10.0-3 install ok installed python-urllib3 python-urllib3 1.19.1-1 install ok installed python2.7 python2.7 2.7.13-2+deb9u3 install ok installed python2.7-minimal python2.7-minimal 2.7.13-2+deb9u3 install ok installed readline-common readline-common 7.0-3 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed 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 xz-utils xz-utils 5.2.2-1.2+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5 0m27.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m27.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'apt-get', 'remove', 'blasr', 'bzip2', 'ca-certificates', 'file', 'hdf5-tools', 'krb5-locales', 'libaec0:amd64', 'libblas-common', 'libblas3', 'libblasr:amd64', 'libcurl3-gnutls:amd64', 'libexpat1:amd64', 'libffi6:amd64', 'libgfortran3:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-100:amd64', 'libhdf5-cpp-100:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3', 'libldap-2.4-2:amd64', 'libldap-common', 'libmagic-mgc', 'libmagic1:amd64', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpbbam:amd64', 'libpbdata:amd64', 'libpbihdf:amd64', 'libpbseq', 'libpsl5:amd64', 'libpython-stdlib: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', 'libssl1.1:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'mime-support', 'openssl', 'publicsuffix', 'python', 'python-avro', 'python-cffi-backend', 'python-chardet', 'python-cryptography', 'python-enum34', 'python-h5py', 'python-idna', 'python-ipaddress', 'python-iso8601', 'python-minimal', 'python-numpy', 'python-openssl', 'python-pbalign', 'python-pbcommand', 'python-pbcore', 'python-pbh5tools', 'python-pkg-resources', 'python-pyasn1', 'python-pysam', 'python-requests', 'python-setuptools', 'python-six', 'python-urllib3', 'python2.7', 'python2.7-minimal', 'readline-common', 'xz-utils', 'pbalign'] 0m29.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: blasr bzip2 ca-certificates file hdf5-tools krb5-locales libaec0 libblas-common libblas3 libblasr libcurl3-gnutls libexpat1 libffi6 libgfortran3 libgmp10 libgnutls30 libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100 libhogweed4 libhts1 libidn11 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libnettle6 libnghttp2-14 libp11-kit0 libpbbam libpbdata libpbihdf libpbseq libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules libsasl2-modules-db libsqlite3-0 libssh2-1 libssl1.1 libsz2 libtasn1-6 libunistring0 mime-support openssl pbalign publicsuffix python python-avro python-cffi-backend python-chardet python-cryptography python-enum34 python-h5py python-idna python-ipaddress python-iso8601 python-minimal python-numpy python-openssl python-pbalign python-pbcommand python-pbcore python-pbh5tools python-pkg-resources python-pyasn1 python-pysam python-requests python-setuptools python-six python-urllib3 python2.7 python2.7-minimal readline-common xz-utils 0 upgraded, 0 newly installed, 87 to remove and 0 not upgraded. After this operation, 109 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 ... 7499 files and directories currently installed.) Removing pbalign (0.3.0-1) ... Removing python-pbalign (0.3.0-1) ... Removing blasr (5.3+0-1) ... Removing bzip2 (1.0.6-8.1) ... Removing python-pbcommand (0.5.3-1) ... Removing python-requests (2.12.4-1) ... Removing ca-certificates (20200601~deb9u1) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing file (1:5.30-1+deb9u3) ... Removing hdf5-tools (1.10.0-patch1+docs-3+deb9u1) ... Removing krb5-locales (1.15-1+deb9u1) ... Removing libpbseq (0~20161219-1) ... Removing libblasr:amd64 (0~20161219-1) ... Removing libpbihdf:amd64 (0~20161219-1) ... Removing libhdf5-cpp-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Removing python-pbh5tools (0.8.0+dfsg-5) ... Removing python-pbcore (1.2.11+dfsg-1) ... Removing python-h5py (2.7.0-1) ... Removing libhdf5-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Removing libsz2:amd64 (0.3.2-1) ... Removing libaec0:amd64 (0.3.2-1) ... Removing python-numpy (1:1.12.1-3) ... Removing liblapack3 (3.7.0-2) ... Removing libblas3 (3.7.0-2) ... Removing libblas-common (3.7.0-2) ... Removing python-pysam (0.10.0+ds-2) ... Removing libpbdata:amd64 (0~20161219-1) ... Removing libpbbam:amd64 (0.7.4+ds-1) ... Removing libhts1:amd64 (1.3.2-2) ... Removing libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Removing python-openssl (16.2.0-1) ... Removing python-cryptography (1.7.1-3+deb9u2) ... Removing python-urllib3 (1.19.1-1) ... Removing python-six (1.10.0-3) ... Removing python-cffi-backend (1.9.1-2) ... Removing python-setuptools (33.1.1-1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Removing libgfortran3:amd64 (6.3.0-18+deb9u1) ... Removing libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Removing libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Removing libpsl5:amd64 (0.17.0-3) ... Removing libidn2-0:amd64 (0.16-1+deb9u1) ... Removing libkrb5-3:amd64 (1.15-1+deb9u1) ... Removing libk5crypto3:amd64 (1.15-1+deb9u1) ... Removing libkrb5support0:amd64 (1.15-1+deb9u1) ... Removing libkeyutils1:amd64 (1.5.9-9) ... Removing libldap-common (2.4.44+dfsg-5+deb9u4) ... Removing libmagic1:amd64 (1:5.30-1+deb9u3) ... Removing libmagic-mgc (1:5.30-1+deb9u3) ... Removing libnghttp2-14:amd64 (1.18.1-1+deb9u1) ... Removing libquadmath0:amd64 (6.3.0-18+deb9u1) ... Removing libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Removing libsasl2-modules:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Removing libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Removing libssh2-1:amd64 (1.7.0-1+deb9u1) ... Removing openssl (1.1.0l-1~deb9u1) ... Removing libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Removing publicsuffix (20190415.1030-0+deb9u1) ... Removing python-avro (1.8.1+dfsg-1) ... Removing python-chardet (2.3.0-2) ... Removing python-enum34 (1.1.6-1) ... Removing python-idna (2.2-1) ... Removing python-ipaddress (1.0.17-1) ... Removing python-iso8601 (0.1.11-1) ... Removing python-pkg-resources (33.1.1-1) ... Removing python-pyasn1 (0.1.9-2) ... Removing xz-utils (5.2.2-1.2+b1) ... Removing python (2.7.13-2) ... Removing python2.7 (2.7.13-2+deb9u3) ... Removing libpython-stdlib:amd64 (2.7.13-2) ... Removing libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ... Removing libexpat1:amd64 (2.2.0-2+deb9u3) ... Removing libgnutls30:amd64 (3.5.8-5+deb9u5) ... Removing libp11-kit0:amd64 (0.23.3-2) ... Removing libffi6:amd64 (3.2.1-6) ... Removing libhogweed4:amd64 (3.3-1+b2) ... Removing libgmp10:amd64 (2:6.1.2+dfsg-1) ... Removing libidn11:amd64 (1.33-1+deb9u1) ... Removing libnettle6:amd64 (3.3-1+b2) ... Removing python-minimal (2.7.13-2) ... Removing python2.7-minimal (2.7.13-2+deb9u3) ... Removing libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) ... Removing libreadline7:amd64 (7.0-3) ... Removing libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Removing libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Removing libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Removing mime-support (3.60) ... Removing readline-common (7.0-3) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'apt-get', 'remove', 'blasr', 'bzip2', 'ca-certificates', 'file', 'hdf5-tools', 'krb5-locales', 'libaec0:amd64', 'libblas-common', 'libblas3', 'libblasr:amd64', 'libcurl3-gnutls:amd64', 'libexpat1:amd64', 'libffi6:amd64', 'libgfortran3:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-100:amd64', 'libhdf5-cpp-100:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3', 'libldap-2.4-2:amd64', 'libldap-common', 'libmagic-mgc', 'libmagic1:amd64', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpbbam:amd64', 'libpbdata:amd64', 'libpbihdf:amd64', 'libpbseq', 'libpsl5:amd64', 'libpython-stdlib: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', 'libssl1.1:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'mime-support', 'openssl', 'publicsuffix', 'python', 'python-avro', 'python-cffi-backend', 'python-chardet', 'python-cryptography', 'python-enum34', 'python-h5py', 'python-idna', 'python-ipaddress', 'python-iso8601', 'python-minimal', 'python-numpy', 'python-openssl', 'python-pbalign', 'python-pbcommand', 'python-pbcore', 'python-pbh5tools', 'python-pkg-resources', 'python-pyasn1', 'python-pysam', 'python-requests', 'python-setuptools', 'python-six', 'python-urllib3', 'python2.7', 'python2.7-minimal', 'readline-common', 'xz-utils', 'pbalign'] 0m29.5s INFO: Running scripts post_remove 0m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_remove_exceptions'] 0m29.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_remove_exceptions'] 0m29.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'dpkg', '--purge', 'blasr', 'bzip2', 'ca-certificates', 'file', 'hdf5-tools', 'krb5-locales', 'libaec0:amd64', 'libblas-common', 'libblas3', 'libblasr:amd64', 'libcurl3-gnutls:amd64', 'libexpat1:amd64', 'libffi6:amd64', 'libgfortran3:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-100:amd64', 'libhdf5-cpp-100:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3', 'libldap-2.4-2:amd64', 'libldap-common', 'libmagic-mgc', 'libmagic1:amd64', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpbbam:amd64', 'libpbdata:amd64', 'libpbihdf:amd64', 'libpbseq', 'libpsl5:amd64', 'libpython-stdlib: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', 'libssl1.1:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'mime-support', 'openssl', 'publicsuffix', 'python', 'python-avro', 'python-cffi-backend', 'python-chardet', 'python-cryptography', 'python-enum34', 'python-h5py', 'python-idna', 'python-ipaddress', 'python-iso8601', 'python-minimal', 'python-numpy', 'python-openssl', 'python-pbalign', 'python-pbcommand', 'python-pbcore', 'python-pbh5tools', 'python-pkg-resources', 'python-pyasn1', 'python-pysam', 'python-requests', 'python-setuptools', 'python-six', 'python-urllib3', 'python2.7', 'python2.7-minimal', 'readline-common', 'xz-utils'] 0m29.7s DUMP: dpkg: warning: ignoring request to remove blasr which isn't installed dpkg: warning: ignoring request to remove bzip2 which isn't installed (Reading database ... 4428 files and directories currently installed.) Purging configuration files for ca-certificates (20200601~deb9u1) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove file which isn't installed dpkg: warning: ignoring request to remove hdf5-tools which isn't installed dpkg: warning: ignoring request to remove krb5-locales which isn't installed dpkg: warning: ignoring request to remove libaec0 which isn't installed dpkg: warning: ignoring request to remove libblas-common which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libblasr which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libffi6 which isn't installed dpkg: warning: ignoring request to remove libgfortran3 which isn't installed dpkg: warning: ignoring request to remove libgmp10 which isn't installed dpkg: warning: ignoring request to remove libgnutls30 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... dpkg: warning: ignoring request to remove libhdf5-100 which isn't installed dpkg: warning: ignoring request to remove libhdf5-cpp-100 which isn't installed dpkg: warning: ignoring request to remove libhogweed4 which isn't installed dpkg: warning: ignoring request to remove libhts1 which isn't installed dpkg: warning: ignoring request to remove libidn11 which isn't installed dpkg: warning: ignoring request to remove libidn2-0 which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed Purging configuration files for libldap-common (2.4.44+dfsg-5+deb9u4) ... dpkg: warning: ignoring request to remove libmagic-mgc which isn't installed Purging configuration files for libmagic1:amd64 (1:5.30-1+deb9u3) ... dpkg: warning: ignoring request to remove libnettle6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libp11-kit0 which isn't installed dpkg: warning: ignoring request to remove libpbbam which isn't installed dpkg: warning: ignoring request to remove libpbdata which isn't installed dpkg: warning: ignoring request to remove libpbihdf which isn't installed dpkg: warning: ignoring request to remove libpbseq which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython-stdlib which isn't installed Purging configuration files for libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) ... dpkg: warning: ignoring request to remove libpython2.7-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline7 which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed Purging configuration files for libsasl2-modules:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed Purging configuration files for libssl1.1:amd64 (1.1.0l-1~deb9u1) ... dpkg: warning: ignoring request to remove libsz2 which isn't installed dpkg: warning: ignoring request to remove libtasn1-6 which isn't installed dpkg: warning: ignoring request to remove libunistring0 which isn't installed Purging configuration files for mime-support (3.60) ... Purging configuration files for openssl (1.1.0l-1~deb9u1) ... dpkg: warning: ignoring request to remove publicsuffix which isn't installed Purging configuration files for python (2.7.13-2) ... dpkg: warning: ignoring request to remove python-avro 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-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-ipaddress which isn't installed dpkg: warning: ignoring request to remove python-iso8601 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-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-pbcore which isn't installed dpkg: warning: ignoring request to remove python-pbh5tools which isn't installed dpkg: warning: ignoring request to remove python-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python-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-setuptools which isn't installed dpkg: warning: ignoring request to remove python-six which isn't installed dpkg: warning: ignoring request to remove python-urllib3 which isn't installed dpkg: warning: ignoring request to remove python2.7 which isn't installed Purging configuration files for python2.7-minimal (2.7.13-2+deb9u3) ... Purging configuration files for readline-common (7.0-3) ... dpkg: warning: ignoring request to remove xz-utils which isn't installed 0m29.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'dpkg', '--purge', 'blasr', 'bzip2', 'ca-certificates', 'file', 'hdf5-tools', 'krb5-locales', 'libaec0:amd64', 'libblas-common', 'libblas3', 'libblasr:amd64', 'libcurl3-gnutls:amd64', 'libexpat1:amd64', 'libffi6:amd64', 'libgfortran3:amd64', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-100:amd64', 'libhdf5-cpp-100:amd64', 'libhogweed4:amd64', 'libhts1:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3', 'libldap-2.4-2:amd64', 'libldap-common', 'libmagic-mgc', 'libmagic1:amd64', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpbbam:amd64', 'libpbdata:amd64', 'libpbihdf:amd64', 'libpbseq', 'libpsl5:amd64', 'libpython-stdlib: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', 'libssl1.1:amd64', 'libsz2:amd64', 'libtasn1-6:amd64', 'libunistring0:amd64', 'mime-support', 'openssl', 'publicsuffix', 'python', 'python-avro', 'python-cffi-backend', 'python-chardet', 'python-cryptography', 'python-enum34', 'python-h5py', 'python-idna', 'python-ipaddress', 'python-iso8601', 'python-minimal', 'python-numpy', 'python-openssl', 'python-pbalign', 'python-pbcommand', 'python-pbcore', 'python-pbh5tools', 'python-pkg-resources', 'python-pyasn1', 'python-pysam', 'python-requests', 'python-setuptools', 'python-six', 'python-urllib3', 'python2.7', 'python2.7-minimal', 'readline-common', 'xz-utils'] 0m29.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'dpkg', '--purge', 'pbalign'] 0m29.7s DUMP: dpkg: warning: ignoring request to remove pbalign which isn't installed 0m29.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'dpkg', '--purge', 'pbalign'] 0m29.7s INFO: Running scripts post_purge 0m29.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_purge_exceptions'] 0m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_purge_exceptions'] 0m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'dpkg', '--purge', '--pending'] 0m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'dpkg', '--purge', '--pending'] 0m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'dpkg', '--remove', '--pending'] 0m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'dpkg', '--remove', '--pending'] 0m29.8s INFO: Running scripts post_test 0m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_test_exceptions'] 0m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'tmp/scripts/post_test_exceptions'] 0m29.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd'] 0m30.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd'] 0m30.4s DEBUG: No broken symlinks as far as we can find. 0m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'dpkg-divert', '--list'] 0m30.4s 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 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'dpkg-divert', '--list'] 0m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'apt-get', 'clean'] 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd', 'apt-get', 'clean'] 0m30.4s DEBUG: Recording chroot state 0m30.8s INFO: PASS: Installation and purging test. 0m31.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/dev/shm'] 0m31.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/dev/shm'] 0m31.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/dev/console'] 0m31.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/dev/console'] 0m31.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/dev/ptmx'] 0m31.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/dev/ptmx'] 0m31.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/dev/pts'] 0m31.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/dev/pts'] 0m31.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/proc'] 0m31.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd/proc'] 0m31.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd'] 0m31.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpy_7qufqd'] 0m31.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpy_7qufqd 0m31.2s INFO: PASS: All tests. 0m31.2s INFO: piuparts run ends. ret=0 End: 2023-02-10 20:49:58 GMT