Your message dated Tue, 22 May 2012 12:33:41 +0000
with message-id <[email protected]>
and subject line Bug#661519: fixed in paml 4.5-1
has caused the Debian Bug report #661519,
regarding paml: error when trying to install together with evolver
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.
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--
661519: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=661519
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: paml
Version: 4.4e-1
Affects: evolver
Severity: serious
User: [email protected]
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:
Unpacking paml (from .../archives/paml_4.4e-1_amd64.deb) ...
dpkg: error processing /var/cache/apt/archives/paml_4.4e-1_amd64.deb (--unpack):
trying to overwrite '/usr/bin/evolver', which is also in package evolver
2.30c.dfsg-3
configured to not write apport reports
dpkg-deb (subprocess): subprocess data was killed by signal (Broken pipe)
dpkg-deb: error: subprocess <decompress> returned error exit status 2
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.
This bug has been filed against the paml package only, unstead of
paml and evolver, since paml is in non-free.
-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: paml
Source-Version: 4.5-1
We believe that the bug you reported is fixed in the latest version of
paml, which is due to be installed in the Debian FTP archive:
paml-doc_4.5-1_all.deb
to non-free/p/paml/paml-doc_4.5-1_all.deb
paml_4.5-1.debian.tar.gz
to non-free/p/paml/paml_4.5-1.debian.tar.gz
paml_4.5-1.dsc
to non-free/p/paml/paml_4.5-1.dsc
paml_4.5-1_amd64.deb
to non-free/p/paml/paml_4.5-1_amd64.deb
paml_4.5.orig.tar.gz
to non-free/p/paml/paml_4.5.orig.tar.gz
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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated paml 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.8
Date: Tue, 15 May 2012 11:10:59 +0200
Source: paml
Binary: paml paml-doc
Architecture: source amd64 all
Version: 4.5-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
paml - Phylogenetic Analysis by Maximum Likelihood (PAML)
paml-doc - Documentation for PAML
Closes: 661519
Changes:
paml (4.5-1) unstable; urgency=low
.
[ Pjotr Prins ]
* Improved long description.
.
[ Andreas Tille ]
* New upstream version
* Fixed watch file
* debian/control: Standards-Version: 3.9.3 (no changes needed)
* debian/rules: remove useless dh-make template
* debian/paml.dirs: removed because unneeded
* debian/{install,links}: install all binaries to
/usr/lib/debian-med/bin and symlink to /usr/bin with the
exception of evolver which has a name space conflict. This
is renamed to /usr/bin/paml-evolver
Closes: #661519
* debian/{paml.docs,paml-doc.docs}:
- Adapted to new names
- do not duplicate the same files into both packages (paml and
paml-doc)
* debian/profile.d/paml: Set PATH to find paml executables under
their expected names
* debian/README.Debian: Document the name space conflict solution
* debian/upstream: Citation information
* debhelper 9 (control+compat)
* debian/patches/hardening.patch: Enable propagation of hardening
flags
Checksums-Sha1:
66b1b2ac747dc623a6fb21ee1668ff0f8c99593c 1414 paml_4.5-1.dsc
b2b9933c883d77a8fc1d1ef8928060d972f43c0b 3485473 paml_4.5.orig.tar.gz
62fecebf1361ccb060a005a16930eda58b80975c 4564 paml_4.5-1.debian.tar.gz
ddfc873a469aaedf712d4f0ed2b405cf5225fae4 945758 paml_4.5-1_amd64.deb
22c491a99906bb174ba6e5fba9d6c226be9373f7 1380048 paml-doc_4.5-1_all.deb
Checksums-Sha256:
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paml_4.5-1.dsc
d53a2bea4f2169ff19c52cb2eeed11cc0d8710318be5af78ee10d8ceb9e3a034 3485473
paml_4.5.orig.tar.gz
feb6fa01a327267b6c47dece7100f2e08fcfb9f7cbe1b8631ad8f0146fdff444 4564
paml_4.5-1.debian.tar.gz
7f08dd16ccdd9c0ea25db53e290074246207702ae5bb308f4c2a62c4ac15d603 945758
paml_4.5-1_amd64.deb
9f9d86bce2cb7232d7ac8197e70e6b921a6bd2ab9c40b40523edfeb749d3f7e8 1380048
paml-doc_4.5-1_all.deb
Files:
714df5723292713b7828bddd937f63df 1414 non-free/science extra paml_4.5-1.dsc
c87ddcf7e993496be30760ecd542113d 3485473 non-free/science extra
paml_4.5.orig.tar.gz
5ab5d87a6215b116a3d655160a0f5e65 4564 non-free/science extra
paml_4.5-1.debian.tar.gz
8da42763f61bd27bce18c398e5778c22 945758 non-free/science extra
paml_4.5-1_amd64.deb
f62d75fc661dbba9ebaf34b6a3cde623 1380048 non-free/doc extra
paml-doc_4.5-1_all.deb
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--- End Message ---
