Package: wnpp
Severity: wishlist
Owner: Charles Plessy ple...@debian.org
Package name: samtools
Version : 0.1.5c-1
Upstream Author : Heng Li, Bob Handsaker, Jue Ruan, Colin Hercus.
URL : http://samtools.sourceforge.net/
License : MIT and NetBSD
diffs.
I have moved the patches from debian/patches to debian/patch, which circumvents
the problem, since there is no will to compromise on either side.
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manintainers. Something with a motivation, a plan, some facts and some
volunteers to get things done.
I have reassigned the bug of my package to dpkg-dev. It is holiday season, so
let's wait for a while and see the answer of the dpkg developers.
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Debian Med packaging
like to provide registration and
bibliographic information) are mostly stored in a Svn, that may not be a
blocker for making a poof of principle…
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{^(\./)?[^/]+/}{$destdir/}) {
$fn2 = $_;
Why not just applying the patches and catch errors if there are, instead of
writing a new patch parser from scratch just to check that it looks like being
in the unified format?
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http
it on the wiki page?
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that is liberal in what it
accepts. (Hence the proposition to accept upstream ‘zip’ archives).
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, that I
think goes in the wrong direction.
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Changed-By: Charles Plessy ple...@debian.org
Description:
embassy-domainatrix - Extra EMBOSS commands to handle domain classification
file
Changes:
embassy-domainatrix (0.1.0+20090715-1) unstable; urgency=low
.
* New upstream release in which the version number
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
libbio-primerdesigner-perl - Perl module to design PCR primers using primer3
and epcr
Changes:
libbio-primerdesigner-perl (0.07-1) unstable; urgency=low
.
* New upstream release (no changes on Linux systems
)’, it is not possible. Do you think it would be possible to
change this behavior or at least to disable the auto-patching facilities? It
would be of course easy to convert the patch, but I would really prefer to stay
as identical to upstream's materials as possible.
Have a nice sunday,
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places like the Ultimate
Debian Database and to keep the information up-to-date, which will be at best
limited to the packages relevant to our projects.
I am therefore seeking comments and insights to better manage our packages
metadata.
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Debian Med packaging team
Le Sun, Aug 02, 2009 at 11:03:11AM +0200, Raphael Hertzog a écrit :
On Sun, 02 Aug 2009, Charles Plessy wrote:
About zip support:
But actually, among the programs that are not distributed upstream in a
tar.gz
format, we in the Debian Med team have as many zip cases as bzip2. Do you
: unstable
Urgency: low
Maintainer: Debian-Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
emboss - the european molecular biology open software suite
emboss-data - data files for the EMBOSS package
emboss-doc
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
libace-perl - Object-Oriented Access to ACEDB Databases
Closes: 535390
Changes:
libace-perl (1.92-2) unstable; urgency=low
.
* debian/rules
- Replaced an echo command by the Perl equivalent in debian/rules
(Closes
is delegated to the menu system itself, be it in Debian or
FreeDesktop standard. I think that what you propose is more their task than the
one of the packaging system.
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), this could be a real plus to become the OS of
choice on that type of machines.
This said, it only represents a small fraction of our user base…
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file for the seaview package:
Source: seaview
Section: non-free/science
Priority: optional
Maintainer: Debian-Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
DM-Upload-Allowed: yes
Uploaders: Charles Plessy ple...@debian.org
Build-Depends: debhelper ( = 7 ), libfltk1.1-dev
popular, a Lintian check will be trivial to
write, to ensure that contrib and non-free packages include the statement
recommended by the Policy.
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Lenny?
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Changed-By: Charles Plessy ple...@debian.org
Description:
velvet - Nucleic acid sequence assembler for very short reads
velvet-example - Example data for the Velvet sequence assembler
Changes:
velvet (0.7.47-1) unstable; urgency=low
.
* New upstream release correcting
RFC-2822 parser can not parse
Debian control files nor DEP 3 patch headers, as it will not preserve CRLF
characters.
What I am simply asking, is that if DEP 3 is not RFC-2822 compliant, it is not
written that it is RFC-2822 compliant.
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Le Fri, Jul 24, 2009 at 01:14:16AM +0200, Raphael Hertzog a écrit :
* Charles Plessy wanted to specify more precisely the format instead
of saying RFC-2822 compliant fields. The discussion went nowhere
and nobody else expressed support for such a change.
Hi Raphaël,
my main concern
expose a flaw: think about
changes in names of binary packages that trigger copyright checks by the FTP
team.
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contains 265 packages, some of them waiting for one month
or more. I disagree with their decision to self-appoint themselves with a new
duty while they are already lacking time for the current one they volunteered
for.
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Changed-By: Charles Plessy ple...@debian.org
Description:
embassy-domalign - Extra EMBOSS commands for protein domain alignment
Changes:
embassy-domalign (0.1.0+20090715-1) unstable; urgency=low
.
* New upstream release in which the version number was unchanged
rejection of packages with errors not justified by overrides is of
course a good idea, but can we get to a compromise where the maintainer is free
to take the responsibility to override errors?
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Description:
maq- maps short fixed-length polymorphic DNA sequence reads to referen
Changes:
maq (0.7.1-3) unstable; urgency=low
.
* Distribute scripts that are not installed by upstream’s
makefile in /usr/share/maq (debian/install
? That is the core
of my suggestion: maye the rejection emails publically available in a central
place so that other developers can learn form them.
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Package: wnpp
Severity: wishlist
Owner: Charles Plessy ple...@debian.org
Dear all,
15th of July is the traditional EMBOSS release (EMBOSS is a set of command line
tools for molecular biologists). Two satellite packages are already present in
Debian and here is the ITP for a third. Package
: unstable
Urgency: low
Maintainer: Debian-Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
emboss - the european molecular biology open software suite
emboss-data - data files for the EMBOSS package
emboss-doc
?
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-By: Charles Plessy ple...@debian.org
Description:
plink - whole-genome association analysis toolset
Changes:
plink (1.06-4) unstable; urgency=low
.
* debian/rules:
- Add support for DEB_BUILD_OPTIONS (Policy § 4.9.1).
- Set FORCE_DYNAMIC=1 instead of patching the Makefile
Changed-By: Charles Plessy ple...@debian.org
Description:
phyml - Phylogenetic estimation using Maximum Likelihood
Closes: 536967
Changes:
phyml (1:200900706-2) unstable; urgency=low
.
* Disable parallel building, that was incorrectly supported and
induced build failures by race
Changed-By: Charles Plessy ple...@debian.org
Description:
seaview- Multiplatform interface for sequence alignment and phylogeny
Changes:
seaview (1:4.1-1) unstable; urgency=low
.
* New upstream version adding nucleotide ambiguity symbols in consensus
DNA sequences.
* debian/control
Changed-By: Charles Plessy ple...@debian.org
Description:
phyml - Phylogenetic estimation using Maximum Likelihood
Changes:
phyml (1:200900706-1) unstable; urgency=low
.
* New upstream release.
* Suppressed unneeded Lintian overrides, and use ‘dh clean’ in debian/rules.
* Checked
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
velvet - Nucleic acid sequence assembler for very short reads
velvet-example - Example data for the Velvet sequence assembler
Changes:
velvet (0.7.44-1) unstable; urgency=low
.
* New upstream release.
* Added
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
libbio-graphics-perl - Generate GD images of Bio::Seq objects
Changes:
libbio-graphics-perl (1.97-1) unstable; urgency=low
.
* New upstream release adding a “feature_limit” option.
* debian/control: incremented
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
r-cran-haplo.stats - GNU R package for haplotype analysis
Changes:
r-cran-haplo.stats (1.4.3-1) unstable; urgency=low
.
* New upstream release.
* debian/control:
- Added myself to the Uploaders
, for the bug 1215086, only the second of the below URLs work:
https://sourceforge.net/tracker/?func=detailaid=1215086
https://sourceforge.net/tracker/?func=detailaid=1215086group_id=133157atid=726404
Have a nice day,
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Debian Med packaging team,
http://www.debian.org/devel/debian-med
.
Unfortunately, it seems that with quilt, it is better ot use $(QUILT_STAMPFN)
in order to avoid a target to become phony. I do not know for other systems.
I just updated http://wiki.debian.org/debian/patches to mention this fact.
Have a nice day,
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Tsurumi, Kanagawa, Japan
Changed-By: Charles Plessy ple...@debian.org
Description:
ncbi-epcr - Tool to test a DNA sequence for the presence of sequence tagged s
Closes: 504849
Changes:
epcr (2.3.12-1) unstable; urgency=low
.
* New upstream release buildable with GCC 4.4 (Closes: #504849)
* Version number updated
Le Tue, Jun 30, 2009 at 08:49:21AM +0200, Raphael Hertzog a écrit :
On Tue, 30 Jun 2009, Charles Plessy wrote:
* “The meta-information would be stored in a set of RFC-2822 compliant
fields.”
RFC-2822 distinguishes between “unstructured” and “structured” fields. The
‘Description’ field
must be escaped by following it by a space. The line that contains that space
is called a continuation line.
- Lines that are not continuation lines and do not start a new field are plain
comments.
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, and most of the time this information is available in the VCS
where the source package is stored.
Have a nice day,
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Changed-By: Charles Plessy ple...@debian.org
Description:
r-cran-qvalue - GNU R package for Q-value estimation for FDR control
Changes:
r-cran-qvalue (1.18.0-1) unstable; urgency=low
.
* New upstream release: changes in documentation and bug corrected
for TCL/Tk support
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
velvet - Nucleic acid sequence assembler for very short reads
velvet-example - Example data for the Velvet sequence assembler
Changes:
velvet (0.7.37-1) unstable; urgency=low
.
* New upstream release.
- Small
. This whole discussion confuses me and I do not
understand if Debian as a project accepts signatures that are not based on a
passport or an ID card. For instance, I have used drivers licenses or social
security cards as well, is that acceptable ?
Have a nice day,
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...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
ssake - genomics application for assembling millions of very short DNA se
ssake-examples - example data for SSAKE, a genomic assembler of short reads
Changes:
ssake (3.4-1) unstable; urgency=low
.
* New upstream release
Le Wed, Jun 17, 2009 at 12:40:01PM +0200, Raphael Hertzog a écrit :
On Tue, 16 Jun 2009, Charles Plessy wrote:
The dh_make template for debian/copyright induces many developers to put
their
packaging work under the GPL, and I have already seen packages whose
license is
otherwise BSD
Changed-By: Charles Plessy ple...@debian.org
Description:
last-align - genome-scale comparison of biological sequences
Changes:
last-align (58-1) unstable; urgency=low
.
* New upstream release able to use sequence quality scores.
Checksums-Sha1:
5871fbf2e3bc5a2ccac43f059f047507f278dad2
Changed-By: Charles Plessy ple...@debian.org
Description:
ncbi-epcr - Tool to test a DNA sequence for the presence of sequence tagged s
Changes:
epcr (2.3.11-1) unstable; urgency=low
.
* New upstream release. When parsing commandline if -d was used before -w or
-f default size was reset
,
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Changed-By: Charles Plessy ple...@debian.org
Description:
wise - comparison of biopolymers, commonly DNA and protein sequences
wise-doc - documentation for the wise package
Closes: 523715
Changes:
wise (2.4.1-7) unstable; urgency=low
.
[ Steffen Moeller ]
* Now builds
Nowhere does it make any mention of source filenames.
Now please drop that shit from your proposal, and maybe we can discuss
it sanely without counting commas.
I am all for making all the fields optional.
This is a major change from Sam‘s original proposal. The reason it has not been
done
Changed-By: Charles Plessy ple...@debian.org
Description:
seaview- Multiplatform interface for sequence alignment and phylogeny
Changes:
seaview (1:4.0-1) unstable; urgency=low
.
* New upstream version
- Computes and draws parsimony, distance and PhyML phylogenetic trees.
- This new
, and don't shoot the messenger’.
Have a nice week-end,
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I limit myself to one message per day in this thread and encourage everybody
else to do so.
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echo
echo --
read
which will fail if using dash as /bin/sh.
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like to suggest to everybody
to try to reduce the number of contributions they send per day. Most of the
answers
we think of will be done by someone else if we wait a few hours, and I think it
is
best if this discussion involves more persons.
Have a nice day,
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Tsurumi
challenging, unless of course we factorize or discard some copyright statements
as described above.
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, but my
feeling is to not enter into such consideration in the specification itself.
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, but I have no clue of what the problem
is, and how important it is. I have read ‘https://wiki.ubuntu.com/DashAsBinSh’,
but found nothing there. Can somebody send me a pointer to some documentation?
Have a nice day,
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http://www.debian.org/devel/debian
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
velvet - Nucleic acid sequence assembler for very short reads
velvet-example - Example data for the Velvet sequence assembler
Changes:
velvet (0.7.34-1) unstable; urgency=low
.
* New upstream release correcting
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
libbio-graphics-perl - Generate GD images of Bio::Seq objects
Changes:
libbio-graphics-perl (1.96-1) unstable; urgency=low
.
* New upstream release improving DAS 1.5 support.
* Documented in debian/copyright files
in WildcardQuery”.
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Changed-By: Charles Plessy ple...@debian.org
Description:
bibus - bibliographic database
bibus-doc-en - Bibus bibliographic database documentation
Changes:
bibus (1.4.3.2-3) unstable; urgency=low
.
[ Jan Beyer ]
* debian/control:
- bibus recommends no longer
Changed-By: Charles Plessy ple...@debian.org
Description:
libmqdb-perl - MappedQueryDB toolkit for federated databases
Changes:
libmqdb-perl (0.954-1) unstable; urgency=low
.
* New upstream release.
Checksums-Sha1:
b59a96dfe514e135b6e80fa76984901858788327 1335 libmqdb-perl_0.954-1.dsc
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
libbio-graphics-perl - Generate GD images of Bio::Seq objects
Changes:
libbio-graphics-perl (1.95-1) unstable; urgency=low
.
* New upstream release, improving SVG support.
Checksums-Sha1
Package: wnpp
Severity: wishlist
Owner: Charles Plessy ple...@debian.org
Package name: staden-io-lib
Version : 1.11.6.1
Programming Lang: C
Description : The Staden io_lib and its associated programs (three binary
packages).
debian/control
--
Source: staden
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
r-cran-epibasix - GNU R Elementary Epidemiological Functions
Changes:
r-cran-epibasix (1.1-1) unstable; urgency=low
.
* New upstream release.
* debian/control:
- Added myself as Uploader.
- Incremented
Changed-By: Charles Plessy ple...@debian.org
Description:
last-align - genome-scale comparison of biological sequences
Changes:
last-align (52-1) unstable; urgency=low
.
* New upstream releases (52 and 51).
- Added maf2html.py: converts MAF-format alignments to coloured HTML
format
: unstable
Urgency: low
Maintainer: Debian-Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
emboss - the european molecular biology open software suite
emboss-data - data files for the EMBOSS package
emboss-doc
Changed-By: Charles Plessy ple...@debian.org
Description:
phyml - Phylogenetic estimation using Maximum Likelihood
Changes:
phyml (1:20090501-1) unstable; urgency=low
.
* New upstream release clarifying the license of the documentation and
switching to a versionning system that can
Changed-By: Charles Plessy ple...@debian.org
Description:
libgd-svg-perl - Seamlessly enable SVG output from scripts written using GD
Changes:
libgd-svg-perl (0.33-1) unstable; urgency=low
.
* New upstream version.
- Can now embed pixmap information inside an SVG (Lincoln Stein
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
libbio-graphics-perl - Generate GD images of Bio::Seq objects
Changes:
libbio-graphics-perl (1.94-1) unstable; urgency=low
.
* New upstream release, adding a “fast” and fixing error in xyplot.
Checksums-Sha1
Changed-By: Charles Plessy ple...@debian.org
Description:
phyml - Phylogenetic estimation using Maximum Likelihood
Closes: 517165
Changes:
phyml (30042009-1) unstable; urgency=low
.
* Initial release (Closes: #517165)
Checksums-Sha1:
7d11108a1e25e07e2681b558fefdd2191e16d49e 1284
as well as the Closes: #n.
This is useful for the security team to track vulnerabilities. If an upload is
made to fix the bug before the advisory ID is known, it is encouraged to modify
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Le Mon, Apr 27, 2009 at 07:36:27PM -0700, Steve Langasek a écrit :
On Sun, Apr 26, 2009 at 08:41:14PM +0900, Charles Plessy wrote:
Le Sat, Apr 25, 2009 at 01:42:04PM +, Joerg Jaspert a écrit :
Hi Maintainer,
rejected, i think we are missing the source for the pdf in doc/.
Almost
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
sigma-align - Simple greedy multiple alignment of non-coding DNA sequences
Changes:
sigma-align (1.1.3-1) unstable; urgency=low
.
* New upstream release.
* Converted the packaging to CDBS.
- debian/rules is much shorter
information for other
developers.
Bonus question: after we shift to the version 3.0 (quilt) of the source
packages, will it be acceptable or not that a file from one tarball has its
source in another one?
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http://www.debian.org/devel/debian-med
Tsurumi
Changed-By: Charles Plessy ple...@debian.org
Description:
libmqdb-perl - MappedQueryDB toolkit for federated databases
Closes: 524998
Changes:
libmqdb-perl (0.953-1) unstable; urgency=low
.
* Initial Release (Closes: #524998).
Checksums-Sha1:
3c012f882b3aa7d55de0352bf9e202050898af95 1335 libmqdb
maintainers start to distribute mktemp in their binary packages).
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a whishlist patch to the BTS. We will
then see if these patches are welcome, and maybe will start a trend. For the
moment, I have the feeling that we are fighting resistance from developpers
whose packages are not an issue for us anyway.
Have a nice day,
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Charles Plessy
Debian Med packaging
Package: wnpp
Severity: wishlist
Owner: Charles Plessy ple...@debian.org
Dear all,
I have packaged a new CPAN module, MappedQueryDB, that will be used by another
software that I intend to package, EdgeExpressDB (more info in its ITP, that I
will post soon).
I will maintain the source package
Le Tue, Apr 21, 2009 at 04:07:44PM +0200, Cyril Brulebois a écrit :
Charles Plessy ple...@debian.org (21/04/2009):
Source: libmqdb-perl
Section: perl
Priority: optional
Build-Depends: debhelper (= 7)
Build-Depends-Indep: libdbd-mysql-perl (= 3.0005),
libdbd-sqlite3-perl (= 1.14
Le Tue, Apr 21, 2009 at 06:22:39PM +0200, Cyril Brulebois a écrit :
Charles Plessy ple...@debian.org (21/04/2009):
libdbd-sqlite3-perl (= 1.14), libdbi-perl (= 1.51), perl (=
5.6.0-12)
^^
WTH?
aqwa
Le Tue, Apr 21, 2009 at 03:27:51PM +0200, Adeodato Simó a écrit :
+ Charles Plessy (Tue, 21 Apr 2009 20:49:27 +0900):
Files: debian/*
Copyright: 2009, Charles Plessy ple...@debian.org
License: PD
Please treat this packaging work as if it were in public domain.
Is such a wording
: unstable
Urgency: low
Maintainer: Debian-Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
emboss - the european molecular biology open software suite
emboss-data - data files for the EMBOSS package
emboss-doc
Changed-By: Charles Plessy ple...@debian.org
Description:
last-align - genome-scale comparison of biological sequences
Changes:
last-align (50-1) unstable; urgency=low
.
* New upstream release (minor changes).
Checksums-Sha1:
263fe840267ed7ff88969ed88cf275192ea612c1 1262 last-align_50-1.dsc
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
embassy-domalign - Extra EMBOSS commands for protein domain alignment
Changes:
embassy-domalign (0.1.0+20080715-1) unstable; urgency=low
.
* New upstream release in which the version number was unchanged
,
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
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Changed-By: Charles Plessy ple...@debian.org
Description:
last-align - genome-scale comparison of biological sequences
Changes:
last-align (48-1) unstable; urgency=low
.
* New upstream release.
- maf-join.py: joins pairwise alignments into multiple alignments.
- Changed lastal
: unstable
Urgency: low
Maintainer: Debian-Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
emboss - the european molecular biology open software suite
emboss-data - data files for the EMBOSS package
emboss-doc
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
libbio-graphics-perl - Generate GD images of Bio::Seq objects
Changes:
libbio-graphics-perl (1.93-1) unstable; urgency=low
.
* New upstream release (corrections and improved documentation).
* debian/copyright made
upload,
won't the BTS expect a NMU acknowledgement anyway?
Have a nice day,
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
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Le Mon, Apr 06, 2009 at 12:52:22PM +0200, Lucas Nussbaum a écrit :
On 06/04/09 at 19:48 +0900, Charles Plessy wrote:
Le Mon, Apr 06, 2009 at 12:13:45PM +0200, Raphael Hertzog a écrit :
On Mon, 06 Apr 2009, Charles Plessy wrote:
I think that it is a good concept, but the linian warning
versioning or add
themselves to Uploaders and hence imply that they're taking ongoing
responsibility for the package.
Hi all,
so in the end, can we use the “ * QA upload.” special first line for
non-uploader uploads without breaking the QA infrastructure?
Have a nice day,
--
Charles Plessy
Debian
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