Your message dated Fri, 02 Mar 2012 05:32:21 +0000
with message-id <e1s3l6l-0002fb...@franck.debian.org>
and subject line Bug#661516: fixed in t-coffee 9.02.r1228-2
has caused the Debian Bug report #661516,
regarding tm-align and t-coffee: error when trying to install together
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
661516: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=661516
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: t-coffee,tm-align
Version: t-coffee/9.02.r1228-1
Version: tm-align/20111012-1
Severity: serious
User: trei...@debian.org
Usertags: edos-file-overwrite
Date: 2012-02-27
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!
libquadmath0 libgfortran3 t-coffee tm-align
Authentication warning overridden.
Can not write log, openpty() failed (/dev/pts not mounted?)
Selecting previously unselected package libquadmath0.
(Reading database ... 10557 files and directories currently installed.)
Unpacking libquadmath0 (from .../libquadmath0_4.6.2-16_amd64.deb) ...
Selecting previously unselected package libgfortran3.
Unpacking libgfortran3 (from .../libgfortran3_4.6.2-16_amd64.deb) ...
Selecting previously unselected package t-coffee.
Unpacking t-coffee (from .../t-coffee_9.02.r1228-1_amd64.deb) ...
Selecting previously unselected package tm-align.
Unpacking tm-align (from .../tm-align_20111012-1_amd64.deb) ...
dpkg: error processing /var/cache/apt/archives/tm-align_20111012-1_amd64.deb
(--unpack):
trying to overwrite '/usr/bin/TMalign', which is also in package t-coffee
9.02.r1228-1
configured to not write apport reports
Processing triggers for man-db ...
Errors were encountered while processing:
/var/cache/apt/archives/tm-align_20111012-1_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/TMalign
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/.
--- End Message ---
--- Begin Message ---
Source: t-coffee
Source-Version: 9.02.r1228-2
We believe that the bug you reported is fixed in the latest version of
t-coffee, which is due to be installed in the Debian FTP archive:
t-coffee-doc_9.02.r1228-2_all.deb
to main/t/t-coffee/t-coffee-doc_9.02.r1228-2_all.deb
t-coffee-examples_9.02.r1228-2_all.deb
to main/t/t-coffee/t-coffee-examples_9.02.r1228-2_all.deb
t-coffee_9.02.r1228-2.debian.tar.gz
to main/t/t-coffee/t-coffee_9.02.r1228-2.debian.tar.gz
t-coffee_9.02.r1228-2.dsc
to main/t/t-coffee/t-coffee_9.02.r1228-2.dsc
t-coffee_9.02.r1228-2_amd64.deb
to main/t/t-coffee/t-coffee_9.02.r1228-2_amd64.deb
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 661...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Charles Plessy <ple...@debian.org> (supplier of updated t-coffee package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Fri, 02 Mar 2012 14:04:20 +0900
Source: t-coffee
Binary: t-coffee t-coffee-examples t-coffee-doc
Architecture: source all amd64
Version: 9.02.r1228-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Charles Plessy <ple...@debian.org>
Description:
t-coffee - Multiple Sequence Alignment
t-coffee-doc - PDF and HTML accompaning documents to T-Coffee
t-coffee-examples - annotated examples for the use of T-Coffee
Closes: 661516
Changes:
t-coffee (9.02.r1228-2) unstable; urgency=low
.
* Recommend tm-align instead of distributing local copy
(debian/control, debian/t-coffee.install, Closes: #661516).
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