Package: gromacs-dev Version: 4.5.5-2 Severity: serious User: debian...@lists.debian.org Usertags: piuparts, broken-symlink, broken-symlink-shared-library
Hi, During a test with piuparts, I noticed your package is responsible for the presence of broken symlinks involving a shared library. Such failures may indicate a significant problem with the package. Usually this is caused by a missing Depends. It may also be triggered if a Recommended or reverse dependency package owning the symlink target file is not yet installed. This type of failure mode needs to be eliminated so that other symlink problems become more visible. In this case, the problem can be resolved by creating a trigger for the target file. See the dpkg triggers documentation[1] and an example on the net[2] for implementation details. This is being filed as Serious because it represents a violation of Policy. Section 8 states "Packages containing shared libraries must be constructed with a little care to make sure that the shared library is always available". A link to the log containing the indicated broken symlinks can be found on piuparts.debian.org[3]. Search for "Warn: Broken Symlinks" to see the failure point. A log showing the broken symlink as an error is appended. The log contains the following 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 [1] - file:///usr/share/doc/dpkg-dev/triggers.txt.gz [2] - http://www.seanius.net/blog/2009/09/dpkg-triggers-howto/ [3] - http://piuparts.debian.org/sid/broken_symlinks_issue.html ---------- Start: 2013-07-05 21:44:14 EST Package: gromacs-dev Source: gromacs Version: 4.5.5-2 Installed-Size: 1380 Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org> 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 piuparts --scriptsdir /etc/piuparts/scripts --skip-logrotatefiles-test --warn-on-others --fail-on-broken-symlinks --mirror http://127.0.0.1/debian --tmpdir /var/tmp --arch amd64 -b /var/cache/piuparts/basetgz/sid.tar.gz -d sid --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 http://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 0.54~201306172307~0.53-14-ge8900a0 starting up. 0m0.0s INFO: Command line arguments: '/usr/sbin/piuparts' '--scriptsdir' '/etc/piuparts/scripts' '--skip-logrotatefiles-test' '--warn-on-others' '--fail-on-broken-symlinks' '--mirror' 'http://127.0.0.1/debian' '--tmpdir' '/var/tmp' '--arch' 'amd64' '-b' '/var/cache/piuparts/basetgz/sid.tar.gz' '-d' 'sid' '--no-upgrade-test' '--apt' 'gromacs-dev=4.5.5-2' 0m0.0s INFO: Running on: Linux debian-testing 3.9-1-amd64 #1 SMP Debian 3.9.8-1 x86_64 0m0.0s DEBUG: Created temporary directory /var/tmp/tmpTYza_H 0m0.0s DEBUG: Unpacking /var/cache/piuparts/basetgz/sid.tar.gz into /var/tmp/tmpTYza_H 0m0.0s DEBUG: Starting command: ['tar', '-C', '/var/tmp/tmpTYza_H', '-zxf', '/var/cache/piuparts/basetgz/sid.tar.gz'] 0m1.4s DEBUG: Command ok: ['tar', '-C', '/var/tmp/tmpTYza_H', '-zxf', '/var/cache/piuparts/basetgz/sid.tar.gz'] 0m1.4s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'mount', '-t', 'proc', 'proc', '/proc'] 0m1.4s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'mount', '-t', 'proc', 'proc', '/proc'] 0m1.4s DEBUG: sources.list: deb http://127.0.0.1/debian sid main deb http://127.0.0.1/debian sid contrib deb http://127.0.0.1/debian sid non-free 0m1.4s DEBUG: Created policy-rc.d and chmodded it. 0m1.4s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'apt-get', 'update'] 0m6.9s DUMP: Get:1 http://127.0.0.1 sid InRelease [205 kB] Get:2 http://127.0.0.1 sid/main amd64 Packages [6398 kB] Get:3 http://127.0.0.1 sid/contrib amd64 Packages [48.5 kB] Get:4 http://127.0.0.1 sid/non-free amd64 Packages [84.6 kB] Get:5 http://127.0.0.1 sid/contrib Translation-en [39.9 kB] Get:6 http://127.0.0.1 sid/main Translation-en [4246 kB] Get:7 http://127.0.0.1 sid/non-free Translation-en [72.7 kB] Fetched 11.1 MB in 4s (2700 kB/s) Reading package lists... 0m6.9s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'apt-get', 'update'] 0m6.9s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'apt-get', '-yf', 'dist-upgrade'] 0m8.3s DUMP: Reading package lists... Building dependency tree... The following packages will be upgraded: apt libapt-pkg4.12 libc-bin libc6 multiarch-support 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 8332 kB of archives. After this operation, 132 kB of additional disk space will be used. Get:1 http://127.0.0.1/debian/ sid/main libc-bin amd64 2.17-7 [1298 kB] Get:2 http://127.0.0.1/debian/ sid/main libc6 amd64 2.17-7 [4624 kB] Get:3 http://127.0.0.1/debian/ sid/main libapt-pkg4.12 amd64 0.9.9 [926 kB] Get:4 http://127.0.0.1/debian/ sid/main apt amd64 0.9.9 [1323 kB] Get:5 http://127.0.0.1/debian/ sid/main multiarch-support amd64 2.17-7 [160 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 8332 kB in 0s (39.4 MB/s) (Reading database ... 6639 files and directories currently installed.) Preparing to replace libc-bin 2.17-6 (using .../libc-bin_2.17-7_amd64.deb) ... Unpacking replacement libc-bin ... Setting up libc-bin (2.17-7) ... (Reading database ... 6639 files and directories currently installed.) Preparing to replace libc6:amd64 2.17-6 (using .../libc6_2.17-7_amd64.deb) ... Unpacking replacement libc6:amd64 ... Setting up libc6:amd64 (2.17-7) ... Processing triggers for libc-bin ... (Reading database ... 6639 files and directories currently installed.) Preparing to replace libapt-pkg4.12:amd64 0.9.8.2 (using .../libapt-pkg4.12_0.9.9_amd64.deb) ... Unpacking replacement libapt-pkg4.12:amd64 ... Setting up libapt-pkg4.12:amd64 (0.9.9) ... Processing triggers for libc-bin ... (Reading database ... 6639 files and directories currently installed.) Preparing to replace apt 0.9.8.2 (using .../archives/apt_0.9.9_amd64.deb) ... Unpacking replacement apt ... Setting up apt (0.9.9) ... gpg: key B98321F9: "Squeeze Stable Release Key <debian-rele...@lists.debian.org>" not changed gpg: key 473041FA: "Debian Archive Automatic Signing Key (6.0/squeeze) <ftpmas...@debian.org>" not changed gpg: key 65FFB764: "Wheezy Stable Release Key <debian-rele...@lists.debian.org>" not changed gpg: key 46925553: "Debian Archive Automatic Signing Key (7.0/wheezy) <ftpmas...@debian.org>" not changed gpg: Total number processed: 4 gpg: unchanged: 4 (Reading database ... 6639 files and directories currently installed.) Preparing to replace multiarch-support 2.17-6 (using .../multiarch-support_2.17-7_amd64.deb) ... Unpacking replacement multiarch-support ... Setting up multiarch-support (2.17-7) ... 0m8.3s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'apt-get', '-yf', 'dist-upgrade'] 0m8.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /var/tmp/tmpTYza_H/tmp/scripts/ 0m8.3s INFO: Running scripts post_setup 0m8.3s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'tmp/scripts/post_setup_experimental'] 0m8.3s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'tmp/scripts/post_setup_experimental'] 0m8.3s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'tmp/scripts/post_setup_forbid_home'] 0m8.4s DUMP: Disabling /home 0m8.4s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'tmp/scripts/post_setup_forbid_home'] 0m8.4s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.4s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.4s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'apt-get', 'clean'] 0m8.4s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'apt-get', 'clean'] 0m9.6s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'dpkg', '--get-selections', '*'] 0m9.6s DUMP: apt install base-files install base-passwd install bash install bsdutils install coreutils install dash install debconf install debconf-i18n install debian-archive-keyring install debianutils install diffutils install dpkg install e2fslibs:amd64 install e2fsprogs install eatmydata install findutils install gcc-4.7-base:amd64 install gcc-4.8-base:amd64 install gnupg install gpgv install grep install gzip install hostname install initscripts install insserv install libacl1:amd64 install libapt-pkg4.12:amd64 install libattr1:amd64 install libblkid1:amd64 install libbz2-1.0:amd64 install libc-bin install libc6:amd64 install libcap2:amd64 install libcomerr2:amd64 install libdb5.1:amd64 install libgcc1:amd64 install liblocale-gettext-perl install liblzma5:amd64 install libmount1 install libncurses5:amd64 install libpam-modules:amd64 install libpam-modules-bin install libpam-runtime install libpam0g:amd64 install libpcre3:amd64 install libreadline6:amd64 install libselinux1:amd64 install libsemanage-common install libsemanage1:amd64 install libsepol1:amd64 install libslang2:amd64 install libss2:amd64 install libstdc++6:amd64 install libtext-charwidth-perl install libtext-iconv-perl install libtext-wrapi18n-perl install libtinfo5:amd64 install libusb-0.1-4:amd64 install libustr-1.0-1:amd64 install libuuid1:amd64 install login install lsb-base install mawk install mount install multiarch-support install ncurses-base install ncurses-bin install passwd install perl-base install readline-common install sed install sensible-utils install sysv-rc install sysvinit install sysvinit-utils install tar install tzdata install util-linux install zlib1g:amd64 install 0m9.6s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'dpkg', '--get-selections', '*'] 0m9.6s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'dpkg-divert', '--list'] 0m9.6s DUMP: diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash diversion of /bin/sh to /bin/sh.distrib by dash 0m9.6s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'dpkg-divert', '--list'] 0m9.6s INFO: Starting install/purge 0m9.6s INFO: apt-cache does not know about any of the requested packages 0m9.6s INFO: Running scripts pre_test 0m9.6s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'tmp/scripts/pre_test_root_password'] 0m9.6s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m9.6s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'tmp/scripts/pre_test_root_password'] 0m9.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/var/tmp/tmpTYza_H'] 0m10.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/var/tmp/tmpTYza_H'] 0m11.0s DEBUG: No broken symlinks as far as we can find. 0m11.0s INFO: Running scripts pre_install 0m11.0s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'tmp/scripts/pre_install_database-server'] 0m11.0s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'tmp/scripts/pre_install_database-server'] 0m11.0s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'tmp/scripts/pre_install_exceptions'] 0m11.0s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'tmp/scripts/pre_install_exceptions'] 0m11.0s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m11.0s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m11.0s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'apt-cache', 'show', 'gromacs-dev'] 0m12.4s DUMP: Package: gromacs-dev Source: gromacs Version: 4.5.5-2 Installed-Size: 1380 Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org> 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. Description-md5: aab3304779c4ebcd0dbb20ae1eb40866 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 0m12.4s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'apt-cache', 'show', 'gromacs-dev'] 0m12.4s DEBUG: Starting command: ['dpkg-deb', '-b', '--nocheck', '/var/tmp/tmpCfaJOS/piuparts-depends-dummy'] 0m12.4s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/var/tmp/tmpCfaJOS/piuparts-depends-dummy.deb'. 0m12.4s DEBUG: Command ok: ['dpkg-deb', '-b', '--nocheck', '/var/tmp/tmpCfaJOS/piuparts-depends-dummy'] 0m12.4s DEBUG: Copying /var/tmp/tmpCfaJOS/piuparts-depends-dummy.deb to /var/tmp/tmpTYza_H/tmp 0m12.4s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m12.4s DUMP: Selecting previously unselected package piuparts-depends-dummy. (Reading database ... 6639 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 0m12.4s DEBUG: Command failed (status=1), but ignoring error: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb'] 0m12.4s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'apt-get', '-yf', 'install'] 0m14.9s 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 libfftw3-double3 libfftw3-long3 libfftw3-quad3 libfftw3-single3 libgomp1 libquadmath0 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 libfftw3-double3 libfftw3-long3 libfftw3-quad3 libfftw3-single3 libgomp1 libquadmath0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxml2 0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded. 1 not fully installed or removed. Need to get 18.0 MB of archives. After this operation, 59.0 MB of additional disk space will be used. Get:1 http://127.0.0.1/debian/ sid/main gromacs-data all 4.5.5-2 [1853 kB] Get:2 http://127.0.0.1/debian/ sid/main libgomp1 amd64 4.8.1-5 [26.8 kB] Get:3 http://127.0.0.1/debian/ sid/main libfftw3-double3 amd64 3.3.3-5 [666 kB] Get:4 http://127.0.0.1/debian/ sid/main libfftw3-single3 amd64 3.3.3-5 [699 kB] Get:5 http://127.0.0.1/debian/ sid/main libfftw3-3 amd64 3.3.3-5 [17.5 kB] Get:6 http://127.0.0.1/debian/ sid/main libxau6 amd64 1:1.0.8-1 [20.7 kB] Get:7 http://127.0.0.1/debian/ sid/main libxdmcp6 amd64 1:1.1.1-1 [26.3 kB] Get:8 http://127.0.0.1/debian/ sid/main libxcb1 amd64 1.9.1-3 [50.3 kB] Get:9 http://127.0.0.1/debian/ sid/main libx11-data all 2:1.6.0-1 [191 kB] Get:10 http://127.0.0.1/debian/ sid/main libx11-6 amd64 2:1.6.0-1 [919 kB] Get:11 http://127.0.0.1/debian/ sid/main libxml2 amd64 2.9.1+dfsg1-2 [911 kB] Get:12 http://127.0.0.1/debian/ sid/main gromacs amd64 4.5.5-2 [9587 kB] Get:13 http://127.0.0.1/debian/ sid/main libfftw3-long3 amd64 3.3.3-5 [304 kB] Get:14 http://127.0.0.1/debian/ sid/main libquadmath0 amd64 4.8.1-5 [138 kB] Get:15 http://127.0.0.1/debian/ sid/main libfftw3-quad3 amd64 3.3.3-5 [541 kB] Get:16 http://127.0.0.1/debian/ sid/main libfftw3-bin amd64 3.3.3-5 [48.8 kB] Get:17 http://127.0.0.1/debian/ sid/main libfftw3-dev amd64 3.3.3-5 [1987 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 18.0 MB in 0s (27.0 MB/s) Selecting previously unselected package gromacs-data. (Reading database ... 6639 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_4.8.1-5_amd64.deb) ... Selecting previously unselected package libfftw3-double3:amd64. Unpacking libfftw3-double3:amd64 (from .../libfftw3-double3_3.3.3-5_amd64.deb) ... Selecting previously unselected package libfftw3-single3:amd64. Unpacking libfftw3-single3:amd64 (from .../libfftw3-single3_3.3.3-5_amd64.deb) ... Selecting previously unselected package libfftw3-3:amd64. Unpacking libfftw3-3:amd64 (from .../libfftw3-3_3.3.3-5_amd64.deb) ... Selecting previously unselected package libxau6:amd64. Unpacking libxau6:amd64 (from .../libxau6_1%3a1.0.8-1_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_1.9.1-3_amd64.deb) ... Selecting previously unselected package libx11-data. Unpacking libx11-data (from .../libx11-data_2%3a1.6.0-1_all.deb) ... Selecting previously unselected package libx11-6:amd64. Unpacking libx11-6:amd64 (from .../libx11-6_2%3a1.6.0-1_amd64.deb) ... Selecting previously unselected package libxml2:amd64. Unpacking libxml2:amd64 (from .../libxml2_2.9.1+dfsg1-2_amd64.deb) ... Selecting previously unselected package gromacs. Unpacking gromacs (from .../gromacs_4.5.5-2_amd64.deb) ... Selecting previously unselected package libfftw3-long3:amd64. Unpacking libfftw3-long3:amd64 (from .../libfftw3-long3_3.3.3-5_amd64.deb) ... Selecting previously unselected package libquadmath0:amd64. Unpacking libquadmath0:amd64 (from .../libquadmath0_4.8.1-5_amd64.deb) ... Selecting previously unselected package libfftw3-quad3:amd64. Unpacking libfftw3-quad3:amd64 (from .../libfftw3-quad3_3.3.3-5_amd64.deb) ... Selecting previously unselected package libfftw3-bin. Unpacking libfftw3-bin (from .../libfftw3-bin_3.3.3-5_amd64.deb) ... Selecting previously unselected package libfftw3-dev:amd64. Unpacking libfftw3-dev:amd64 (from .../libfftw3-dev_3.3.3-5_amd64.deb) ... Setting up gromacs-data (4.5.5-2) ... Setting up libgomp1:amd64 (4.8.1-5) ... Setting up libfftw3-double3:amd64 (3.3.3-5) ... Setting up libfftw3-single3:amd64 (3.3.3-5) ... Setting up libfftw3-3:amd64 (3.3.3-5) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up libxdmcp6:amd64 (1:1.1.1-1) ... Setting up libxcb1:amd64 (1.9.1-3) ... Setting up libx11-data (2:1.6.0-1) ... Setting up libx11-6:amd64 (2:1.6.0-1) ... Setting up libxml2:amd64 (2.9.1+dfsg1-2) ... Setting up gromacs (4.5.5-2) ... Setting up libfftw3-long3:amd64 (3.3.3-5) ... Setting up libquadmath0:amd64 (4.8.1-5) ... Setting up libfftw3-quad3:amd64 (3.3.3-5) ... Setting up libfftw3-bin (3.3.3-5) ... Setting up libfftw3-dev:amd64 (3.3.3-5) ... Setting up piuparts-depends-dummy (0.invalid.0) ... Processing triggers for libc-bin ... 0m14.9s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'apt-get', '-yf', 'install'] 0m14.9s INFO: Installation of ['tmp/piuparts-depends-dummy.deb'] ok 0m14.9s DEBUG: Removing /var/tmp/tmpTYza_H/tmp/piuparts-depends-dummy.deb 0m14.9s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m14.9s DUMP: (Reading database ... 8168 files and directories currently installed.) Removing piuparts-depends-dummy ... 0m14.9s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m14.9s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'apt-get', 'clean'] 0m14.9s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'apt-get', 'clean'] 0m16.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/var/tmp/tmpTYza_H'] 0m16.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/var/tmp/tmpTYza_H'] 0m17.7s DEBUG: No broken symlinks as far as we can find. 0m17.7s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'apt-cache', 'policy'] 0m18.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://127.0.0.1/debian/ sid/non-free Translation-en 500 http://127.0.0.1/debian/ sid/main Translation-en 500 http://127.0.0.1/debian/ sid/contrib Translation-en 500 http://127.0.0.1/debian/ sid/non-free amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=non-free origin 127.0.0.1 500 http://127.0.0.1/debian/ sid/contrib amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=contrib origin 127.0.0.1 500 http://127.0.0.1/debian/ sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main origin 127.0.0.1 Pinned packages: 0m18.9s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'apt-cache', 'policy'] 0m18.9s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'apt-cache', 'policy', 'gromacs-dev'] 0m18.9s DUMP: gromacs-dev: Installed: (none) Candidate: 4.5.5-2 Version table: 4.5.5-2 0 500 http://127.0.0.1/debian/ sid/main amd64 Packages 0m18.9s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'apt-cache', 'policy', 'gromacs-dev'] 0m18.9s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'apt-get', '-y', 'install', 'gromacs-dev=4.5.5-2'] 0m19.5s 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://127.0.0.1/debian/ sid/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 (6541 kB/s) Selecting previously unselected package gromacs-dev. (Reading database ... 8168 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) ... 0m19.5s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'apt-get', '-y', 'install', 'gromacs-dev=4.5.5-2'] 0m19.5s INFO: Running scripts post_install 0m19.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/var/tmp/tmpTYza_H'] 0m20.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/var/tmp/tmpTYza_H'] 0m21.1s ERROR: FAIL: 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 0m21.5s DEBUG: Starting command: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'umount', '/proc'] 0m21.5s DEBUG: Command ok: ['chroot', '/var/tmp/tmpTYza_H', 'eatmydata', 'umount', '/proc'] 0m21.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/var/tmp/tmpTYza_H'] 0m21.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/var/tmp/tmpTYza_H'] 0m21.6s DEBUG: Removed directory tree at /var/tmp/tmpTYza_H 0m21.6s ERROR: piuparts run ends. ret=1 End: 2013-07-05 21:44:36 EST -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of "unsubscribe". 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