[Debichem-devel] Bug#715068: Broken library symlink detected in gromacs-dev
David Steele
dsteele at gmail.com
Sat Jul 6 05:01:14 UTC 2013
Package: gromacs-dev
Version: 4.5.5-2
Severity: serious
User: debian-qa at 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-devel at 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-release at lists.debian.org>" not changed
gpg: key 473041FA: "Debian Archive Automatic Signing Key (6.0/squeeze) <ftpmaster at debian.org>" not changed
gpg: key 65FFB764: "Wheezy Stable Release Key <debian-release at lists.debian.org>" not changed
gpg: key 46925553: "Debian Archive Automatic Signing Key (7.0/wheezy) <ftpmaster at 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-devel at 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
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