Le Thu, Feb 23, 2012 at 08:45:00AM +0100, Andreas Tille a écrit :
>
> From my perceptions this case is one more prove for the fact that
> debcheckout for our purpose is weaker than directly inspecting VCS
> content.
Hi Andreas,
the two approaches have symmetrical flaws:
- VCS URLs may be wrong
Le Sat, Feb 18, 2012 at 07:40:41PM +0100, Andreas Tille a écrit :
> On Sat, Feb 18, 2012 at 04:53:40PM +0100, Andreas Tille wrote:
> > I noticed this. I just verified the current data in UDD and noticed
> > that some packages are lacking information even if the upstream file
> > just has it (for i
Le Tue, Feb 21, 2012 at 09:21:51PM +0100, Andreas Tille a écrit :
>
> I can't see a reason to hold back something that fixes a problem. I'm
> pretty sure Charles will inspect your change in Git and so it is safe if
> you just go for it (in this and in similar future cases).
Thanks Carlos for you
Hi Andreas and Yaroslav,
I started to write an answer this morning, but I can not keep up the rythm of
the discussion ! Below I wrap up what I drafted, and the summary is that I
will work on gathering the debian/upstream files in a single VCS on
collab-maint as well.
I will then focus on the oth
Le Mon, Feb 20, 2012 at 09:43:09AM +0100, Andreas Tille a écrit :
>
> there are tools which assemble informations for Sources.gz files - I guess
> this could be implemented if say 20% of the packages will contain such a
> file.
In such a model, the packages need to be uploaded so that Sources.g
Le Sun, Feb 19, 2012 at 03:13:19PM +0100, Andreas Tille a écrit :
>
> I somehow assumed that if
> I'm editing a debian/upstream file and commit it to our Vcs after some
> delay (say 1 day) this change would be reflected in Umegaya and (in the
> worst case one day later) the UDD bibref gatherer wou
Le Sun, Feb 19, 2012 at 03:15:00PM +0100, Andreas Tille a écrit :
> On Sun, Feb 19, 2012 at 10:12:33AM +0900, Charles Plessy wrote:
>
> > If we can assemble a longer list of similarly non-free packages,
> > perhaps their rescue could be wrapped as a summer of code project
Le Sat, Feb 18, 2012 at 04:53:40PM +0100, Andreas Tille a écrit :
>
> I noticed this. I just verified the current data in UDD and noticed
> that some packages are lacking information even if the upstream file
> just has it (for instance mira-assembler has only DOI in UDD). May be
> we could trac
Le Sat, Feb 18, 2012 at 03:03:36PM +0100, Andreas Tille a écrit :
> On Sat, Feb 18, 2012 at 10:52:50AM +0100, Alex Mestiashvili wrote:
> > I started work on bowtie2 packaging and I see that bowtie is already
> > packaged in svn [2].
> > I am wondering if any packaging job has already been done on b
Le Sat, Feb 18, 2012 at 07:30:17PM +0100, Andreas Tille a écrit :
>
> IMHO it might be worth trying to contact the author of this > 10 year
> old code to verify whether this phrase remains valid these days. Any
> volunteer to free cufflinks (or did I missed something)?
Hi Andreas,
this did not
Hi Andreas,
I have a working implementation as a Debian package that will allow us to
transfer easily the Umegaya gatherer for bibliographic information to
debian-med.debian.net. I do not remember if I have the root access to
that machine... Can you add me to the sudo group ?
Once installed ther
Le Tue, Feb 14, 2012 at 01:04:22PM +0100, Andreas Tille a écrit :
> Hi Charles,
>
> the description is a bit sparse for the package itself as for the task
> where I would like to include it. Could you please try to be a bit
> more verbose for the general Debian user audience?
How about this ?
Package: wnpp
Severity: wishlist
Owner: Charles Plessy
Package name: vegan
Version : 2.0-2
Upstream Author : Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre
Legendre, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M.
Henry H. Stevens, H
Package: wnpp
Severity: wishlist
Owner: Charles Plessy
Package name: permute
Version : 0.6-3
Upstream Author : Gavin L. Simpson
URL : http://cran.r-project.org/web/packages/permute/
License : GPL-2
Programming Lang: R
Description : R functions
url
svn+ssh://ple...@svn.debian.org/svn/debian-med/trunk/packages/pscoils/trunk
This is why I recommend debcheckout in our group policy.
http://debian-med.alioth.debian.org/docs/policy.html#source
Have a nice week-end,
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Debian Med packaging team,
http://www.de
Le Wed, Feb 08, 2012 at 04:54:51PM +0100, Andreas Tille a écrit :
>
> No, the "Files: debian/*" are needing a license. I usually choose "Same
> as packaged software itself". Deleting this part is no option because
> it will not pass ftpmaster. I recently learned that even "Public
> domain" is n
Le Wed, Feb 08, 2012 at 10:38:50AM -0500, Carlos Borroto a écrit :
>
> I made a mistake here. At one point after pushing the initial
> repository and forgetting to push tags, I mess up my local repository
> so I erased and recloned. This means I don't have access to the tags
> created be git-impor
Le Wed, Feb 08, 2012 at 02:16:56PM +0900, Charles Plessy a écrit :
>
> I uploaded r-cran-rsqlite. I noted that you forgot to push your tags; please
> push them.
Sorry for the noise, I also forgot the following.
The license you chose for the Debian packaging (GPL-2+) is more restric
Dear Carlos,
I uploaded r-cran-rsqlite. I noted that you forgot to push your tags; please
push them.
I have the impression that the package uses the code copy of SQLite instead of
the material provided by libsqlite3-dev. That would definitely be something to
solve, as otherwise it means that ea
possible as
cufflinks is very unfortunately non-free. Also, if nothing in the tophat
package calls programs from the cufflinks package, the relationship would
rather be that tophat Enhances: cufflinks and cufflinks Depends: tophat.
Have a nice day,
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Tsurumi, Kanagawa, Japan
Le Mon, Feb 06, 2012 at 09:09:44AM -0500, Carlos Borroto a écrit :
>
> I just notice that we are only recommending bowtie, but bowtie is
> actually needed by tophat. All the actual mapping is done by bowtie. I
> think we should have bowtie as a dependency of the binary package. I
> have the commit
most of my packages, I gave
up writing manpages. The problem is when upstream is not interested in
maintaining them.
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Le Sun, Feb 05, 2012 at 03:04:44PM -0500, Carlos Borroto a écrit :
>
> Is only missing manpages. I talked to Alexandre about it and it seems
> we would have to use something like help2man. Upstream doesn't
> includes any manpage.
Dear Carlos and everybody,
I just uploaded tophat after correcting
check grep, or vice-versa. But I
found proofchecking strictly necessary to not be embarassed too often in front
of the FTP team. Peer review also helps.
I will sponsor r-cran-rsqlite (tomorrow).
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Tsurumi, Kana
hand in debian/control.
>
> I remember when we started using this trick about 3 years ago (at least
> my feeling says so) that Charles Plessy who invented this trick said
> that you would not be particularly happy about this trick. Otherwise it
> would have been included into
Hi An
two packages would not
be identical.
Have a nice day,
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-cran-proto.git/
Dear Carlos,
no need to use mentors.debian.org in our case. I have uploaded the package
after documenting more files in debian/copyright (see commit list). Many
thanks for all the new R packages you are preparing !
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Le Sat, Jan 28, 2012 at 02:23:03PM +0100, Andreas Tille a écrit :
> On Fri, Jan 27, 2012 at 11:07:38AM +0900, Charles Plessy wrote:
> > http://anonscm.debian.org/gitweb/?p=users/plessy/snappy-java.git
>
> For some reason I can not commit to this:
>
> $ git push
> C
Package: wnpp
Severity: wishlist
Owner: Charles Plessy
Package name: umegaya
Version : 0
Upstream Author : Charles Plessy
URL : http://upstream-metadata.debian.net/
License : BOLA-1.1
Programming Lang: Perl
Description : Umegaya is a MEtadata
gs.debian.org/634607
By the way, the syntax of the machine-readable copyright files can be validated
with the config-edit command, from the libconfig-model-perl package.
http://ddumont.wordpress.com/2011/01/13/debian-copyright-dep5-parsereditorvalidatormigrator-is-released/
Cheers,
--
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Le Sun, Jan 22, 2012 at 06:30:28PM -0500, Dominique Belhachemi a écrit :
>
> For now (if you are using Lucid) you can change the debhelper version
> in debian/control to "debhelper (>= 7)" and write a 7 in
> debian/compat.
Hi all,
note that the debian-med PPA contains a backport of debhelper 8 f
Le Wed, Jan 25, 2012 at 07:39:04PM +0100, Alex Mestiashvili a écrit :
>
> taken from http://pkg-perl.alioth.debian.org/git.html
> almost the same is written in the debian-med policy but I liked the way
> it is written here :)
Hi all,
please do not hesitate to suggest improvements for the wording
Le Fri, Jan 27, 2012 at 03:01:21PM +0900, Charles Plessy a écrit :
>
> I reviewed your package, and will upload it shortly after updating the
> format of its copyright file.
… I missed the copyright of Adam Kennedy, and other copyrights as not all files
under /inc are part of Modu
n the Perl build system itself.
Have a nice week-end,
Charles
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easy problem for one of you, I would be
really greatful if you could give it a try !
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uildpackage do so. In your
case, you would have needed “pristine-tar checkout
liboptions-java_0.0.20120113.orig.tar.gz”, but I would prefer to not mention it
in our group policy, exactly for the reason that it complicates things.
Just use git-buildpackage as you would use dpkg-buildpackage. For inst
Le Sun, Jan 15, 2012 at 07:57:54PM -0500, Yaroslav Halchenko a écrit :
> To me, it is not just typing: trying to explain structure of debian/ to
> a new contributor/user is already quite evolved, and having something
> like "umegaya" might take additional few minutes to explain and would
> work ag
Le Sun, Jan 15, 2012 at 02:40:12PM -0500, Yaroslav Halchenko a écrit :
> if you are talking about getting a shorter adequate name, why not
> just to go with something which fits better among the list of what we
> carry under debian/: simply debian/upstream ? atm I don't see any
> package which wo
xcept perhaps that it may be preferable to first fix the
details in Debian Med before going on a larger scale.
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w
Le Thu, Jan 12, 2012 at 08:15:37AM +0100, Andreas Tille a écrit :
>
> > Lastly, since upstream-metadata.yaml is long to type, I have been tempted to
> > rename the logistics around the file ‘umegaya’ for Upstream MEtadata
> > GAthereing
> > with YAml.
>
> This would finally spare me copy-n-past
Hi Andreas,
Sorry, the data was actually rotten for multiple reasons. First, the machine
running upstream-metadata.debian.net stopped keeping dep-src entries in its
sources.list, so debcheckout was not working anymore, and my rudimentary
scripts did not catch the error. I added error-catching to
Le Fri, Jan 13, 2012 at 10:37:31AM +0100, Andreas Tille a écrit :
> On Fri, Jan 13, 2012 at 05:22:23PM +0900, Charles Plessy wrote:
> >
> > You must have a git-buildpackage configuration file somewhere that has some
> > non-standard options enabled. On my system, it doe
Le Fri, Jan 13, 2012 at 08:54:22AM +0100, Andreas Tille a écrit :
>
> > Perhaps you did not update the pristine-tar branch before trying to build
> > the
> > package ? The commande ‘gbp-pull’ will do this conveniently for you.
>
> I simply assumed that a `git pull` would simply do the right th
,
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Le Thu, Jan 12, 2012 at 11:04:36PM +0100, Andreas Tille a écrit :
>
> $ git checkout pristine-tar
> Switched to branch 'pristine-tar'
> $ ls *
> clinica_0.2.1~dfsg.orig.tar.bz2.delta clinica_0.2.1.orig.tar.gz.delta
> clinica_0.2.1~dfsg.orig.tar.bz2.id clinica_0.2.1.orig.tar.gz.id
> $ pristine
t hook that does this when
debian/upstream-metadata.yaml is refreshed.
Lastly, since upstream-metadata.yaml is long to type, I have been tempted to
rename the logistics around the file ‘umegaya’ for Upstream MEtadata GAthereing
with YAml.
Cheers,
--
Charles Plessy
Debian Med packaging team,
h
I would try
Cytoscape or some R plugins. See the shamefully outdated following page for
examples.
http://wiki.debian.org/DebianSystemsBiology
I propose to delete phylographer from our repository's trunk. It stays in its
history anyway, so no work is lost.
Cheers,
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Deb
Le Tue, Jan 10, 2012 at 07:48:40PM +, Andreas Tille a écrit :
> Modified:
>trunk/packages/phylographer/trunk/debian/compat
>trunk/packages/phylographer/trunk/debian/control
> Log:
> Fixed cut-n-pasto in Vcs fields, packaging updates - does anybody care about
> this package??
Hi Andrea
ated to the Judy library. Do you think
I can link safely to Debian's version (1.0.5) ?
Have a nice day,
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with a
eplot versions
> from?
Hello Andreas and Olivier,
I think that I lost momentum in 2008 when I was interacting with Olivier. I
hope that this was not the reason for not going ahead with the upload. If that
was the case, I am really sorry.
In any case, I am available to resume the work on treeplot
Le Mon, Jan 09, 2012 at 03:51:14PM +0100, Andreas Tille a écrit :
>
>git-buildpackage --debsign-k "Andreas Tille "
It is even simpler:
git-buildpackage -k "Andreas Tille "
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Le Mon, Jan 09, 2012 at 12:21:16PM +0100, Andreas Tille a écrit :
>
> it was repackages as required by ftpmaster. Even if it might be
> fine now because git-buildpackage works and is able to create the
> pristine tarball it is not the very best idea to have a different
> tarball without having a
Le Mon, Jan 09, 2012 at 07:49:09AM -0500, SRA Toolkit Development Group a écrit
:
>
> Can you be more specific? There was no intentional loss of dynamic
> linking, and we still build our system dynamically.
The following commands give me different results on 2.1.2 and 2.1.3.
make dynamic
e
Andreas and Leonardo,
indeed, the problem is rather that the files that are checked in the
repository, and the files that are in the upstream archive downloaded by uscan,
do not match. Probably the archive that was checked in the repository was
repacked ?
Have a nice day,
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Debian M
system to resolve the problem myself.
Can you help us ?
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, remove the --user option.
But Andreas, note anyway that if you have the original upstream sources in the
parent directory, after running uscan or apt-get source accordingly, then you
can work without the upstream and pristine-tar branches as well.
Have a nice Sunday,
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Deb
replacing it ?
http://lists.debian.org/20111210150746.ga32...@merveille.plessy.net
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Le Thu, Jan 05, 2012 at 03:34:21PM +0100, Alex Mestiashvili a écrit :
> Hello ,
> There is a new upstream release ,
> Lintian seems to be clean , please review and sponsor it .
I will, tomorrow.
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e recently I started to commit directly
patches to the master branch and expose them in debian/patches for
http://patch-tracker.debian.org/.
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target, which is implicitely passed to
dh, does not depend on a target that applies the patch. For local builds, it
just happens by chance that they are applied, because the source package is
built before the binary packages.
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day,
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not
auto-built).
I have corrected this in the Git repository.
Have a nice day and a happy new year !
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or a makefile.
For the source, if it is still available, why not committing the data and the
script that produces the PDF. (Althouth of course the real source would be a
snapshot of the UDD at the time, and the source of that UDD snapshot would be…
complex.) On the other hand, if the source is not a
Le Sun, Dec 11, 2011 at 12:07:46AM +0900, Charles Plessy a écrit :
>
> It is a bit late so I will not upload this night, but if nobody sends a patch
> until tomorrow morning, I will upload the package as it is. Let's ask
> Upstream
> to replace locfit, which is also the ca
gt; Please stop doing this.
Hi Steve, Thorsten and everybody,
just in case, I reworded a bit our group policy to make sure it does not
suggest we are using mergeWithUpstream everywhere.
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Le Sat, Dec 10, 2011 at 01:44:30PM +0100, Alex Mestiashvili a écrit :
> On 12/10/2011 01:13 PM, Charles Plessy wrote:
> >
> > I had a look at cufflinks, and I think it can be uploaded to non-free.
> >
> > The only issue I found is that it ignores the CFLAGS passed by
>
honor Debian's CFLAGS…
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to contact the cufflinks authors and as them if they can
help or replace locfit.
We can definitely upload to non-free in the meantime.
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heless, even if it
would allow cheaters to inspect the chocolates in advance, I would
advocate putting a link to the source somewhere (on the star ?). That
would be the cherry on the cake.
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ive enough. Please do
not hesitate to let us know when you feel that our documentation is unclear or
too dry.
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Dear all,
here is a proposition of release goal that was posted on debian-devel.
The Debian Med packages that would need to be corrected are the following:
Debian Med Packaging Team
amap-align
amide
bioruby
boxshade
clustalx
dicomscope
emboss
g2
igraph
libace-perl
biocooca.app will always be
distributed in archive.debian.org and snapshot.debian.org. If for some reason
you would like to ask us to reconsider our decision, please do not hesitate to
contact us on our mailing list.
Have a nice week-end,
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stenAlteholz:
> http://wiki.debian.org/DebianMedQAWorkflow
>
> New page:
> = Workflow for Debian Med packages =
Hi Thorsten.
this is a nice documentation. I feel however that there are some part that are
redundant with our group policy
(http://debian-med.alioth.debian.org/docs/policy.html).
How a
f the Debian Pure Blends, it
operates from whithin Debian. It should really be nothing more than a simple
preseed file, with no programmatic parts. In that sense, I think that
CloudBioLinux can also benefit from this approach as it will simplify
operations a lot.
Cheers,
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D
Le Tue, Oct 11, 2011 at 11:21:43AM +0200, Andreas Tille a écrit :
> Hi Charles,
>
> On Tue, Oct 11, 2011 at 03:42:38PM +0900, Charles Plessy wrote:
> > here is a link to an article that illustrates in what context a Debian Med
> > machine image with the ‘cloud’ task l
Hello everybody,
here is a link to an article that illustrates in what context a Debian Med
machine image with the ‘cloud’ task loaded would be useful.
http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002147
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http
2.0. So, could you
> please upload those packages for me ?
Bonjour Olivier,
I uploaded the Mobyle packages.
It really looks nice. A Mobyle-powered live or cloud image would be a great
presentation of what Debian Med offers for sequence analysis !
Cheers,
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: to the former (and cc:ing its maintainer).
Thanks a lot Luca for doing the Right Thing.
Actually, my motivation when following tightly recent upstream releases of
MAFFT (we often skip some as they are quite frequent) was to see if the ia64
build failure was reproducible. Unfortunately it i
an-devel if there are new points
of view to consider. Since I am busy with another work involving the Policy
team, DEP 5, I will wait for that project to be completed before going to the
CTTE.
Have a nice day,
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Tsu
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team this is rarely the case.
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Le Mon, Sep 19, 2011 at 09:43:51PM +0200, Thorsten Alteholz a écrit :
>
> On Sat, 17 Sep 2011, Charles Plessy wrote:
> >sorry to be a bit late to realise: I remember why I was putting files like
> >trunk/debian/RETIRED in the Subversion repositories of packages I migrated to
&g
Hi Olivier,
> For link issues, I think your refer to the links to the program examples.
> But programs are installed with the mobyle-programs package.
> By default, no program is installed, so links in example tutorial will fail.
> I have added in man page a hint about this requirement.
I install
Le Mon, Sep 19, 2011 at 12:05:32AM +0200, Andreas Tille a écrit :
>
> I somehow feel this is the right moment to let molphy die. This
> non-free, non-maintained upstream piece of very old code just drained a
> lot of my time to fix totally broken code. While arb rdepends from
> molphy (actually
Le Sun, Sep 18, 2011 at 11:08:13AM +0900, Charles Plessy a écrit :
>
> I had a look at mobyle.
Hi again,
I tried to test Mobyle. http://localhost/mobyle gives “403 Forbidden”.
Links in http://localhost/mobyle/portal/help/stepbystep did not work, and
http://localhost/mobyle/porta
hrough debian/mobyle.links ?
chown -R www-data:www-data /var/log/mobyle
chown -R www-data:www-data /var/lib/mobyle
If the mobyle package is the only one to create these directories, then their
group can be set in the binary package directly.
Bon dimanche,
Charles
--
Charles Plessy
the Subversion repositories of packages I migrated to
Git: deleting the trunk directory without waiting for a release cycle will
break the VCS URLs in the stable release.
Cheers,
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
--
compatible version 2.0 is needed to extend it :)
Perhaps you can have a look at my “UMEGAYA”, UPstream MEtadata GAthered with
YAml project, which I unfortunately neglected recently for expriments on the
Amazon computer cloud and DEP 5.
http://upstream-metadata.debian.net/
Cheers,
Charles
--
Charl
Le Wed, Sep 07, 2011 at 09:52:30AM +0200, Andreas Tille a écrit :
> On Wed, Sep 07, 2011 at 03:47:42PM +0900, Charles Plessy wrote:
> > Some of the programs names are not generic, some are borderline and some are
> > clearly generic. I do not want to make the call. Also, each time
the current system is designed to carry only one publication per package.
Your email reminds me that I need to make a nice proof of principle now that
the data is loaded in the UDD. Perhaps we can consider increasing the
complexity
of the system only after that ?
Have a nice day,
--
Ch
about it direcly after Debconf,
but since nothing seems to have happened, perhaps it is time to accept the fait
accompli and use the http://anonscm.debian.org/viewvc/ base URL instead.
Have a nice day,
--
Charles Plessy
Tsurumi, Kanagawa, Japan
--
To UNSUBSCRIBE, email to debian-med-requ...@l
asks.debian.org/home/groups. That would allow to execute
commit hooks on vasks and serve the result on wagner. Let's see if this is
accepted.
Have a nice week-end,
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
--
To UNSUBS
build-time regression tests. This suggest that it will be difficult to get
some help to fix the bug.
Please remove t-coffee on armel from unstable.
Have a nice day,
--
Charles Plessy
Debian Med packaging team
Tsurumi, Kanagawa, Japan
--
To UNSUBSCRIBE, email to debian-med-requ
channel money into Debian Med would be to
sell it as a shelf product or as a book describing how to use it. That would
be a big project, but that may help research labs to contribute by buying
the product. It would also cut some trees, but that is another story ;)
Have a nice day,
--
Charles
Le Sat, Aug 13, 2011 at 05:25:03PM +0200, Olivier Sallou a écrit :
> no problem for rename, however you should rename it also in control file as
> it is a circos dependency (it is needed by circos main package)
Et voilà, uploaded :)
Thanks again for your perseverance with the fonts, and bon diman
e tag. Would you mind if I
rename it otf-symbols-circos ?
Cheers,
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
--
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of "unsubscribe". Trouble? Contac
d forwarded message -
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
--
To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org
with a subject of "unsubscribe". Trouble? Contact listmas...@lists.deb
eam's bugtracker, I would be happy to apply it to our Debian package.
http://sourceforge.net/tracker/?func=detail&aid=3356549&group_id=93181&atid=603358
With its Popcon install and vote scores above 250 and 150 respectively,
perlprimer is one of our star packages.
Cheer
Hello everybody,
here is some advertisement for a software that I will not have time to package.
http://www.openfreezer.org/
OpenFreezer Laboratory Reagent Tracking and Workflow Management System is an
open-source information management system for biological laboratories. The
system tracks
Le Mon, Aug 01, 2011 at 09:11:07AM +0200, Olivier Sallou a écrit :
>
> Where did you see that other fonts do not allow modification?
> I see no such mention in text files.
Hi Olivier,
this is exactly the problem: if it is not mentionned, it may not be allowed.
In particular for fonts, I think th
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