[Debian-med-packaging] Bug#758648: mapsembler2 and discosnp: error when trying to install together

[Ralf Treinen]

Package: discosnp,mapsembler2
Version: discosnp/1.2.3-1
Version: mapsembler2/2.2.1+dfsg-1
Severity: serious
User: treinen at debian.org
Usertags: edos-file-overwrite

Date: 2014-08-19
Architecture: amd64
Distribution: sid

Hi,

automatic installation tests of packages that share a file and at the
same time do not conflict by their package dependency relationships has
detected the following problem:


Selecting previously unselected package gcc-4.9-base:amd64.
(Reading database ... 10861 files and directories currently installed.)
Preparing to unpack .../gcc-4.9-base_4.9.1-7_amd64.deb ...
Unpacking gcc-4.9-base:amd64 (4.9.1-7) ...
Setting up gcc-4.9-base:amd64 (4.9.1-7) ...
(Reading database ... 10868 files and directories currently installed.)
Preparing to unpack .../libstdc++6_4.9.1-7_amd64.deb ...
Unpacking libstdc++6:amd64 (4.9.1-7) over (4.8.2-19) ...
Setting up libstdc++6:amd64 (4.9.1-7) ...
Processing triggers for libc-bin (2.19-9) ...
Selecting previously unselected package libdb5.3:amd64.
(Reading database ... 10881 files and directories currently installed.)
Preparing to unpack .../libdb5.3_5.3.28-5_amd64.deb ...
Unpacking libdb5.3:amd64 (5.3.28-5) ...
Selecting previously unselected package libexpat1:amd64.
Preparing to unpack .../libexpat1_2.1.0-6_amd64.deb ...
Unpacking libexpat1:amd64 (2.1.0-6) ...
Selecting previously unselected package libffi6:amd64.
Preparing to unpack .../libffi6_3.1-2_amd64.deb ...
Unpacking libffi6:amd64 (3.1-2) ...
Selecting previously unselected package libquadmath0:amd64.
Preparing to unpack .../libquadmath0_4.9.1-7_amd64.deb ...
Unpacking libquadmath0:amd64 (4.9.1-7) ...
Selecting previously unselected package libgfortran3:amd64.
Preparing to unpack .../libgfortran3_4.9.1-7_amd64.deb ...
Unpacking libgfortran3:amd64 (4.9.1-7) ...
Selecting previously unselected package libhdf5-7:amd64.
Preparing to unpack .../libhdf5-7_1.8.12+docs-1.1+b1_amd64.deb ...
Unpacking libhdf5-7:amd64 (1.8.12+docs-1.1+b1) ...
Selecting previously unselected package libpython2.7-minimal:amd64.
Preparing to unpack .../libpython2.7-minimal_2.7.8-5_amd64.deb ...
Unpacking libpython2.7-minimal:amd64 (2.7.8-5) ...
Selecting previously unselected package python2.7-minimal.
Preparing to unpack .../python2.7-minimal_2.7.8-5_amd64.deb ...
Unpacking python2.7-minimal (2.7.8-5) ...
Selecting previously unselected package bc.
Preparing to unpack .../bc_1.06.95-9_amd64.deb ...
Unpacking bc (1.06.95-9) ...
Selecting previously unselected package mime-support.
Preparing to unpack .../mime-support_3.56_all.deb ...
Unpacking mime-support (3.56) ...
Selecting previously unselected package libpython2.7-stdlib:amd64.
Preparing to unpack .../libpython2.7-stdlib_2.7.8-5_amd64.deb ...
Unpacking libpython2.7-stdlib:amd64 (2.7.8-5) ...
Selecting previously unselected package python2.7.
Preparing to unpack .../python2.7_2.7.8-5_amd64.deb ...
Unpacking python2.7 (2.7.8-5) ...
Selecting previously unselected package python-minimal.
Preparing to unpack .../python-minimal_2.7.8-1_amd64.deb ...
Unpacking python-minimal (2.7.8-1) ...
Selecting previously unselected package libpython-stdlib:amd64.
Preparing to unpack .../libpython-stdlib_2.7.8-1_amd64.deb ...
Unpacking libpython-stdlib:amd64 (2.7.8-1) ...
Selecting previously unselected package python.
Preparing to unpack .../python_2.7.8-1_amd64.deb ...
Unpacking python (2.7.8-1) ...
Selecting previously unselected package discosnp.
Preparing to unpack .../discosnp_1.2.3-1_amd64.deb ...
Unpacking discosnp (1.2.3-1) ...
Selecting previously unselected package mapsembler2.
Preparing to unpack .../mapsembler2_2.2.1+dfsg-1_amd64.deb ...
Unpacking mapsembler2 (2.2.1+dfsg-1) ...
dpkg: error processing archive /var/cache/apt/archives/mapsembler2_2.2.1+dfsg-1_amd64.deb (--unpack):
 trying to overwrite '/usr/bin/kissreads', which is also in package discosnp 1.2.3-1
dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)
Processing triggers for man-db (2.6.7.1-1) ...
Processing triggers for install-info (5.2.0.dfsg.1-4) ...
Errors were encountered while processing:
 /var/cache/apt/archives/mapsembler2_2.2.1+dfsg-1_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)


This is a serious bug as it makes installation fail, and violates
sections 7.6.1 and 10.1 of the policy. An optimal solution would
consist in only one of the packages installing that file, and renaming
or removing the file in the other package. Depending on the
circumstances you might also consider Replace relations or file
diversions. If the conflicting situation cannot be resolved then, as a
last resort, the two packages have to declare a mutual
Conflict. Please take into account that Replaces, Conflicts and
diversions should only be used when packages provide different
implementations for the same functionality.

Here is a list of files that are known to be shared by both packages
(according to the Contents file for sid/amd64, which may be
slightly out of sync):

  /usr/bin/kissreads
  /usr/share/man/man1/kissreads.1.gz

This bug has been filed against both packages. If you, the maintainers of
the two packages in question, have agreed on which of the packages will
resolve the problem please reassign the bug to that package. You may then
also register in the BTS that the other package is affected by the bug.

-Ralf.

PS: for more information about the detection of file overwrite errors
of this kind see http://edos.debian.net/file-overwrites/.