Re: blast+ packaging

2011-05-29 Thread Olivier Sallou
Hi, please feel free to commit in my dir. It will indeed be easier than merging. Your deep knowledge of compilation stuff of blast is one of the reason I asked you to review the package. I am sure that your updates will be perfect. For dir updates, be it ncbi-blast+ or ncbi-blast-plus, I would ra

Re: trouble committing to svn.d.o/svn/debian-med

2011-05-29 Thread Stephen Gran
This one time, at band camp, Aaron M. Ucko said: > [Sorry if this is a known issue; I don't run IRC.] > > I'm trying to commit some changes to the debian-med Subversion > repository. The first few went through fine (most recently at 18:56 > UTC), but since then I've been hitting permission errors

bmaj watcher packaging

2011-05-29 Thread Olivier Sallou
Hi, following your remarks, I am looking at adding binary dependencies source code. However, after a look, source dependency is quite huge (GWT/SmartGWT, others are fine). I wonder if I really need to add source code for those in my package, or if a reference to source code URL would be fi

Re: blast+ packaging

2011-05-29 Thread George Marselis
since we are on the subject, i have been trying to compile ncbi-blast on my own, for my own use. i would like to enable ever single one of it's features; eg, UUIDs . or xalan. I cannot find any info on how to activate UUIDs (it's not an option in ./configure --help) and I cannot find the proper de

Re: blast+ packaging

2011-05-29 Thread Olivier Sallou
Hi, are you talking of blast or blast+ ? Regarding features, I do not see what you mean by xalan feature, or uuid (sounds like java packages). Olivier - Mail original - > De: "George Marselis" > À: "Debian Med Project List" > Envoyé: Dimanche 29 Mai 2011 13:57:28 > Objet: Re: blast+ p

Re: libbam-dev ships sam.h in /usr/include/samtools

2011-05-29 Thread Charles Plessy
Dear Alex, I reviewed the licenses in the sources of Cufflinks and found that the files under src/locfit are not free, because their license forbids to make benchmarks… http://anonscm.debian.org/gitweb/?p=debian-med/cufflinks.git;a=blob;f=debian/copyright;h=af50c87d0a97f9db7c35b77e7af3f9ee321d4f6

Re: blast+ packaging

2011-05-29 Thread George Marselis
ncbi-blast+ . am I mistaken? On Sun, May 29, 2011 at 3:04 PM, Olivier Sallou wrote: > Hi, > are you talking of blast or blast+ ? > > Regarding features, I do not see what you mean by xalan feature, or uuid > (sounds like java packages). > > Olivier > > - Mail original - >> De: "George Ma

Re: blast+ packaging

2011-05-29 Thread Aaron M. Ucko
Olivier Sallou writes: > please feel free to commit in my dir. It will indeed be easier than merging. Done, thanks. I also threw in some improvements to the copyright file that I'd meant to propose earlier: * Remove the stanza for (c++/)scripts/projects/xmlwrapp/*, whose LICENSE file documen

Re: rev 6863 (Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6)

2011-05-29 Thread Sebastian Hilbert
Am Sonntag, 29. Mai 2011, 05:27:08 schrieb Steve M. Robbins: > On Sat, May 28, 2011 at 05:45:26PM +0200, Andreas Tille wrote: > > On Sat, May 28, 2011 at 05:29:35PM +0200, Mathieu Malaterre wrote: > > > I tried building Ginkgo-CADx and it looks ok to me now. So I agree > > > with question r6861 :)

Re: rev 6863 (Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6)

2011-05-29 Thread Steve M. Robbins
On Sun, May 29, 2011 at 08:51:45PM +0200, Sebastian Hilbert wrote: > Am Sonntag, 29. Mai 2011, 05:27:08 schrieb Steve M. Robbins: > > OK, I built and uploaded it. > Thanks a lot. > > http://ftp-master.debian.org/new.html > > When does it usually show up ? In this specific instance, unfortunate

Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6

2011-05-29 Thread Carlos Barrales
Hi Mathieu, We have not a exact release date planed yet, but it could be during next month. For sure, the debian directory will be removed. Kind Regards. -- Carlos Barrales Ruiz. MetaEmotion HealthCare. carlos.barra...@metaemotion.com http://healthcare.metaemotion.com On Sat, May 28, 2011 at 8:

Final take on Ginkgo-CADx - any volunteer (Was: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6)

2011-05-29 Thread Andreas Tille
Hi On Mon, May 30, 2011 at 08:27:26AM +0200, Carlos Barrales wrote: > We have not a exact release date planed yet, but it could be during next > month. > For sure, the debian directory will be removed. Great. Anyway, is there any volunteer to work down the copyright issues mentioned in the rejec

Re: rev 6863 (Re: Ginkgo-CADx package - was: Install on ubuntu 10.04.2 or debian 6)

2011-05-29 Thread Andreas Tille
Hi, I just added the Build-Depends in SVN to make sure the build will not fail on testing machines. Hoping for somebody who cares about the copyright file now ... Kind regards Andreas. On Sun, May 29, 2011 at 08:03:52AM +0200, Andreas Tille wrote: > On Sat, May 28, 2011 at 06:06:04PM +0