to
the gain for everybody.
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and the hppa porters, which like every
other group in Debian severely lack manpower.
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uploads.
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Changed-By: Charles Plessy ple...@debian.org
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
samtools (0.1.7a~dfsg-1) unstable; urgency=low
.
* New upstream
will complain. So why not ?
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of the architecture-independant packages
happens. Could we have a bit more details on the buildd(s) and arch(es)
involved, the contact points in case of breakage, etc…
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to increase their number, not to
correct their behaviour.
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the binary packages is and should stay the first (and not only) check
before doing an upload. But there are situations, discussed on this list, where
a source upload can be useful. Even without binary building before. That what
the current binNMU system is doing anyway.
Have a nice day,
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when they process the packages a few
days later (even on amd64 this month, see
https://buildd.debian.org/pkg.cgi?pkg=r-cran-spatial).
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Oh no, please, Please, PLEASE, *PLEASE* do not cross-post the discussions
between debian-vote and debian-devel. There is no point having separated lists
otherwise.
Have a nice day,
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-By: Charles Plessy ple...@debian.org
Description:
bwa- Burrows-Wheeler Aligner
Changes:
bwa (0.5.5-1) unstable; urgency=low
.
* New upstream release.
* Using Dpkg source format version ‘3.0 (quilt)’ (debian/source/format).
Checksums-Sha1:
5682ca38dead1c2b9beebbe2a535e1bfd3165e1f 1266
Le Mon, Nov 09, 2009 at 10:24:39AM +0100, Stefano Zacchiroli a écrit :
On Sun, Nov 08, 2009 at 12:09:28AM +0900, Charles Plessy wrote:
Still, having /usr/share/www as a document root does not prevent complex
packages to be fragmented between /usr/share, /usr/lib/cgi-bin/, /var/lib/,
/var
: 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
/webserver/conf.d will still be
necessary for these packages to work, there will little benefit in moving files
to /usr/share/www.
Anyway, thank you very much for your initiative. Exploring new directions is
good !
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, because on computers with a short name,
only a few keystrokes in the browser bar can call it. Switching from “foo/dc”
to “foo/vendors-apps/dc” is unfun, expecially since the ‘-’ sign is a moving
target on heterogeneous keyboard environments.
Have a nice day,
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Debian Med packaging team
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
libbio-samtools-perl - read SAM/BAM nucleotide sequence aligment database files
Changes:
libbio-samtools-perl (1.06-1) unstable; urgency=low
.
* New Upstream Version (Bio::DB::Sam modified to work with GBrowse 1
that may allow to] remove them from the archive.
Do you understand why people are getting annoyed ?
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Le Mon, Nov 02, 2009 at 08:49:40AM -0800, Russ Allbery a écrit :
I'm not seeing where he's doing any significant harm
By killing the discusssion with a flood of emails. Here are the top posters for
this month in this thread:
3 Charles Plessy (+1 with this one)
3 Michael Banck
getting around to filing bugs on policy MUST violations and others that
make the package too buggy to be in Debian
Wow, time goes so fast, it is already the season for attempting to delay the
release!
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that Stefano's proposition to implicate the QA team
in the management of which tag gets in the blacklist makes a lot of sense, as
it will help the people who will do the hard work of orphaning, MIA checking,
and bug fixing to prioritise and orgainse their efforts.
Have a nice day,
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Le Fri, Oct 30, 2009 at 09:35:58AM -0500, Manoj Srivastava a écrit :
The interface definition behind this is:
That ‘make -f debian/rules’ is not present anywhere in the Policy demonstrates
it is not the interface.
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example of how the Policy is sometimes going too
far in
chosing how developers should implement interfaces, instead of simply
specifying the interface.
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Changed-By: Charles Plessy ple...@debian.org
Description:
r-cran-bitops - GNU R package implementing bitwise operations
Changes:
bitops (1.0-4.1-1) unstable; urgency=low
.
* New upstream release.
* debian/changelog:
- New maintainer: the Debian Med packaging team.
- Added
Le Tue, Oct 27, 2009 at 04:26:58PM +0900, Charles Plessy a écrit :
Le Mon, Oct 26, 2009 at 11:07:19PM +, Roger Leigh a écrit :
While most developers are conscientious enough to make sure their
packages build, one does see enough crap packages that IMO this
(minimal) bar should
.
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Changed-By: Charles Plessy ple...@debian.org
Description:
r-cran-epitools - GNU R Epidemiology Tools for Data and Graphics
Changes:
r-cran-epitools (0.5.3-2) unstable; urgency=low
.
* Rebuilt against R 2.10.0 (new documentation system).
* debian/changelog:
- Added myself
if there are developpers who are
obviously careless, would be far more efficient than our current procedure.
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creates a more complex mechanism at
our archive level, which raises the bar for new contributors.
I really feel sorry for the Lintian maintianers who will get most of the flames
in the future.
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Changed-By: Charles Plessy ple...@debian.org
Description:
r-cran-g.data - GNU R package for delayed-data
Changes:
r-cran-g.data (2.0-2) unstable; urgency=low
.
* Rebuilt against R 2.10.0 (new documentation system).
* Incremented Standards-Version to reflect compliance with Policy 3.8.3
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
r-cran-combinat - GNU R package with utilities for combinatorics
Changes:
r-cran-combinat (0.0-7-1) unstable; urgency=low
.
* New upstream release.
* Converted debian/copyright to experimental machine-readable format
details about packaging issues.
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Changed-By: Charles Plessy ple...@debian.org
Description:
r-cran-rocr - GNU R package to prepare and display ROC curves
Changes:
r-cran-rocr (1.0-2-2) unstable; urgency=low
.
* Rebuilt against R 2.10.0 because of changes in the documentation system.
* Converted debian/copyright
...@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 (1.4.4-1) unstable; urgency=low
.
* New upstream release (documentation update).
* Updated Standards-Version to reflect
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
r-cran-randomforest - GNU R package implementing the random forest
classificator
Changes:
r-cran-randomforest (4.5-33-1) unstable; urgency=low
.
* New upstream release.
* Added comment on trademarks in debian
...@lists.alioth.debian.org
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 (1.18.0-2) unstable; urgency=low
.
* Rebuilt against R 2.10.0 because of its new documentation system.
* debian/control
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
r-other-bio3d - GNU R package for biological structure analysis
Closes: 551414
Changes:
r-other-bio3d (1.0-6-1) unstable; urgency=low
.
* New upstream release.
* Mended debian/watch thanks to Yan Morin (Closes: #551414
Changed-By: Charles Plessy ple...@debian.org
Description:
clustalx - Multiple alignment of nucleic acid and protein sequences (graphic
Closes: 550893
Changes:
clustalx (2.0.12-1) unstable; urgency=low
.
* New upstream release (LP: #423648, #393769):
- Uses Qt instead of lesstif
also completely untie the update of upstream metadata from package upload, and
if the file is managed in a VCS, it would be easy to revert mistakes and find
misusers, if somebody ever dares.
Have a nice day
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Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi
Changed-By: Charles Plessy ple...@debian.org
Description:
seaview- Multiplatform interface for sequence alignment and phylogeny
Changes:
seaview (1:4.2-1) unstable; urgency=low
.
* New upstream release.
* debian/control:
- Build depend on unversionned libjpeg-dev package.
- Added
-By: Charles Plessy ple...@debian.org
Description:
bwa- Burrows-Wheeler Aligner
Changes:
bwa (0.5.4-1) unstable; urgency=low
.
* New upstream release, see ‘/usr/share/doc/bwa/NEWS.gz’.
* Refreshed debian/copyright.
* Reflected the rename of dBWT-Sw to BWA-SW in the package's
-license/
There is also the CC0, which is supposed to mean something similar to the
above:
http://creativecommons.org/publicdomain/zero/1.0/legalcode
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will be
raised of course).
Dear Steffen,
shouldn’t the upstream maintainer(s) be warned before the security issue is
advertised in public?
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Changed-By: Charles Plessy ple...@debian.org
Description:
clustalw - global multiple nucleotide or peptide sequence alignment
Closes: 550895
Changes:
clustalw (2.0.12-1) unstable; urgency=low
.
* New upstream release fixing many bugs
(see /usr/share/doc/clustalw/CHANGELOG).
* Updated
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
mummer - Efficient sequence alignment of full genomes
mummer-doc - Documentation for MUMmer
Changes:
mummer (3.22~dfsg-1) unstable; urgency=low
.
* New upstream release:
3.22
- Significant 'dnadiff' bug
package to remove a similar clause, by referring to the following essay on the
FSF website: http://www.fsf.org/licensing/essays/bsd.html. Maybe you can give
it a try?
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Debian Med packaging team,
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, but the only persons
who veto packages in Debian are our archive administrators, an none of them has
objected against libjs-extjs. In my opinion, just go ahead and it will be fine
:)
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Changed-By: Charles Plessy ple...@debian.org
Description:
infernal - inference of RNA secondary structural alignments
infernal-doc - inference of RNA secondary structural alignments – documentatio
Closes: 550253
Changes:
infernal (1.0-2) unstable; urgency=low
.
* Switch
-By: Charles Plessy ple...@debian.org
Description:
bwa- Burrows-Wheeler Aligner
Closes: 548719
Changes:
bwa (0.5.3-1) unstable; urgency=low
.
* Initial release (Closes: #548719)
Checksums-Sha1:
b938813d9a1cf740a3e47f6e29148ff8c5ad62c9 1236 bwa_0.5.3-1.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 (1.982-1) unstable; urgency=low
.
* New upstream release fixing DAS stylesheet support.
* Enhances: gbrowse (debian
programs
and I will stop following this Policy directive. In my opinion, the choice is
to be left to the maintainer, and this is not well reflected by using a
’should’ directive in the Policy. I would like to see it rephrased as a best
practice or removed.
Have a nice day,
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Le Tue, Sep 29, 2009 at 01:12:14PM -0500, Manoj Srivastava a écrit :
On Mon, Sep 28 2009, Paul Wise wrote:
On Tue, Sep 29, 2009 at 9:37 AM, Charles Plessy ple...@debian.org wrote:
in my first experimentations I used DEB_BUILD_OPTIONS, but this leads
to the possibility of clashing
Package: wnpp
Severity: wishlist
Owner: Charles Plessy ple...@debian.org
Package name: bwa
Version : 0.5.3
Upstream Author : Heng Li and others, see:
http://bio-bwa.sourceforge.net/bwa.shtml
URL : http://bio-bwa.sourceforge.net
License : GPL
with no
options. In the case I presented here, the goal is to help the maintainer to
make tests that are not possible on our build network.
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for not including extension in program names
upstream, but in my opinion removing them before upstream creates more
problems than it solves…
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http://www.debian.org/devel/debian-med
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in a controlled environment
http://lists.debian.org/debian-announce/2009/msg00010.html
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that is detected in
debian/rules.
I was just wondering if other people were using something similar and if there
would be ground for standardisation.
Have a nice day,
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Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
libbio-samtools-perl - read SAM/BAM nucleotide sequence aligment database files
Changes:
libbio-samtools-perl (1.05-1) UNRELEASED; urgency=low
.
* New upstream release.
- Bio::DB::Sam-seq_id() method no longer lower
maintainers?/long-shot
Hi Javier,
it is an interesting idea to define a set of criteria that data package must
follow, but I think it will be much easier for everybody to have this enforced
by a policy rather than by tools.
Have a nice day,
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Debian Med packaging team,
http
-By: Charles Plessy ple...@debian.org
Description:
bioperl- Perl tools for computational molecular biology
Changes:
bioperl (1.6.0-3) unstable; urgency=low
.
[ David Paleino ]
* Removed myself from Uploaders
.
[ Charles Plessy ]
* debian/control:
- Added libdata-stag-perl
the problem could simply solved by renaming one of the two concepts?
Native format could be called ‘direct’, or native packages could be called
’original’, for instance. This would help the Project to keep track of what
programs it is upstream for.
Have a nice day,
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Tsurumi, Kanagawa
, statistics,
checking, …)
Have a nice day,
PS: please notify me in private if you think I am using the wrong list for this
discussion, or if you think that I should keep on posting on -devel even if
others think I am using the wrong list…
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Tsurumi, Kanagawa, Japan
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
libbio-samtools-perl - read SAM/BAM nucleotide sequence aligment database files
Closes: 543487
Changes:
libbio-samtools-perl (1.04-1) unstable; urgency=low
.
* Initial Release (Closes: #543487).
Checksums-Sha1
. Everybody is welcome to contribute! Everybody is also welcome to add
their name to the Drivers field if they see themselves as drivers, in the
spirit of DEP 0.
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...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
samtools (0.1.6~dfsg-1) unstable; urgency=low
.
* New upstream
subscribed to -devel with the digest option, I will patiently
wait for the next digest to arrive before answering to your other email.]
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-gain the momentum that led this bug to be closed.
So from the point of view of this experience, I definitely support the idea of
having a mechanism to contact all the contributors to a bug, although I am
unsure if it would be a good default.
Have a nice day,
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Tsurumi, Kanagawa
,
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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 (0.7.53-1) unstable; urgency=low
.
* New upstream release:
- Ignored
, it is for sure
a good thing, but in the case when the package maintainer sits on the
translations, like for sbackup, this is clearly a problem.
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Changed-By: Charles Plessy ple...@debian.org
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
samtools (0.1.5c-2) unstable; urgency=low
.
* Rebuilt with -fPIC
...@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 (0.7.52-1) unstable; urgency=low
.
* New upstream release:
V 0.7.51
Changed-By: Charles Plessy ple...@debian.org
Description:
bioperl-run - Wrapper modules for BioPerl
Closes: 541274
Changes:
bioperl-run (1.6.1-1) unstable; urgency=low
.
* New upstream release.
* debian/patches/10-wrong-path-for-interpreter.patch: removed
(fixed upstream
Le Tue, Sep 01, 2009 at 11:21:37AM +0200, Vincent Danjean a écrit :
Josselin Mouette wrote:
Le mardi 01 septembre 2009 à 09:49 +0900, Charles Plessy a écrit :
I started to write a message about to ask upstream why they do not make a
shared version of libbam, but I am blocked because I
Le Mon, Aug 31, 2009 at 01:23:39AM +0100, Stephen Gran a écrit :
This one time, at band camp, Charles Plessy said:
Le Sat, Aug 29, 2009 at 08:06:09PM -0700, Steve Langasek a écrit :
On Sun, Aug 30, 2009 at 11:56:58AM +0900, Charles Plessy wrote:
as per Policy § 10.2, I would like to know
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
libsrf-dev - C++ implementation of the SRF format for DNA sequence data
srf-doc- specification documents for the SRF format DNA sequence data
Closes: 489983
Changes:
srf (0.1+dfsg-1) unstable; urgency=low
.
* Initial
Le Sat, Aug 29, 2009 at 08:06:09PM -0700, Steve Langasek a écrit :
On Sun, Aug 30, 2009 at 11:56:58AM +0900, Charles Plessy wrote:
as per Policy § 10.2, I would like to know if everybody agrees if I change
the
libbam-dev package to compile libbam.a with -fPIC.
What are the reasons
; let's all
cooperate to reduce the traffic on this list).
Have a nice week-end,
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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:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Closes: 540453
Changes:
samtools (0.1.5c-1) unstable; urgency=low
.
* Initial
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
embassy-phylip - EMBOSS conversions of the programs in the phylip package
Closes: 493977
Changes:
embassy-phylip (3.68-1) unstable; urgency=low
.
* Initial release (Closes: #493977)
Checksums-Sha1
Package: wnpp
Severity: wishlist
Owner: Charles Plessy ple...@debian.org
Package name: libbio-samtools-perl
Version : 1.03
Upstream Author : Lincoln Stein
URL : http://search.cpan.org/dist/Bio-SamTools/
License : Artistic version 2, or GNU GPL version 1
: 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:
libgo-perl - perl modules for GO and other OBO ontologies
Changes:
libgo-perl (0.10-1) unstable; urgency=low
.
* New upstream version.
* debian/rules, debian/control and debian/compat and debian/watch
refreshed with dh-make-perl
...@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 (1.981-1) unstable; urgency=low
.
* New upstream release fixing bugs in wiggle_xyplot and improving
documentation
...@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 (0.7.50-1) UNRELEASED; urgency=low
.
* New upstream release:
V 0.7.49
: http://blitiri.com.ar/p/bola/
Have a nice day,
--
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:
libbio-scf-perl - Perl extension for reading and writting SCF sequence files
Closes: 513303
Changes:
libbio-scf-perl (1.01-1) unstable; urgency=low
.
* Initial Release. (Closes: #513303)
Checksums-Sha1
Team
debian-med-packag...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
libstaden-read-dev - development files for libstaden-read
libstaden-read1 - Staden library for reading and writing DNA sequencing results
staden-io-lib-utils - programs for maniuplating
Team
debian-med-packag...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
libstaden-read-dev - development files for libstaden-read
libstaden-read1 - Staden library for reading and writing DNA sequencing results
staden-io-lib-utils - programs for maniuplating
Packaging Team
debian-med-packag...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
libstaden-read-dev - development files for libstaden-read
libstaden-read0 - Staden library for reading and writing DNA sequencing results
staden-io-lib-utils - programs for maniuplating
...@lists.alioth.debian.org
Changed-By: Charles Plessy ple...@debian.org
Description:
embassy-domsearch - Extra EMBOSS commands to search for protein domains
Closes: 537204
Changes:
embassy-domsearch (0.1.0+20980715-1) unstable; urgency=low
.
* Initial release (Closes: #537204).
Checksums-Sha1
to developer-oriented metadata.
Have a nice day,
--
Charles Plessy
Tsurumi, Kanagawa, Japan
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, I am sure, thank you’.
This would have saved us your digressions about lies and expulsions. Please
consider that this list is high traffic and try to limit your messages in
quantity.
It may even help you to have a nice day.
--
Charles Plessy
Tsurumi, Kanagawa, Japan
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meta-data like the VSC, Homepage, Section
and Description fields, the Debtags, etc.
Have a nice day,
--
Charles Plessy
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...@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 (0.7.48-1) unstable; urgency=low
.
* New upstream release
-efficient for
everybody.
Leafs are what give trees their nice colors :)
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
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,
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
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-{'DOI'}' samtools/debian/upstream-metadata.yaml
10.1093/bioinformatics/btp352
I am unsure if it is a good idea to manage multi-line upstream meta-data
anyway. Are there other opinions on this ?
Have a nice day,
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
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