Start: 2018-02-24 14:08:50 UTC Package: gromacs-dev Source: gromacs Version: 4.5.5-2 Installed-Size: 1380 Maintainer: Debichem Team Architecture: amd64 Depends: gromacs (= 4.5.5-2), fftw3-dev Recommends: gromacs-data Suggests: gromacs-mpich (= 4.5.5-2) | gromacs-openmpi (= 4.5.5-2), libmpich2-dev, lesstif2-dev, libx11-dev, zlib1g-dev Description: GROMACS molecular dynamics sim, development kit Homepage: http://www.gromacs.org/ Description-md5: aab3304779c4ebcd0dbb20ae1eb40866 Tag: devel::lang:c, devel::library, field::biology, field::chemistry, implemented-in::c, role::devel-lib Section: devel Priority: extra Filename: pool/main/g/gromacs/gromacs-dev_4.5.5-2_amd64.deb Size: 291724 MD5sum: 52fa07d86a1b8a6a80c8ec284c819f5f SHA1: 23e84010e9267229c421fae777d156eb2668c471 SHA256: 901a17e2ba8fa358f10befaf77f5ad6d0cb32cb4f2ce072aef10b3f046d390e7 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python2.7/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --skip-logrotatefiles-test --warn-on-others --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --scriptsdir /etc/piuparts/scripts-wheezy --warn-on-debsums-errors --warn-on-install-over-symlink --mirror 'http://mirror.bm.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz -d wheezy --no-upgrade-test --apt gromacs-dev=4.5.5-2 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 0.84~201801121530~0.83-4-g6e16ed9a starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --skip-logrotatefiles-test --warn-on-others --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --scriptsdir /etc/piuparts/scripts-wheezy --warn-on-debsums-errors --warn-on-install-over-symlink --mirror 'http://mirror.bm.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz -d wheezy --no-upgrade-test --apt gromacs-dev=4.5.5-2 0m0.0s INFO: Running on: Linux piu-slave-bm-a 4.9.0-6-amd64 #1 SMP Debian 4.9.82-1+deb9u2 (2018-02-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpYBRXaJ 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpYBRXaJ 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz'] 0m1.9s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/wheezy_amd64.tar.gz'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/proc'] 0m2.0s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/proc'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/dev/pts'] 0m2.0s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/dev/pts'] 0m2.0s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/dev/ptmx'] 0m2.0s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/dev/ptmx'] 0m2.0s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/dev/console'] 0m2.0s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/dev/console'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/run/shm'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/run/shm'] 0m2.1s DEBUG: sources.list: deb http://mirror.bm.debian.org/debian/ wheezy main 0m2.1s DEBUG: Created policy-rc.d and chmodded it. 0m2.1s DEBUG: Created resolv.conf. 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpYBRXaJ/tmp/scripts/ 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts-wheezy to /srv/piuparts.debian.org/tmp/tmpYBRXaJ/tmp/scripts/ 0m2.1s INFO: Running scripts post_chroot_unpack 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-get', 'update'] 0m4.8s DUMP: Hit http://mirror.bm.debian.org wheezy Release.gpg Hit http://mirror.bm.debian.org wheezy Release Hit http://mirror.bm.debian.org wheezy/main amd64 Packages Hit http://mirror.bm.debian.org wheezy/main Translation-en Reading package lists... 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-get', 'update'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-get', '-yf', 'dist-upgrade'] 0m5.2s DUMP: Reading package lists... Building dependency tree... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-get', '-yf', 'dist-upgrade'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.6s DUMP: 0c96df6df725ee7ec7aebd2b6a77fb72 - 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.6s INFO: Running scripts post_setup 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_setup_dummy_users'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_setup_dummy_users'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_setup_experimental'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_setup_experimental'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_setup_forbid_home'] 0m6.7s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_setup_forbid_home'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_setup_force-unsafe-io'] 0m6.7s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' `/bin/sync' -> `true' 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_setup_force-unsafe-io'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_setup_minimize'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_setup_minimize'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_setup_squeeze-backports'] 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_setup_squeeze-backports'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_setup_wheezy-fake-essential'] 0m8.0s DUMP: *** Adding fake essential packages *** Reading package lists... Building dependency tree... Suggested packages: perl-modules The following NEW packages will be installed: adduser ucf 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 335 kB of archives. After this operation, 1327 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ wheezy/main adduser all 3.113+nmu3 [264 kB] Get:2 http://mirror.bm.debian.org/debian/ wheezy/main ucf all 3.0025+nmu3 [70.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 335 kB in 0s (18.9 MB/s) Selecting previously unselected package adduser. (Reading database ... 6639 files and directories currently installed.) Unpacking adduser (from .../adduser_3.113+nmu3_all.deb) ... Selecting previously unselected package ucf. Unpacking ucf (from .../ucf_3.0025+nmu3_all.deb) ... Moving old data out of the way Setting up adduser (3.113+nmu3) ... Setting up ucf (3.0025+nmu3) ... 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_setup_wheezy-fake-essential'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_setup_zz_backports'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_setup_zz_backports'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-get', 'clean'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-get', 'clean'] 0m8.0s DEBUG: Recording chroot state 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.8s DUMP: install ok installed adduser adduser 3.113+nmu3 install ok installed apt apt 0.9.7.9+deb7u7 install ok installed base-files base-files 7.1wheezy11 install ok installed base-passwd base-passwd 3.5.26 install ok installed bash bash 4.2+dfsg-0.1+deb7u3 install ok installed bsdutils bsdutils 1:2.20.1-5.3 install ok installed coreutils coreutils 8.13-3.5 install ok installed dash dash 0.5.7-3 install ok installed debconf debconf 1.5.49 install ok installed debconf-i18n debconf-i18n 1.5.49 install ok installed debian-archive-keyring debian-archive-keyring 2014.3~deb7u1 install ok installed debianutils debianutils 4.3.2 install ok installed diffutils diffutils 1:3.2-6 install ok installed dpkg dpkg 1.16.18 install ok installed e2fslibs:amd64 e2fslibs 1.42.5-1.1+deb7u1 install ok installed e2fsprogs e2fsprogs 1.42.5-1.1+deb7u1 install ok installed findutils findutils 4.4.2-4 install ok installed gcc-4.7-base:amd64 gcc-4.7-base 4.7.2-5 install ok installed gnupg gnupg 1.4.12-7+deb7u7 install ok installed gpgv gpgv 1.4.12-7+deb7u7 install ok installed grep grep 2.12-2 install ok installed gzip gzip 1.5-1.1 install ok installed hostname hostname 3.11 install ok installed initscripts initscripts 2.88dsf-41+deb7u1 install ok installed insserv insserv 1.14.0-5 install ok installed libacl1:amd64 libacl1 2.2.51-8 install ok installed libapt-pkg4.12:amd64 libapt-pkg4.12 0.9.7.9+deb7u7 install ok installed libattr1:amd64 libattr1 1:2.4.46-8 install ok installed libblkid1:amd64 libblkid1 2.20.1-5.3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-4 install ok installed libc-bin libc-bin 2.13-38+deb7u10 install ok installed libc6:amd64 libc6 2.13-38+deb7u10 install ok installed libcomerr2:amd64 libcomerr2 1.42.5-1.1+deb7u1 install ok installed libdb5.1:amd64 libdb5.1 5.1.29-5 install ok installed libgcc1:amd64 libgcc1 1:4.7.2-5 install ok installed liblocale-gettext-perl liblocale-gettext-perl 1.05-7+b1 install ok installed liblzma5:amd64 liblzma5 5.1.1alpha+20120614-2 install ok installed libmount1 libmount1 2.20.1-5.3 install ok installed libncurses5:amd64 libncurses5 5.9-10 install ok installed libpam-modules:amd64 libpam-modules 1.1.3-7.1 install ok installed libpam-modules-bin libpam-modules-bin 1.1.3-7.1 install ok installed libpam-runtime libpam-runtime 1.1.3-7.1 install ok installed libpam0g:amd64 libpam0g 1.1.3-7.1 install ok installed libreadline6:amd64 libreadline6 6.2+dfsg-0.1 install ok installed libselinux1:amd64 libselinux1 2.1.9-5 install ok installed libsemanage-common libsemanage-common 2.1.6-6 install ok installed libsemanage1:amd64 libsemanage1 2.1.6-6 install ok installed libsepol1:amd64 libsepol1 2.1.4-3 install ok installed libslang2:amd64 libslang2 2.2.4-15 install ok installed libss2:amd64 libss2 1.42.5-1.1+deb7u1 install ok installed libstdc++6:amd64 libstdc++6 4.7.2-5 install ok installed libtext-charwidth-perl libtext-charwidth-perl 0.04-7+b1 install ok installed libtext-iconv-perl libtext-iconv-perl 1.7-5 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-7 install ok installed libtinfo5:amd64 libtinfo5 5.9-10 install ok installed libusb-0.1-4:amd64 libusb-0.1-4 2:0.1.12-20+nmu1 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-3 install ok installed libuuid1:amd64 libuuid1 2.20.1-5.3 install ok installed login login 1:4.1.5.1-1 install ok installed lsb-base lsb-base 4.1+Debian8+deb7u1 install ok installed mawk mawk 1.3.3-17 install ok installed mount mount 2.20.1-5.3 install ok installed multiarch-support multiarch-support 2.13-38+deb7u10 install ok installed ncurses-base ncurses-base 5.9-10 install ok installed ncurses-bin ncurses-bin 5.9-10 install ok installed passwd passwd 1:4.1.5.1-1 install ok installed perl-base perl-base 5.14.2-21+deb7u3 install ok installed readline-common readline-common 6.2+dfsg-0.1 install ok installed sed sed 4.2.1-10 install ok installed sensible-utils sensible-utils 0.0.7 install ok installed sysv-rc sysv-rc 2.88dsf-41+deb7u1 install ok installed sysvinit sysvinit 2.88dsf-41+deb7u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-41+deb7u1 install ok installed tar tar 1.26+dfsg-0.1 install ok installed tzdata tzdata 2016d-0+deb7u1 install ok installed ucf ucf 3.0025+nmu3 install ok installed util-linux util-linux 2.20.1-5.3 install ok installed xz-utils xz-utils 5.1.1alpha+20120614-2 install ok installed zlib1g:amd64 zlib1g 1:1.2.7.dfsg-13 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg-divert', '--list'] 0m9.9s DUMP: diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg-divert', '--list'] 0m9.9s INFO: Running scripts is_testable 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/is_testable_uninstallable'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/is_testable_uninstallable'] 0m9.9s INFO: apt-cache does not know about any of the requested packages 0m9.9s INFO: Running scripts pre_test 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_test_exceptions'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_test_exceptions'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_test_root_password'] 0m9.9s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_test_root_password'] 0m9.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ'] 0m10.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ'] 0m12.6s DEBUG: No broken symlinks as far as we can find. 0m12.6s INFO: Running scripts pre_install 0m12.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_install_database-server'] 0m12.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_install_database-server'] 0m12.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_install_exceptions'] 0m12.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_install_exceptions'] 0m12.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_install_extras'] 0m12.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_install_extras'] 0m12.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_install_foreign_architecture'] 0m12.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_install_foreign_architecture'] 0m12.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m12.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m12.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-cache', 'show', 'gromacs-dev=4.5.5-2'] 0m14.4s DUMP: Package: gromacs-dev Source: gromacs Version: 4.5.5-2 Installed-Size: 1380 Maintainer: Debichem Team Architecture: amd64 Depends: gromacs (= 4.5.5-2), fftw3-dev Recommends: gromacs-data Suggests: gromacs-mpich (= 4.5.5-2) | gromacs-openmpi (= 4.5.5-2), libmpich2-dev, lesstif2-dev, libx11-dev, zlib1g-dev Description-en: GROMACS molecular dynamics sim, development kit GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. . It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non- biological systems, e.g. polymers. . This package contains header files and static libraries for development purposes, plus sample Makefiles. Development components for MPI-enabled GROMACS builds also require their respective packages. Homepage: http://www.gromacs.org/ Description-md5: aab3304779c4ebcd0dbb20ae1eb40866 Tag: devel::lang:c, devel::library, field::biology, field::chemistry, implemented-in::c, role::devel-lib Section: devel Priority: extra Filename: pool/main/g/gromacs/gromacs-dev_4.5.5-2_amd64.deb Size: 291724 MD5sum: 52fa07d86a1b8a6a80c8ec284c819f5f SHA1: 23e84010e9267229c421fae777d156eb2668c471 SHA256: 901a17e2ba8fa358f10befaf77f5ad6d0cb32cb4f2ce072aef10b3f046d390e7 0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-cache', 'show', 'gromacs-dev=4.5.5-2'] 0m14.4s DEBUG: metapackage: Package: piuparts-depends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: piuparts developers team Description: Dummy package to satisfy dependencies - created by piuparts This package was created automatically by piuparts and can safely be removed Depends: gromacs (= 4.5.5-2), fftw3-dev 0m14.4s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpyZ7hh2/piuparts-depends-dummy'] 0m14.4s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmpyZ7hh2/piuparts-depends-dummy.deb'. 0m14.4s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpyZ7hh2/piuparts-depends-dummy'] 0m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m14.4s DUMP: 0.9.7.9+deb7u7 0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m14.4s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmpyZ7hh2/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmpYBRXaJ/tmp 0m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg', '-i', './tmp/piuparts-depends-dummy.deb'] 0m14.5s DUMP: Selecting previously unselected package piuparts-depends-dummy. (Reading database ... 6768 files and directories currently installed.) Unpacking piuparts-depends-dummy (from .../tmp/piuparts-depends-dummy.deb) ... dpkg: dependency problems prevent configuration of piuparts-depends-dummy: piuparts-depends-dummy depends on gromacs (= 4.5.5-2); however: Package gromacs is not installed. piuparts-depends-dummy depends on fftw3-dev; however: Package fftw3-dev is not installed. dpkg: error processing piuparts-depends-dummy (--install): dependency problems - leaving unconfigured Errors were encountered while processing: piuparts-depends-dummy 0m14.5s DEBUG: Command failed (status=1), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg', '-i', './tmp/piuparts-depends-dummy.deb'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-get', '-yf', 'install'] 0m18.0s DUMP: Reading package lists... Building dependency tree... Reading state information... Correcting dependencies... Done The following extra packages will be installed: gromacs gromacs-data libfftw3-3 libfftw3-bin libfftw3-dev libgomp1 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxml2 Suggested packages: tcsh c-shell Recommended packages: cpp xml-core The following NEW packages will be installed: gromacs gromacs-data libfftw3-3 libfftw3-bin libfftw3-dev libgomp1 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxml2 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 1 not fully installed or removed. Need to get 17.2 MB of archives. After this operation, 52.1 MB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ wheezy/main gromacs-data all 4.5.5-2 [1853 kB] Get:2 http://mirror.bm.debian.org/debian/ wheezy/main libgomp1 amd64 4.7.2-5 [27.5 kB] Get:3 http://mirror.bm.debian.org/debian/ wheezy/main libfftw3-3 amd64 3.3.2-3.1 [1665 kB] Get:4 http://mirror.bm.debian.org/debian/ wheezy/main libxau6 amd64 1:1.0.7-1 [18.8 kB] Get:5 http://mirror.bm.debian.org/debian/ wheezy/main libxdmcp6 amd64 1:1.1.1-1 [26.3 kB] Get:6 http://mirror.bm.debian.org/debian/ wheezy/main libxcb1 amd64 1.8.1-2+deb7u1 [50.2 kB] Get:7 http://mirror.bm.debian.org/debian/ wheezy/main libx11-data all 2:1.5.0-1+deb7u2 [194 kB] Get:8 http://mirror.bm.debian.org/debian/ wheezy/main libx11-6 amd64 2:1.5.0-1+deb7u2 [901 kB] Get:9 http://mirror.bm.debian.org/debian/ wheezy/main libxml2 amd64 2.8.0+dfsg1-7+wheezy5 [906 kB] Get:10 http://mirror.bm.debian.org/debian/ wheezy/main gromacs amd64 4.5.5-2 [9587 kB] Get:11 http://mirror.bm.debian.org/debian/ wheezy/main libfftw3-bin amd64 3.3.2-3.1 [202 kB] Get:12 http://mirror.bm.debian.org/debian/ wheezy/main libfftw3-dev amd64 3.3.2-3.1 [1767 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 17.2 MB in 0s (18.4 MB/s) Selecting previously unselected package gromacs-data. (Reading database ... 6768 files and directories currently installed.) Unpacking gromacs-data (from .../gromacs-data_4.5.5-2_all.deb) ... Selecting previously unselected package libgomp1:amd64. Unpacking libgomp1:amd64 (from .../libgomp1_4.7.2-5_amd64.deb) ... Selecting previously unselected package libfftw3-3:amd64. Unpacking libfftw3-3:amd64 (from .../libfftw3-3_3.3.2-3.1_amd64.deb) ... Selecting previously unselected package libxau6:amd64. Unpacking libxau6:amd64 (from .../libxau6_1%3a1.0.7-1_amd64.deb) ... Selecting previously unselected package libxdmcp6:amd64. Unpacking libxdmcp6:amd64 (from .../libxdmcp6_1%3a1.1.1-1_amd64.deb) ... Selecting previously unselected package libxcb1:amd64. Unpacking libxcb1:amd64 (from .../libxcb1_1.8.1-2+deb7u1_amd64.deb) ... Selecting previously unselected package libx11-data. Unpacking libx11-data (from .../libx11-data_2%3a1.5.0-1+deb7u2_all.deb) ... Selecting previously unselected package libx11-6:amd64. Unpacking libx11-6:amd64 (from .../libx11-6_2%3a1.5.0-1+deb7u2_amd64.deb) ... Selecting previously unselected package libxml2:amd64. Unpacking libxml2:amd64 (from .../libxml2_2.8.0+dfsg1-7+wheezy5_amd64.deb) ... Selecting previously unselected package gromacs. Unpacking gromacs (from .../gromacs_4.5.5-2_amd64.deb) ... Selecting previously unselected package libfftw3-bin. Unpacking libfftw3-bin (from .../libfftw3-bin_3.3.2-3.1_amd64.deb) ... Selecting previously unselected package libfftw3-dev:amd64. Unpacking libfftw3-dev:amd64 (from .../libfftw3-dev_3.3.2-3.1_amd64.deb) ... Setting up gromacs-data (4.5.5-2) ... Setting up libgomp1:amd64 (4.7.2-5) ... Setting up libfftw3-3:amd64 (3.3.2-3.1) ... Setting up libxau6:amd64 (1:1.0.7-1) ... Setting up libxdmcp6:amd64 (1:1.1.1-1) ... Setting up libxcb1:amd64 (1.8.1-2+deb7u1) ... Setting up libx11-data (2:1.5.0-1+deb7u2) ... Setting up libx11-6:amd64 (2:1.5.0-1+deb7u2) ... Setting up libxml2:amd64 (2.8.0+dfsg1-7+wheezy5) ... Setting up gromacs (4.5.5-2) ... Setting up libfftw3-bin (3.3.2-3.1) ... Setting up libfftw3-dev:amd64 (3.3.2-3.1) ... Setting up piuparts-depends-dummy (0.invalid.0) ... 0m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-get', '-yf', 'install'] 0m18.0s INFO: Installation of ['./tmp/piuparts-depends-dummy.deb'] ok 0m18.0s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmpYBRXaJ/./tmp/piuparts-depends-dummy.deb 0m18.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m18.0s DUMP: piuparts-depends-dummy install ok installed 0m18.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m18.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m18.1s DUMP: (Reading database ... 8260 files and directories currently installed.) Removing piuparts-depends-dummy ... 0m18.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m18.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-get', 'clean'] 0m18.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-get', 'clean'] 0m18.1s DEBUG: Recording chroot state 0m20.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ'] 0m21.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ'] 0m23.2s DEBUG: No broken symlinks as far as we can find. 0m23.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-cache', 'policy'] 0m24.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror.bm.debian.org/debian/ wheezy/main Translation-en 500 http://mirror.bm.debian.org/debian/ wheezy/main amd64 Packages release v=7.11,o=Debian,a=oldoldstable,n=wheezy,l=Debian,c=main origin mirror.bm.debian.org Pinned packages: 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-cache', 'policy'] 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-cache', 'policy', 'gromacs-dev'] 0m24.6s DUMP: gromacs-dev: Installed: (none) Candidate: 4.5.5-2 Version table: 4.5.5-2 0 500 http://mirror.bm.debian.org/debian/ wheezy/main amd64 Packages 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-cache', 'policy', 'gromacs-dev'] 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-get', '-y', 'install', 'gromacs-dev=4.5.5-2'] 0m25.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Suggested packages: gromacs-mpich gromacs-openmpi libmpich2-dev lesstif2-dev libx11-dev zlib1g-dev The following NEW packages will be installed: gromacs-dev 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 292 kB of archives. After this operation, 1413 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian/ wheezy/main gromacs-dev amd64 4.5.5-2 [292 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 292 kB in 0s (12.4 MB/s) Selecting previously unselected package gromacs-dev. (Reading database ... 8260 files and directories currently installed.) Unpacking gromacs-dev (from .../gromacs-dev_4.5.5-2_amd64.deb) ... Setting up gromacs-dev (4.5.5-2) ... 0m25.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-get', '-y', 'install', 'gromacs-dev=4.5.5-2'] 0m25.5s INFO: Running scripts post_install 0m25.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_install_exceptions'] 0m25.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_install_exceptions'] 0m25.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ'] 0m26.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ'] 0m28.7s ERROR: WARN: Broken symlinks: /usr/lib/libgmx_mpi.mpich.so -> libgmx_mpi.mpich.so.6 /usr/lib/libgmx_mpi_d.mpich.so -> libgmx_mpi_d.mpich.so.6 /usr/lib/libgmxpreprocess_mpi.mpich.so -> libgmxpreprocess_mpi.mpich.so.6 /usr/lib/libgmxpreprocess_mpi_d.mpich.so -> libgmxpreprocess_mpi_d.mpich.so.6 /usr/lib/libmd_mpi.mpich.so -> libmd_mpi.mpich.so.6 /usr/lib/libmd_mpi_d.mpich.so -> libmd_mpi_d.mpich.so.6 /usr/lib/libgmx_mpi.openmpi.so -> libgmx_mpi.openmpi.so.6 /usr/lib/libgmx_mpi_d.openmpi.so -> libgmx_mpi_d.openmpi.so.6 /usr/lib/libgmxpreprocess_mpi.openmpi.so -> libgmxpreprocess_mpi.openmpi.so.6 /usr/lib/libgmxpreprocess_mpi_d.openmpi.so -> libgmxpreprocess_mpi_d.openmpi.so.6 /usr/lib/libmd_mpi.openmpi.so -> libmd_mpi.openmpi.so.6 /usr/lib/libmd_mpi_d.openmpi.so -> libmd_mpi_d.openmpi.so.6 0m28.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m28.7s DUMP: install ok installed adduser adduser 3.113+nmu3 install ok installed apt apt 0.9.7.9+deb7u7 install ok installed base-files base-files 7.1wheezy11 install ok installed base-passwd base-passwd 3.5.26 install ok installed bash bash 4.2+dfsg-0.1+deb7u3 install ok installed bsdutils bsdutils 1:2.20.1-5.3 install ok installed coreutils coreutils 8.13-3.5 install ok installed dash dash 0.5.7-3 install ok installed debconf debconf 1.5.49 install ok installed debconf-i18n debconf-i18n 1.5.49 install ok installed debian-archive-keyring debian-archive-keyring 2014.3~deb7u1 install ok installed debianutils debianutils 4.3.2 install ok installed diffutils diffutils 1:3.2-6 install ok installed dpkg dpkg 1.16.18 install ok installed e2fslibs:amd64 e2fslibs 1.42.5-1.1+deb7u1 install ok installed e2fsprogs e2fsprogs 1.42.5-1.1+deb7u1 install ok installed findutils findutils 4.4.2-4 install ok installed gcc-4.7-base:amd64 gcc-4.7-base 4.7.2-5 install ok installed gnupg gnupg 1.4.12-7+deb7u7 install ok installed gpgv gpgv 1.4.12-7+deb7u7 install ok installed grep grep 2.12-2 install ok installed gromacs gromacs 4.5.5-2 install ok installed gromacs-data gromacs-data 4.5.5-2 install ok installed gromacs-dev gromacs-dev 4.5.5-2 install ok installed gzip gzip 1.5-1.1 install ok installed hostname hostname 3.11 install ok installed initscripts initscripts 2.88dsf-41+deb7u1 install ok installed insserv insserv 1.14.0-5 install ok installed libacl1:amd64 libacl1 2.2.51-8 install ok installed libapt-pkg4.12:amd64 libapt-pkg4.12 0.9.7.9+deb7u7 install ok installed libattr1:amd64 libattr1 1:2.4.46-8 install ok installed libblkid1:amd64 libblkid1 2.20.1-5.3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-4 install ok installed libc-bin libc-bin 2.13-38+deb7u10 install ok installed libc6:amd64 libc6 2.13-38+deb7u10 install ok installed libcomerr2:amd64 libcomerr2 1.42.5-1.1+deb7u1 install ok installed libdb5.1:amd64 libdb5.1 5.1.29-5 install ok installed libfftw3-3:amd64 libfftw3-3 3.3.2-3.1 install ok installed libfftw3-bin libfftw3-bin 3.3.2-3.1 install ok installed libfftw3-dev:amd64 libfftw3-dev 3.3.2-3.1 install ok installed libgcc1:amd64 libgcc1 1:4.7.2-5 install ok installed libgomp1:amd64 libgomp1 4.7.2-5 install ok installed liblocale-gettext-perl liblocale-gettext-perl 1.05-7+b1 install ok installed liblzma5:amd64 liblzma5 5.1.1alpha+20120614-2 install ok installed libmount1 libmount1 2.20.1-5.3 install ok installed libncurses5:amd64 libncurses5 5.9-10 install ok installed libpam-modules:amd64 libpam-modules 1.1.3-7.1 install ok installed libpam-modules-bin libpam-modules-bin 1.1.3-7.1 install ok installed libpam-runtime libpam-runtime 1.1.3-7.1 install ok installed libpam0g:amd64 libpam0g 1.1.3-7.1 install ok installed libreadline6:amd64 libreadline6 6.2+dfsg-0.1 install ok installed libselinux1:amd64 libselinux1 2.1.9-5 install ok installed libsemanage-common libsemanage-common 2.1.6-6 install ok installed libsemanage1:amd64 libsemanage1 2.1.6-6 install ok installed libsepol1:amd64 libsepol1 2.1.4-3 install ok installed libslang2:amd64 libslang2 2.2.4-15 install ok installed libss2:amd64 libss2 1.42.5-1.1+deb7u1 install ok installed libstdc++6:amd64 libstdc++6 4.7.2-5 install ok installed libtext-charwidth-perl libtext-charwidth-perl 0.04-7+b1 install ok installed libtext-iconv-perl libtext-iconv-perl 1.7-5 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-7 install ok installed libtinfo5:amd64 libtinfo5 5.9-10 install ok installed libusb-0.1-4:amd64 libusb-0.1-4 2:0.1.12-20+nmu1 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-3 install ok installed libuuid1:amd64 libuuid1 2.20.1-5.3 install ok installed libx11-6:amd64 libx11-6 2:1.5.0-1+deb7u2 install ok installed libx11-data libx11-data 2:1.5.0-1+deb7u2 install ok installed libxau6:amd64 libxau6 1:1.0.7-1 install ok installed libxcb1:amd64 libxcb1 1.8.1-2+deb7u1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.1-1 install ok installed libxml2:amd64 libxml2 2.8.0+dfsg1-7+wheezy5 install ok installed login login 1:4.1.5.1-1 install ok installed lsb-base lsb-base 4.1+Debian8+deb7u1 install ok installed mawk mawk 1.3.3-17 install ok installed mount mount 2.20.1-5.3 install ok installed multiarch-support multiarch-support 2.13-38+deb7u10 install ok installed ncurses-base ncurses-base 5.9-10 install ok installed ncurses-bin ncurses-bin 5.9-10 install ok installed passwd passwd 1:4.1.5.1-1 install ok installed perl-base perl-base 5.14.2-21+deb7u3 install ok installed readline-common readline-common 6.2+dfsg-0.1 install ok installed sed sed 4.2.1-10 install ok installed sensible-utils sensible-utils 0.0.7 install ok installed sysv-rc sysv-rc 2.88dsf-41+deb7u1 install ok installed sysvinit sysvinit 2.88dsf-41+deb7u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-41+deb7u1 install ok installed tar tar 1.26+dfsg-0.1 install ok installed tzdata tzdata 2016d-0+deb7u1 install ok installed ucf ucf 3.0025+nmu3 install ok installed util-linux util-linux 2.20.1-5.3 install ok installed xz-utils xz-utils 5.1.1alpha+20120614-2 install ok installed zlib1g:amd64 zlib1g 1:1.2.7.dfsg-13 0m28.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m30.0s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', '-ac', '--ignore-obsolete'] 0m31.5s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', '-ac', '--ignore-obsolete'] 0m31.5s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m31.5s DUMP: 0.15.1 0m31.5s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m31.5s INFO: Running adequate version 0.15.1 now. 0m31.5s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'gromacs-dev'] 0m31.6s DUMP: gromacs-dev: broken-symlink /usr/lib/libmd_mpi_d.openmpi.so -> libmd_mpi_d.openmpi.so.6 gromacs-dev: broken-symlink /usr/lib/libmd_mpi.openmpi.so -> libmd_mpi.openmpi.so.6 gromacs-dev: broken-symlink /usr/lib/libgmxpreprocess_mpi_d.openmpi.so -> libgmxpreprocess_mpi_d.openmpi.so.6 gromacs-dev: broken-symlink /usr/lib/libgmxpreprocess_mpi.openmpi.so -> libgmxpreprocess_mpi.openmpi.so.6 gromacs-dev: broken-symlink /usr/lib/libgmx_mpi_d.openmpi.so -> libgmx_mpi_d.openmpi.so.6 gromacs-dev: broken-symlink /usr/lib/libgmx_mpi.openmpi.so -> libgmx_mpi.openmpi.so.6 gromacs-dev: broken-symlink /usr/lib/libmd_mpi_d.mpich.so -> libmd_mpi_d.mpich.so.6 gromacs-dev: broken-symlink /usr/lib/libmd_mpi.mpich.so -> libmd_mpi.mpich.so.6 gromacs-dev: broken-symlink /usr/lib/libgmxpreprocess_mpi_d.mpich.so -> libgmxpreprocess_mpi_d.mpich.so.6 gromacs-dev: broken-symlink /usr/lib/libgmxpreprocess_mpi.mpich.so -> libgmxpreprocess_mpi.mpich.so.6 gromacs-dev: broken-symlink /usr/lib/libgmx_mpi_d.mpich.so -> libgmx_mpi_d.mpich.so.6 gromacs-dev: broken-symlink /usr/lib/libgmx_mpi.mpich.so -> libgmx_mpi.mpich.so.6 0m31.6s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'gromacs-dev'] 0m31.6s ERROR: WARN: Inadequate results from running adequate! gromacs-dev: broken-symlink /usr/lib/libmd_mpi_d.openmpi.so -> libmd_mpi_d.openmpi.so.6 gromacs-dev: broken-symlink /usr/lib/libmd_mpi.openmpi.so -> libmd_mpi.openmpi.so.6 gromacs-dev: broken-symlink /usr/lib/libgmxpreprocess_mpi_d.openmpi.so -> libgmxpreprocess_mpi_d.openmpi.so.6 gromacs-dev: broken-symlink /usr/lib/libgmxpreprocess_mpi.openmpi.so -> libgmxpreprocess_mpi.openmpi.so.6 gromacs-dev: broken-symlink /usr/lib/libgmx_mpi_d.openmpi.so -> libgmx_mpi_d.openmpi.so.6 gromacs-dev: broken-symlink /usr/lib/libgmx_mpi.openmpi.so -> libgmx_mpi.openmpi.so.6 gromacs-dev: broken-symlink /usr/lib/libmd_mpi_d.mpich.so -> libmd_mpi_d.mpich.so.6 gromacs-dev: broken-symlink /usr/lib/libmd_mpi.mpich.so -> libmd_mpi.mpich.so.6 gromacs-dev: broken-symlink /usr/lib/libgmxpreprocess_mpi_d.mpich.so -> libgmxpreprocess_mpi_d.mpich.so.6 gromacs-dev: broken-symlink /usr/lib/libgmxpreprocess_mpi.mpich.so -> libgmxpreprocess_mpi.mpich.so.6 gromacs-dev: broken-symlink /usr/lib/libgmx_mpi_d.mpich.so -> libgmx_mpi_d.mpich.so.6 gromacs-dev: broken-symlink /usr/lib/libgmx_mpi.mpich.so -> libgmx_mpi.mpich.so.6 0m31.6s ERROR: WARN: Running adequate resulted in less interesting tags found: broken-symlink 0m31.6s INFO: Running scripts pre_remove 0m31.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m31.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m31.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m31.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m31.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m33.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m33.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m33.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m33.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m33.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m33.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_remove_exceptions'] 0m33.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/pre_remove_exceptions'] 0m33.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-get', 'remove', 'libx11-data', 'gromacs', 'libxdmcp6:amd64', 'gromacs-data', 'libx11-6:amd64', 'libxau6:amd64', 'libgomp1:amd64', 'libfftw3-dev:amd64', 'libfftw3-3:amd64', 'libfftw3-bin', 'libxcb1:amd64', 'libxml2:amd64', 'gromacs-dev'] 0m34.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: gromacs gromacs-data gromacs-dev libfftw3-3 libfftw3-bin libfftw3-dev libgomp1 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxml2 0 upgraded, 0 newly installed, 13 to remove and 0 not upgraded. After this operation, 53.5 MB disk space will be freed. (Reading database ... 8502 files and directories currently installed.) Removing gromacs-dev ... Removing gromacs ... Removing gromacs-data ... Removing libfftw3-dev:amd64 ... Removing libfftw3-bin ... Removing libfftw3-3:amd64 ... Removing libgomp1:amd64 ... Removing libx11-6:amd64 ... Removing libx11-data ... Removing libxcb1:amd64 ... Removing libxau6:amd64 ... Removing libxdmcp6:amd64 ... Removing libxml2:amd64 ... 0m34.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-get', 'remove', 'libx11-data', 'gromacs', 'libxdmcp6:amd64', 'gromacs-data', 'libx11-6:amd64', 'libxau6:amd64', 'libgomp1:amd64', 'libfftw3-dev:amd64', 'libfftw3-3:amd64', 'libfftw3-bin', 'libxcb1:amd64', 'libxml2:amd64', 'gromacs-dev'] 0m34.7s INFO: Running scripts post_remove 0m34.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_remove_exceptions'] 0m34.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_remove_exceptions'] 0m34.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_remove_extras'] 0m34.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_remove_extras'] 0m34.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg', '--purge', 'libx11-data', 'gromacs', 'libxdmcp6:amd64', 'gromacs-data', 'libx11-6:amd64', 'libxau6:amd64', 'libgomp1:amd64', 'libfftw3-dev:amd64', 'libfftw3-3:amd64', 'libfftw3-bin', 'libxcb1:amd64', 'libxml2:amd64'] 0m34.7s DUMP: dpkg: warning: ignoring request to remove libx11-data which isn't installed (Reading database ... 6768 files and directories currently installed.) Removing gromacs ... Purging configuration files for gromacs ... Removing libxdmcp6:amd64 ... Purging configuration files for libxdmcp6:amd64 ... dpkg: warning: ignoring request to remove gromacs-data which isn't installed Removing libx11-6:amd64 ... Purging configuration files for libx11-6:amd64 ... Removing libxau6:amd64 ... Purging configuration files for libxau6:amd64 ... Removing libgomp1:amd64 ... Purging configuration files for libgomp1:amd64 ... dpkg: warning: ignoring request to remove libfftw3-dev which isn't installed Removing libfftw3-3:amd64 ... Purging configuration files for libfftw3-3:amd64 ... dpkg: warning: ignoring request to remove libfftw3-bin which isn't installed Removing libxcb1:amd64 ... Purging configuration files for libxcb1:amd64 ... Removing libxml2:amd64 ... Purging configuration files for libxml2:amd64 ... 0m34.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg', '--purge', 'libx11-data', 'gromacs', 'libxdmcp6:amd64', 'gromacs-data', 'libx11-6:amd64', 'libxau6:amd64', 'libgomp1:amd64', 'libfftw3-dev:amd64', 'libfftw3-3:amd64', 'libfftw3-bin', 'libxcb1:amd64', 'libxml2:amd64'] 0m34.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg', '--purge', 'gromacs-dev'] 0m34.8s DUMP: dpkg: warning: ignoring request to remove gromacs-dev which isn't installed 0m34.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg', '--purge', 'gromacs-dev'] 0m34.8s INFO: Running scripts post_purge 0m34.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_purge_exceptions'] 0m34.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_purge_exceptions'] 0m34.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg', '--purge', '--pending'] 0m34.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg', '--purge', '--pending'] 0m34.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg', '--remove', '--pending'] 0m34.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg', '--remove', '--pending'] 0m34.8s INFO: Running scripts post_test 0m34.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_test_exceptions'] 0m34.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'tmp/scripts/post_test_exceptions'] 0m34.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ'] 0m35.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ'] 0m37.5s DEBUG: No broken symlinks as far as we can find. 0m37.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg-divert', '--list'] 0m37.5s DUMP: diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m37.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'dpkg-divert', '--list'] 0m37.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-get', 'clean'] 0m37.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ', 'apt-get', 'clean'] 0m37.5s DEBUG: Recording chroot state 0m40.1s INFO: PASS: Installation and purging test. 0m41.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/run/shm'] 0m41.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/run/shm'] 0m41.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/dev/console'] 0m41.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/dev/console'] 0m41.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/dev/ptmx'] 0m41.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/dev/ptmx'] 0m41.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/dev/pts'] 0m41.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/dev/pts'] 0m41.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/proc'] 0m41.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ/proc'] 0m41.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ'] 0m41.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpYBRXaJ'] 0m41.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpYBRXaJ 0m41.4s INFO: PASS: All tests. 0m41.4s INFO: piuparts run ends. ret=0 End: 2018-02-24 14:09:32 UTC