Le Mon, Sep 28, 2009 at 07:07:28AM +, Andreas Tille a écrit :
> -mafft (6.240-3) UNRELEASED; urgency=low
> +mafft (6.713-1) UNRELEASED; urgency=low
Hi Andreas,
many thanks for your help on upgrading the packages, I got quite dispersed
those days and did not find time for some of them.
In the
Le Fri, Sep 18, 2009 at 09:11:27PM +0900, Charles Plessy a écrit :
> Le Fri, Sep 18, 2009 at 09:11:50AM +0200, Andreas Tille a écrit :
> >
> > I'm personally quite sloppy to add usertags to WNPP bugs because for *me*
> > the
> > tasks pages serve the same purp
Le Fri, Sep 18, 2009 at 09:11:50AM +0200, Andreas Tille a écrit :
>
> I'm personally quite sloppy to add usertags to WNPP bugs because for *me* the
> tasks pages serve the same purpose. On the other hand there is nothing
> against to be strict with the WNPP usertags - but I have no time to deal w
hive
administrators that it is needed to keep the GPL boilerplate. Can you restore
it? (and actually repair it, as it was lacking ‘or (at your option) any later
version.’).
Lastly, how about the R igraph package? Are you intersted to package it?
Have a nice day,
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Debian
s
keep the secret that we do not provide their sources untill we really want to
have a strong discussion on the matter ;)
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runk/packages/R/r-other-mott-happy/trunk/debian/#_trunk_packages_R_r-other-mott-happy_trunk_debian_
and I could check it out:
svn co
svn+ssh://svn.debian.org/svn/debian-med/trunk/packages/R/r-other-mott-happy/trunk/
r-other-mott-happy
Have a nice day,
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Debian Med packa
Le Fri, Aug 21, 2009 at 10:52:57AM +0900, Charles Plessy a écrit :
> Le Thu, Aug 20, 2009 at 03:15:40PM +0200, Anthony Boureux a écrit :
> >
> > May be it is time for me to contribute to debian.
> > So, I will present myself : I'm doing research and teaching in
>
: dependency_libs depended-on
zbar: dependency_libs depended-on
zinnia:
zorp: dependency_libs depended-on
zvbi:
zziplib: dependency_libs depended-on
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aybe better to not trigger
the creation of the meta-package with the generalist network drawing packages.
Alternatively, a purely graph-oriented metapackage could be made for debian
science, and med-bio-systems could depend on it later.
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htt
Le Mon, Aug 24, 2009 at 11:35:18AM +0200, Andreas Tille a écrit :
> On Mon, Aug 24, 2009 at 06:27:05PM +0900, Charles Plessy wrote:
> > these programs could be used to generate pictures similar to what you can
> > see in the following Google images search:
> >
> > http
e images search:
http://images.google.com/images?q=biological+network
Unsurprisingly, the packaged ones are generalist tools, while the ones for
biologists are not yet packaged. This said, given how Java is popular among
them, there was a good reason until the Lenny release.
Have a nice day,
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ever, I do not think that altree 1.1.0 should be packaged : they
> are still bugs in the new method added in altree 1.1.0 and the doc is not
> updated.
Good to know. Just ping us on this list or through the BTS when you thing a new
upstream release is ready for upload.
Have a nice week-end,
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to ask plenty of questions, and many thanks for offering your
help.
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ed by other software? If yes, I will try to RFP it first and see if
there are volunteers on debian-scie...@l.d.o.
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them.
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ee that it is time to remove biomode from Debian.
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u when I will split the biology task file, but I am not
sure when I will start this.
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with a su
Le Sun, Aug 09, 2009 at 12:08:54PM +0900, Charles Plessy a écrit :
>
> time flies fast and we are already between one third and the half of this
> release cycle. I propose that we discuss what are the goals that we would like
> to acheive in Debian Squeeze.
OK, I guess it is my
Le Mon, Aug 10, 2009 at 04:21:40PM +0200, Mathieu Malaterre a écrit :
> On Mon, Aug 10, 2009 at 6:54 AM, Charles Plessy wrote:
>
> > (And for the licensing of the packaging, I always recommend to use the same
> > terms as upstream's work unless the upstream license is non-
erimental instead of unstable until Upstream releases a first stable
version.
(And for the licensing of the packaging, I always recommend to use the same
terms as upstream's work unless the upstream license is non-free).
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http://
;,\n"' | sed 's/guest@/gu...@alioth./'
I hope your mailboxes will forgive me.
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Package: wnpp
Severity: wishlist
Owner: Charles Plessy
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
Programming Lang: C, Perl
up a more detailed proposal, and submit it on
-blends and -science and then on -devel.
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with a subj
Le Sat, Aug 01, 2009 at 11:29:18PM +0900, Charles Plessy a écrit :
>
> I think that the issue of managing package metadata goes beyond homepage and
> registration, I propose to start a discussion on the subject on debian-devel,
> and to fall back on using the debian/control
calloc ( 2*(N+1) , sizeof(char) ) ) ;
+
+ assert ( SIZE_MAX >> 1 >= (M+1) ) ;
+ Show_A = (char *) calloc ( 2*(M+1) , sizeof(char) ) ;
+ assert ( Show_A ) ;
+ Show_B = (char *) calloc ( 2*(N+1) , sizeof(char) ) ;
+ assert ( Show_B ) ;
D [0] [0] = 0;
Op [0] [0] = 'a';
Have
Le Thu, Jul 30, 2009 at 11:25:02PM +0200, Andreas Tille a écrit :
> I was wondering how we might come up
> with some resonable default for command line applications. The only idea
> I had was to call the application by using the option which prints some
> help screen. This gives two pieces of inf
o start a discussion on the subject on debian-devel,
and to fall back on using the debian/control file if this discussion is not
fruitful.
The key problem is that the metadata can evolve independantly of the source
code, and that updating the binary packages just for changing URLs is not
suitable.
Hav
Le Tue, Jul 28, 2009 at 12:50:08PM +0100, James Bonfield a écrit :
>
> Following on from this I'm pleased to say the upstream staden-read
> library now has incorporated full libtool support and I hope
> appropriate versioning too. (Thanks Charles for the patches.)
Thank you very much, I have upda
Le Wed, Jul 29, 2009 at 02:00:35PM +0200, Steffen Moeller a écrit :
>
> In principle, Debian-Med could have its own PayPal account to collect
> donations, but this would take much of the fun away, I think. Money should
> go to upstream directly and unconditionally.
Hi Steffen,
I think that there
al solution.
Have a nice day,
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let us know if you find a more complex alternative that you would like
to see redistributed in Debian.
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ill reach the archives and our metapackages are
rebuilt (this is not automatic). This metapackage contains Pondus, Cycle and
Mencal, which are other tools oriented at the end-user and not the doctor.
If you are looking for a place to store your source package, it is welcome in
our team’s reposi
rtbug for reporting bug, what tool can I use for this kind of
> task ?
Hi Mathieu,
I completely overlooked that version information may be manipulable by
pseudoheaders, and do this usually with control commands (the ones we CC to
cont...@bugs.debian.org).
Have a nice day,
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> On Fri, May 29, 2009 at 02:25:26PM +0900, Charles Plessy wrote:
> > I almost finished to package Staden's io_lib. In contrary to Upstream's
> > defaults, the Debian package builds a dynamic library. Could somebody help
> > me
> > to figure out the Right
Package: wnpp
Severity: wishlist
Owner: Charles Plessy
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 structure is trivial
Le Mon, Jul 06, 2009 at 11:38:51AM -0500, Boyd Stephen Smith Jr. a écrit :
> In <20090704120642.gh6...@kunpuu.plessy.org>, Charles Plessy wrote:
> >we have a patch in the Debian package mummer for which we lost origin and
> >detailed description. I would like to forward it
Package: plink
Version: 1.06-1
Severity: serious
Justification: no longer builds from source
thanks
Le Sat, Jul 11, 2009 at 12:06:21PM +0200, Luk Claes a écrit :
> Charles Plessy wrote:
> > Le Fri, Jul 10, 2009 at 08:56:31PM +, DDPOMail robot a écrit :
> >> === plink:
>
Alioth users can gain write access to collab-maint by joining the group.
(DDs have write access by default so they do not need).
Have a nice day,
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Debian Med packaging team,
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Tsurumi, Kanagawa, Japan
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Hello everybody,
The 20th International Conference on Genome Informatics will be held at
PACIFICO YOKOHAMA, Japan on December 14-16, 2009.
Their call for poster and software demonstrations is open until October 1st.
http://giw.ims.u-tokyo.ac.jp/giw2009/cfposter.html
See you there ?
--
Charles
on mips and mipsel?
Have a nice week-end,
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Tsurumi, Kanagawa, Japan
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contradicts
Debian's goals of being usable on a broad range of hardwares. Also, it may
create the conditions for a buffer overflow.
Best regards,
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Tsurumi, Kanagawa, Japan
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a buffer overflow.
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Le Sat, Jul 04, 2009 at 09:14:46AM -0300, Nelson A. de Oliveira a écrit :
>
> It will dynamically allocate space for the strings, instead allocating
> a predefined size.
Hi Nelson,
thank you very much for the help.
And only now I found that you forwarded it upstream five years ago :)
https://so
//lists.debian.org/debian-devel/2005/06/msg00037.html
The take-home message is of course: DEP3 is good for you!
http://dep.debian.net/deps/dep3/
Have a nice day,
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Le Thu, Jul 02, 2009 at 09:20:47AM +0200, Andreas Tille a écrit :
> On Thu, Jul 02, 2009 at 01:47:12PM +0900, Charles Plessy wrote:
> > http://patch-tracking.debian.net/patch/series/view/mummer/3.20-3/01sm_src_tigr.diff
>
> See
>
>http://lists.debian.org/debian-med/2007
versions, or forward the Bourne versions
upstream and ask permission for using them?
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with a subject of
one version in Debian to build against at
a given time.
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e something temporally strange on
> ftp-master?
Hi Jan,
It is strange as the key 0CA6B4AA is in the DM keyring. Maybe it was a
temporary failure? I suggest to retry.
Good luck :)
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Debian Med packaging team,
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Tsurumi, Kanagawa, Jap
aging Team ’,
then that list gets copies of rejection emails.
http://lists.alioth.debian.org/pipermail/debian-med-packaging/2009-June/003961.html
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Le Tue, Jun 23, 2009 at 10:14:24AM +0200, Mathieu Malaterre a écrit :
> 'lo,
>
> I had some issue uploading another release of gdcm, and had to do a
> dcut to remove some old gdcm files and then another dupload ... gdcm
> 2.0.10-5 has been seating in the UploadQueue overnight, is this
> somethin
d sponsoring.
Have a nice day,
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packages have a very slow turnover.
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- 2.0.11: new output format incompatible with 2.0.10.
Have a nice day,
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he Debian archive is about the sonames. Are there values that you recommend,
or should Debian use values lower than 1 before you provide upstream support
for dynamic io_lib ?
Have a nice day,
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Debian Med packaging team,
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Tsurumi, Kanagawa, Japan
er on top
of them… Maybe Upstream updated his tarball without incrementing the version
number? Did they have this header when you prepared the package?
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tion? With
Seqan in Debian, we could then start to package Bowtie.
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Le Mon, May 25, 2009 at 06:09:58PM +0200, David Paleino a écrit :
> On Mon, 25 May 2009 23:01:08 +0900, Charles Plessy wrote:
>
> > I am sure that there would be a lot of experience and kudos to gain by
> > helping
> > us to establish a ‘blends+mr’ workflow. Actually
debian.net/debian/pool/main/s/staden-io-lib/staden-io-lib_1.11.6.1-1~rc1.dsc
Everything is of course in our Subversion repository as well.
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Package: wnpp
Severity: wishlist
Owner: Charles Plessy
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-io-lib
Section
Le Wed, May 27, 2009 at 10:04:28AM +0200, Andreas Tille a écrit :
> On Wed, May 27, 2009 at 10:25:53AM +0900, Charles Plessy wrote:
> > I uploaded a new upstream version of SeaView, which unfortunately became
> > non-free as it uses files from the PHYLIP package, that does not all
Le Wed, May 27, 2009 at 10:25:53AM +0900, Charles Plessy a écrit :
>
> All of this is reflected in debian/copyright and the seaview(1) manual page.
… That I will commit this evening because I forgot this morning.
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have
triple-checked with Upstream that an exemption is given to use the
GPL-incompatible files.
All of this is reflected in debian/copyright and the seaview(1) manual page.
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ebian.org/developer.php?packages=clamtk+bpython+…
If he complains, send him to us so that we can tell him how happy we are to
work with you :)
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for all the packages we recommend in
our Blend, not only the ones we package by ourselves.
Have a nice sunday,
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with a
important package for many people.
*OTOH, there was a stable release with a long freeze during this time
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=
"Imagination is more important than knowledge" A.Einstein
----- End forwarded message -
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am the lead
uploader. Commits are much appreciated.
I will maybe have some free time the 10th in the afternoon and the evening. If
some Debian enthousiasts are located are located around Cold Spring Harbor, I
would be happy to meet them.
Have a nice day
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Debian Med packaging
Le Sat, May 02, 2009 at 11:35:49PM +0900, Charles Plessy a écrit :
>
> 2) Epigrass has a new major release, but the tarball strangely misses many
> files. I have tried to contact Upstream in a Launchpad where he asks for the
> update of the Ubuntu package.
>
> https://bugs.la
that
would happen to be helpful for understanding better the current flu variant,
please let us know.
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Le Fri, May 01, 2009 at 02:48:24PM +0200, Andreas Tille a écrit :
> On Thu, 30 Apr 2009, Charles Plessy wrote:
>
>> Modified: trunk/packages/phyml/trunk/debian/changelog
>> ===
>> --- trunk/packages/phym
Dear all,
I recommend to have a look to Sean Eddy's slides on his blog:
http://selab.janelia.org/people/eddys/blog/?p=123
I am sure that Debian Med is well on the way to fit somewhere in the big
picture.
Have a nice day,
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Debian Med packaging team,
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Hi all,
Le Fri, Apr 24, 2009 at 04:10:59PM +0200, Steffen Moeller a écrit :
> Package: wnpp
> Severity: wishlist
> Owner: Steffen Moeller
>
> * Package name: profit
> * License : non-free, non-redistributable
“ProFit is freely available for use by not-for-profit organisations”
Mayb
.
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Hi all,
I added the following advertisement for the proposed GSoC projects this year:
http://www.debian.org/devel/debian-med/News/2009/20090328
Feel free suggest any necessary correction.
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e
other project in getting accepted.
Lastly, as a caveat I must say that to use the Amazon computer cloud, one has
to install some non-free software written in Java…
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Hi all,
I registered my GPG key in the backports.org system. Please let me know in the
future when there is user demand for some backports.
Have a nice week-end,
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Le Fri, Mar 27, 2009 at 02:22:35PM +0100, Andreas Tille a écrit :
>
> the raise of several R packages which are also useful for medical
> applications lets me wonder whether we should create a statistics
> task. I'd regard
>
> r-cran-qvalue
> r-cran-randomforest
>
> would be perfect target
Le Thu, Mar 26, 2009 at 10:24:41PM +0100, Andreas Tille a écrit :
>
> you did not answered this request from Charles. Please keep
> us informed if you do something about this or whether somebody
> of us should contact the author. Please keep in mind the
> more work you might take from our shoulde
actually lacking BioCocoa 1 itself.
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Most of them do not have a biological background, so take this
into account when answering, and when writing your application.
Good luck, and do not hesitate to ask as many questions as you like on this
list.
Have a nice day,
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g-exppsy/odin.git gives an empty
directory… is 'git checkout debian/1.7.0-1' the correct command to populate it?
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ll we remove it from Alioth? We did the
same for pkg-emboss some time ago. I can browse the list archives, identify the
monthes that are 100% spam, and backup the rest in another place, such as
Debian Med's Alioth web site.
Have a nice day,
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Debian Med packaging team,
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t make sense to have a Debian package for cran2deb, or is it too early?
Have a nice day,
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Le Mon, Mar 16, 2009 at 10:45:06PM +0100, Andreas Tille a écrit :
>
> I admit I'm keen on seeing a bioc2deb and I would even consider
> baby sitting the resulting packages through new etc - perhaps Charles
> Plessy might share some experiences from Debian Perl group how they ha
Hi all,
I uploaded PhyML to NEW.
For peer-review purposes, I uploaded an exact copy to Mentors:
http://mentors.debian.net/debian/pool/main/p/phyml/
Have a nice day,
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Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
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let you know, so that we can package the necessary Perl
modules. This will take us a few weeks as well anyway.
Have a nice day,
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Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
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kage, if
> I understood it.
> But there are packages that aren't available on Debian, like
> libcgi-validop-perl
Hi all,
I have packaged a lot of Perl libraries recently and could do the job quite
quiclky if the source package of elementalclinic is uncovered.
Have a nice day,
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Le Sat, Feb 28, 2009 at 06:15:35PM +0100, Steffen Moeller a écrit :
> Hi Charles,
>
> Charles Plessy wrote:
> > I would like to start a discussion about the possiblity to propose
> > project(s)
> > for the Google Summer of Code 2009. Last year the project I proposed
the bottom-up approach for the defintion of the project. Any idea ?
Of course, if you have a strong interst in the Summer of Code, do not hesitate
to candidate as a mentor as well.
Have a nice day,
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Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi
Package: wnpp
Severity: wishlist
Owner: Charles Plessy
Hello everybody,
Here is another Perl library that is needed for the Generic Genome Browser
(version 2).
I will inject the package soon in the pkg-perl repository.
Have a nice day,
-- Charles Plessy
Source: libgd-svg-perl
Section: perl
Package: wnpp
Severity: wishlist
Owner: Charles Plessy
Hello everybody,
I intend to package Phyml, as it is necessary for upgrading SeaView to version
4.0. As usual, the source of the PDF manual was omitted from the Upstream
tarball. I am working on this issue.
Have a nice day,
-- Charles
Le Sat, Feb 14, 2009 at 05:18:21PM +0100, Andreas Tille a écrit :
>
> Do you intend to copy dmstats1.pdf and authorstat_med.pdf to devel/debian-med
> or would you use explicite links? Currently the links are not working.
Hi Andreas,
I just commited the corrected WML document with the PDF files i
Hi all,
After a five-month lapse, I tried to finish the redaction of the news for the
release of Debian Med for Lenny. I attached the WML source to this email.
Have a nice day,
(and let's keep finger crossed ;)
--
Charles
What is new for Debian Med in Lenny ?
2009-02-15
#use wml::debian::news
Le Wed, Feb 11, 2009 at 09:34:26PM +0100, Andreas Tille a écrit :
> Hi,
>
> I like to foreward this ITP for your interst. Does anybody think
> that we should mention this in our metapackages and which one
> might be the best?
Hi Andreas,
I think we should leave it out unless we have a user reque
Hi Andreas,
Le Wed, Feb 11, 2009 at 11:49:41AM +0100, Andreas Tille a écrit :
> ...
> AddLanguage pl .pl
> ...
>
> which works for all languages except for Polish.
Maybe because it looks like perl script ?
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Charles
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Le Tue, Feb 10, 2009 at 10:45:47PM -0600, Lukasz Szybalski a écrit :
> On Tue, Feb 10, 2009 at 8:57 PM, Charles Plessy wrote:
> >
> >> ps. As a side note, it would be grate if debian had a working .deb files
> >> for
> &g
t is something to keep in mind, especially if
infrastructure makes it transparent. Can debtorrent work with the torrenting
facilities of the Amazon Simple Storage system ?
Lastly, BitTorrent is strictly forbidden in some workplaces (like where I
work), so it will have to be optional.
Have a nice d
ti effect. But
be sure that I welcome all feedback!
Have a nice day,
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Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
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I am exploring the possibility to to use it to produce binary
packages but no source packages. Would it be compatible with your plans?
Have a nice day,
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Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
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al public and our future users.
PS: if you think the above information is missing from the wiki, please feel
free to paste it :)
Have a nice day,
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Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
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is example needs CDBS)
Have a nice day,
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Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
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