[Pkg-scicomp-devel] Bug#568841: libparmetis-dev and libscotchmetis-dev: error when trying to install together

[Ralf Treinen]

Package: libscotchmetis-dev,libparmetis-dev
Version: libscotchmetis-dev/5.1.7.dfsg-1
Version: libparmetis-dev/3.1.1-1
Severity: serious
User: treinen at debian.org
Usertags: edos-file-overwrite

Date: 2010-02-07
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:


WARNING: The following packages cannot be authenticated!
  libc-dev-bin linux-libc-dev libc6-dev libgfortran3 zlib1g-dev libibverbs1
  libibverbs-dev libopenmpi1.3 openmpi-common libopenmpi-dev mpi-default-dev
  libparmetis3.1 libparmetis-dev libscotch-5.1 libscotch-dev
  libscotchmetis-dev
W: cowdancer: unsupported operation flock, read-only open and fchown/fchmod/flock are not supported: tried openning dev:inode of 2055:5408551
W: cowdancer: unsupported operation flock, read-only open and fchown/fchmod/flock are not supported: tried openning dev:inode of 2055:5407760
W: cowdancer: unsupported operation flock, read-only open and fchown/fchmod/flock are not supported: tried openning dev:inode of 2055:3588098
Authentication warning overridden.
Can not write log, openpty() failed (/dev/pts not mounted?)
Selecting previously deselected package libc-dev-bin.
(Reading database ... 12292 files and directories currently installed.)
Unpacking libc-dev-bin (from .../libc-dev-bin_2.10.2-6_amd64.deb) ...
Selecting previously deselected package linux-libc-dev.
Unpacking linux-libc-dev (from .../linux-libc-dev_2.6.32-7_amd64.deb) ...
Selecting previously deselected package libc6-dev.
Unpacking libc6-dev (from .../libc6-dev_2.10.2-6_amd64.deb) ...
Selecting previously deselected package libgfortran3.
Unpacking libgfortran3 (from .../libgfortran3_4.4.3-2_amd64.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_amd64.deb) ...
Selecting previously deselected package libibverbs1.
Unpacking libibverbs1 (from .../libibverbs1_1.1.3-2_amd64.deb) ...
Selecting previously deselected package libibverbs-dev.
Unpacking libibverbs-dev (from .../libibverbs-dev_1.1.3-2_amd64.deb) ...
Selecting previously deselected package libopenmpi1.3.
Unpacking libopenmpi1.3 (from .../libopenmpi1.3_1.3.3-4_amd64.deb) ...
Selecting previously deselected package openmpi-common.
Unpacking openmpi-common (from .../openmpi-common_1.3.3-4_all.deb) ...
Selecting previously deselected package libopenmpi-dev.
Unpacking libopenmpi-dev (from .../libopenmpi-dev_1.3.3-4_amd64.deb) ...
Selecting previously deselected package mpi-default-dev.
Unpacking mpi-default-dev (from .../mpi-default-dev_0.6_amd64.deb) ...
Selecting previously deselected package libparmetis3.1.
Unpacking libparmetis3.1 (from .../libparmetis3.1_3.1.1-1_amd64.deb) ...
Selecting previously deselected package libparmetis-dev.
Unpacking libparmetis-dev (from .../libparmetis-dev_3.1.1-1_amd64.deb) ...
Selecting previously deselected package libscotch-5.1.
Unpacking libscotch-5.1 (from .../libscotch-5.1_5.1.7.dfsg-1_amd64.deb) ...
Selecting previously deselected package libscotch-dev.
Unpacking libscotch-dev (from .../libscotch-dev_5.1.7.dfsg-1_amd64.deb) ...
Selecting previously deselected package libscotchmetis-dev.
Unpacking libscotchmetis-dev (from .../libscotchmetis-dev_5.1.7.dfsg-1_amd64.deb) ...
dpkg: error processing /var/cache/apt/archives/libscotchmetis-dev_5.1.7.dfsg-1_amd64.deb (--unpack):
 trying to overwrite '/usr/include/metis/metis.h', which is also in package libparmetis-dev 0:3.1.1-1
Processing triggers for man-db ...
W: cowdancer: unsupported operation flock, read-only open and fchown/fchmod/flock are not supported: tried openning dev:inode of 2055:5408551
W: cowdancer: unsupported operation flock, read-only open and fchown/fchmod/flock are not supported: tried openning dev:inode of 2055:5407760
W: cowdancer: unsupported operation flock, read-only open and fchown/fchmod/flock are not supported: tried openning dev:inode of 2055:3588098
Errors were encountered while processing:
 /var/cache/apt/archives/libscotchmetis-dev_5.1.7.dfsg-1_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)
cow-shell unlink .ilist: No such file or directory


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/include/metis/metis.h
  /usr/lib/libmetis.a
  /usr/lib/libmetis.so

This bug is assigned to 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.

-Ralf.

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