Re: Problems with libmtj-java and new version of beast-mcmc

On 09/04/2015 08:04 AM, Andreas Tille wrote: > On Fri, Sep 04, 2015 at 05:09:45AM +, olivier sallou wrote: >>> Do you want me to work on the todo list (which looks a bit scary to me - >>> but I might try to have a look). >> Nope, for the moment I will continue. >> But will take time. It needs

Re: Trinityrnaseq status

On 08/22/2015 09:34 PM, Michael Crusoe wrote: > On Sat, Aug 22, 2015 at 6:49 AM Andreas Tille > wrote: > > Hi, > > On Sat, Aug 22, 2015 at 12:57:20AM +, Michael Crusoe wrote: > > > > trinityrnaseq: waiting on libjung-free-java, rsem, express, and >

Re: Help needed to update to latest fastqc

On 08/22/2015 03:35 PM, Andreas Tille wrote: > Hi, > > On Sat, Aug 22, 2015 at 08:27:39AM +, olivier sallou wrote: >> As libsis-base-java and libsis-jhdf5-java are in our git repo and seem to >> be fine, you may want to build/install them locally to test your fastqc >> update ? >> >> As it ma

Re: libsis-base-java switched to git

libsis-jhdf5 is on git: Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/libsis-jhdf5-java.git Vcs-Git: git://anonscm.debian.org/debian-med/libsis-jhdf5-java.git I have updated DEP3 patches headers and a few things. Should we for upload of sis-base and sis-jhdf5 ? Olivier On 08/21/

Re: libjung-java build to be in free

On 08/21/2015 11:26 AM, Andreas Tille wrote: > On Fri, Aug 21, 2015 at 08:21:02AM +, olivier sallou wrote: >> Hi, >> to avoid dependency licensing issue of libjung (related to dependency >> libjai-core-java), we could package libjung with the removal >> of jung-jai-contrib-2.0.1-sources >> an

Re: Lena licensing, how to patch?

On 08/20/2015 10:05 PM, Ghislain Vaillant wrote: > On 20/08/15 20:54, olivier sallou wrote: >> Hi, >> I have a colleague who have the lena image licensing issue in his >> package. >> He tried to patch it but get fuzzing issue when building the package. >> As it is a binary file and never patched

Re: python-cobra seems to resist backporting :-( [python-cobra_0.4.0b2-1~bpo8+1_amd64.changes REJECTED]

On 08/17/2015 01:39 PM, Andreas Tille wrote: > I've never seen this. :-( > > Any idea > Andreas. > > - Forwarded message from Debian FTP Masters > - > > Date: Mon, 17 Aug 2015 09:22:57 + > From: Debian FTP Masters > To: Debian Med Packaging Team , > Afif Elghraoui > , t

Re: Help needed to update to latest fastqc

lp (failed to instanciate). If you want to have a look I gonna continue ot investiguate. Olivier > > Cheers, > > TIM > > On Fri, 2015-08-14 at 08:16 +0200, olivier.sal...@codeless.fr wrote: >> On 08/13/2015 05:20 PM, Tim Booth wrote: >> >>> Hi Olivier, >

Re: Help needed to update to latest fastqc

On 08/13/2015 05:20 PM, Tim Booth wrote: > Hi Olivier, > > Looks like Bernd Rinn is making positive noises regarding a DFSG version > of the library, so hopefully once he provides code you can take what I > have done and make use of it. I committed to SVN because it's so much > easier than pushing

Re: Help needed to update to latest fastqc

On 08/12/2015 08:43 PM, Tim Booth wrote: > Hi, > > After a fair amount of struggling I conclude that I do not have all the > code required to build this thing from source. > > The distribution of JHDF5 from > https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=26609113 > contains some Java sou

Re: Help needed to update to latest fastqc

On 08/12/2015 12:44 PM, Tim Booth wrote: > Hi Andreas and Olivier, > > I'm going to have a crack at the FastQC update. I've been poking at the > HDF5 packages and here are my conclusions so far: I already had a look and started some work. In fact I expected to progress on it during Debconf, but

Re: python-cobra 0.4.0b2 ready for upload

On 08/10/2015 02:50 PM, Andreas Tille wrote: > On Mon, Aug 10, 2015 at 09:16:26PM +0900, Charles Plessy wrote: >> Le Mon, Aug 10, 2015 at 02:28:37AM -0700, Afif Elghraoui a écrit : >>> Hi, Andreas, >>> I've completed packaging the latest upstream release of python-cobra. >>> Would you be able to

Re: python-cobra 0.4.0b2 ready for upload

On 08/10/2015 02:50 PM, Andreas Tille wrote: > On Mon, Aug 10, 2015 at 09:16:26PM +0900, Charles Plessy wrote: >> Le Mon, Aug 10, 2015 at 02:28:37AM -0700, Afif Elghraoui a écrit : >>> Hi, Andreas, >>> I've completed packaging the latest upstream release of python-cobra. >>> Would you be able to

Re: fastq status?

On 05/14/2015 06:22 PM, Andreas Tille wrote: > On Thu, May 14, 2015 at 08:57:43AM +0200, olivier.sal...@codeless.fr wrote: >>> Debian Science team. In other words: While you stated that what we >>> need is probably a different code base than we need for fastqc the >&g

Fwd: Re: fastq status?

CC'ing list... Forwarded Message Subject:Re: fastq status? Date: Thu, 14 May 2015 08:57:43 +0200 From: olivier.sal...@codeless.fr To: Andreas Tille On 05/13/2015 10:43 AM, Andreas Tille wrote: > Hi Olivier, > > On Wed, May 13, 2015 at 05

Re: DebianMed Sprint network issue

On 12/12/2014 11:36 AM, Andreas Tille wrote: > Hi, > > On Fri, Dec 12, 2014 at 09:48:00AM +0100, olivier.sal...@codeless.fr wrote: >>> If it helps I can send you a pair of PowerLAN adapters. >> I tried to propose this solution but it seems that their box is too far >

Re: DebianMed Sprint network issue

On 12/11/2014 04:09 PM, Andreas Tille wrote: > Hi Olivier, > > On Thu, Dec 11, 2014 at 12:29:12PM +, olivier sallou wrote: >> Hi, >> I just talked with the hotel and they still have wifi access issues (though >> it was supposed to be solved). So it is almost plain sure that wifi won't >> be ac

Re: DebianMed Sprint network issue

On 12/11/2014 05:48 PM, Sebastian Hilbert wrote: > Am Donnerstag, 11. Dezember 2014, 17:33:44 schrieb Karsten Hilbert: >> On Thu, Dec 11, 2014 at 04:09:34PM +0100, Andreas Tille wrote: I just talked with the hotel and they still have wifi access issues (though it was supposed to be

Re: Licensing terms for data derived from ARB/SILVA data

On 11/29/2014 12:29 PM, Sascha Steinbiss wrote: > Hi all, > >>> But we would like to ask you to clearly indicate that the profiles are >>> only free for non-commercial usage, commercial users need a licence. >>> The easiest approach is to add a reference to the SILVA terms of >>> license assigned t

Re: Licensing terms for data derived from ARB/SILVA data

On 11/28/2014 04:48 PM, Frank Oliver Glöckner wrote: > Dear Sascha Steinbiss, > thanks for the information. > We discussed it and in general we agree that the HMM profiles derived > from LSURef_115_tax_silva_full_align_trunc.fasta can be distributed. > But we would like to ask you to clearly indic

Re: Need some help for Java package

On 02/09/2014 12:57 AM, Andreas Tille wrote: > Hi, > > On Sat, Feb 08, 2014 at 06:12:07PM +0100, olivier.sal...@codeless.fr wrote: >>> I found some reference here: >>> >>>http://bioinf.hutton.ac.uk/tablet/svn.txt >>> >>> which belongs to

Next sprint proposal

Hi, sorry if mail is a duplicate, I had an issue when I sent my previous mail. After our nice sprint in Stonehaven, I come with a proposal (well ideas in fact) for the next sprint in France. There are several options: 1) in Brittany, in Saint Malo [0]. This is a really nice place (old town from

Re: Need some help for Java package

On 02/08/2014 04:54 PM, Andreas Tille wrote: > Hi Olivier, > > On Sat, Feb 08, 2014 at 09:11:15AM +0100, olivier.sal...@codeless.fr wrote: >> I've gone furher, remove cplex, but there is still an issue. Code >> references: >> >> CigarParser.extractAllAlignDi

Re: Need some help for Java package

On 02/08/2014 10:57 AM, Andreas Tille wrote: > Hi again, > > On Sat, Feb 08, 2014 at 09:11:15AM +0100, olivier.sal...@codeless.fr wrote: >>> I gonna test this. >> I've gone furher, remove cplex, but there is still an issue. Code >> references: >> >>

Re: Need some help for Java package

On 02/08/2014 08:42 AM, olivier.sal...@codeless.fr wrote: > On 02/08/2014 12:16 AM, Andreas Tille wrote: >> Hi, >> >> I need to package a Java package without build system. I prepared the >> packaging at >> >> git://anonscm.debian.org/debian-med/giir

Re: Need some help for Java package

On 02/08/2014 12:16 AM, Andreas Tille wrote: > Hi, > > I need to package a Java package without build system. I prepared the > packaging at > > git://anonscm.debian.org/debian-med/giira.git > > and need to reconstruct the file GIIRA.jar which is part of > > http://sourceforge.net/projects

Re: Need some help for Java package

On 02/08/2014 12:16 AM, Andreas Tille wrote: > Hi, > > I need to package a Java package without build system. I prepared the > packaging at > > git://anonscm.debian.org/debian-med/giira.git > > and need to reconstruct the file GIIRA.jar which is part of > > http://sourceforge.net/projects

Re: Chances for cooperation between OSDDLinux and Debian

On 11/21/2013 02:00 PM, Andreas Tille wrote: > Hi Raghava, > > On Thu, Nov 21, 2013 at 04:40:52PM +0530, G P S Raghava wrote: >> Dear Andreas >> >> Thanks for your email and detail response to my quiries. We have >> created debian package for our number of software, though they are not >> perfect

Re: (Java-)Help with ne version of igv needed

On 09/13/2013 08:57 PM, Andreas Tille wrote: > Hi Olivier, > > On Fri, Sep 13, 2013 at 05:02:14PM +0200, Olivier Sallou wrote: >> hi, >> I just updated the git repo on my computer and tried a build, and it >> works fine, I could build the package. >> However, I had to download the upstream tar wit

bugs about "crashed with exit code 139"

Hi, you all have seen many many bugs from forallsecure, getting all the same crash exit code. Does anymore has a hint on the root cause of this? I can't imagine this does not come from the same root cause considering the numerous bugs found. Olivier -- gpg key id: 4096R/326D8438 (keyring.debia

IGV package ready

Hi Andreas, the package libbc-prov dependency update I was waiting for has been done. I have made a few updates on IGV and it should be "ok" now for non-free. However, dependency has been pushed to experimental. As IGV will go to non-free, it will have to be pushed to non-free/experimental too. D

Re: [z...@debian.org: Availability of Debian official cloud images from debian.org]

Le 3/16/13 6:40 AM, Charles Plessy a écrit : > Le Fri, Mar 15, 2013 at 09:25:55AM +0100, olivier.sal...@codeless.fr a écrit : >> Le 3/15/13 8:13 AM, Andreas Tille a écrit : >>> Hi, >>> >>> any volunteer to join this effort to create such images featuring >&g

Re: [z...@debian.org: Availability of Debian official cloud images from debian.org]

Le 3/15/13 8:13 AM, Andreas Tille a écrit : > Hi, > > any volunteer to join this effort to create such images featuring > med-cloud packages? What would be a med-cloud image ? (but an image containing med-cloud packages) I would gladly help such thing with debian-cloud team when debian-cloud team

Re: FWD Next BioPerl release

Le 2/6/13 5:43 AM, Charles Plessy a écrit : > Hi all, > > for your information, there is a new BioPerl release scheduled soon. > > I a still very busy at work and may not be able to push it in Debian quickly. > Also, we need to ensure compatibility with the reverse dependancies. What do you propos

Re: please upgrade libbio-graphics-perl

Le 12/15/12 9:37 AM, Charles Plessy a écrit : > Le Sat, Dec 15, 2012 at 09:15:59AM +0100, olivier.sal...@codeless.fr a écrit : >> could you please upgrade libbio-graphics-perl? New GBrowse needs at >> least v2.31. >> >> If you do not have time, please tell me and I

Re: please upgrade libbio-graphics-perl

Le 12/15/12 9:37 AM, Charles Plessy a écrit : > Le Sat, Dec 15, 2012 at 09:15:59AM +0100, olivier.sal...@codeless.fr a écrit : >> could you please upgrade libbio-graphics-perl? New GBrowse needs at >> least v2.31. >> >> If you do not have time, please tell me and I

please upgrade libbio-graphics-perl

Hi Charles, could you please upgrade libbio-graphics-perl? New GBrowse needs at least v2.31. If you do not have time, please tell me and I 'll try to update it myself. Thanks Olivier -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB

Re: Fwd: RFS: scscp-imcce/0.7.0+ds-1 [ITP] -- IMCCE SCSCP C Library

Le 8/28/12 10:54 PM, Jerome BENOIT a écrit : > Hello: > > On 28/08/12 12:16, olivier.sal...@codeless.fr wrote: >> >> Le 8/28/12 12:12 PM, Steffen Möller a écrit : >>> Hello, >>> >>> I am totally swamped, but also like seeing so many astronom

please upgrade libbio-graphics-perl

Hi Charles, would you mond upgrading libbio-graphics-perl to latest version? I need at least version 2.28 (current 2.29) for gbrowse. Thanks Olivier -- gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, em

Bug#686938: ITP: libvm-ec2-perl

Package: wnpp Severity: wishlist Owner: Olivier Sallou X-Debbugs-Cc: debian-med@lists.debian.org * Package name: libvm-ec2-perl Version : 1.17 Upstream Author : Lincoln D. Stein * URL : http://search.cpan.org/~lds/VM-EC2-1.02/ * License : Artistic 1 and GPL-1

Re: libsnappy1.0.3 and picard-tools ok

Le 9/6/12 6:59 AM, Charles Plessy a écrit : > Le Mon, Sep 03, 2012 at 08:53:39AM +0200, Olivier Sallou a écrit : >> I have just uploaded libsnappy1.0.3-java_1.0.3-rc3~dfsg-3 which does >> not conflict anymore on maven repo. >> >> I use it against picard-tools, with additiona patches for jbzip2 u

Re: snappy uploaded and picard-tools can be build against it

Le 8/29/12 7:07 AM, Charles Plessy a écrit : > Le Tue, Aug 28, 2012 at 12:49:59PM +0200, olivier.sal...@codeless.fr a écrit : >> Hi, >> I have uploaded libsnappy1.0.3-java package for picard-tools. >> I could successfully build picard-tools with this package. >> >&

Re: snappy uploaded and picard-tools can be build against it

Le 8/29/12 7:07 AM, Charles Plessy a écrit : > Le Tue, Aug 28, 2012 at 12:49:59PM +0200, olivier.sal...@codeless.fr a écrit : >> Hi, >> I have uploaded libsnappy1.0.3-java package for picard-tools. >> I could successfully build picard-tools with this package. >> >&

Re: snappy uploaded and picard-tools can be build against it

Le 8/28/12 2:36 PM, Andreas Tille a écrit : > On Tue, Aug 28, 2012 at 12:49:59PM +0200, olivier.sal...@codeless.fr wrote: >> Hi, >> I have uploaded libsnappy1.0.3-java package for picard-tools. >> I could successfully build picard-tools with this package. > Cool. Tha

fixed picard-tools

Hi, I have updated picard-tools on Debian git to use libsnappy1.0.3. I updated the patches and files to use version 1.75 (latest). Package build correctly, however it would be fine to test the package (I do not know picard-tools) before uploading it. Charles, could you have a look? Thanks Olivi

snappy uploaded and picard-tools can be build against it

Hi, I have uploaded libsnappy1.0.3-java package for picard-tools. I could successfully build picard-tools with this package. picard-tools still need to be updated to get latest release and use snappy1.0.3-java.jar file (update of the patch) Olivier -- gpg key id: 4096R/326D8438 (keyring.debia

Re: status on picard-tools and issue with libsnappy-java

Le 8/14/12 10:57 AM, Andreas Tille a écrit : > Hi, > > On Tue, Aug 14, 2012 at 09:06:46AM +0200, olivier.sal...@codeless.fr wrote: >> Le 8/13/12 1:35 PM, Andreas Tille a écrit : >>> On Mon, Aug 13, 2012 at 08:07:22PM +0900, Charles Plessy wrote: >>>> For libsna

Re: status on picard-tools and issue with libsnappy-java

Le 8/14/12 10:57 AM, Andreas Tille a écrit : > Hi, > > On Tue, Aug 14, 2012 at 09:06:46AM +0200, olivier.sal...@codeless.fr wrote: >> Le 8/13/12 1:35 PM, Andreas Tille a écrit : >>> On Mon, Aug 13, 2012 at 08:07:22PM +0900, Charles Plessy wrote: >>>> For libsna

Re: status on picard-tools and issue with libsnappy-java

Le 8/13/12 1:35 PM, Andreas Tille a écrit : > On Mon, Aug 13, 2012 at 08:07:22PM +0900, Charles Plessy wrote: >> For libsnappy-java, since it still only has 10 Popcon users, of which I >> already >> contribute 2 or 3 points because I develop on multiple machines, we can also >> do >> something v

Re: Ping: Help for non-technical task needed (Was: License of colt [colt_1.2.0~dfsg-1_amd64.changes REJECTED)

Le 8/13/12 10:58 AM, Andreas Tille a écrit : > On Mon, Aug 13, 2012 at 09:15:47AM +0200, olivier.sal...@codeless.fr wrote: >>>> I have sent a message via Facebook to one of the author but I am afraid >>>> that it will be complicated >>> Any answe

Re: status on picard-tools and issue with libsnappy-java

Le 8/13/12 11:08 AM, Andreas Tille a écrit : > On Mon, Aug 13, 2012 at 09:27:50AM +0200, olivier.sal...@codeless.fr wrote: >> I copy below the answer from upstream team. >> They will not go to latest snappy version. Seems it was quite difficult >> to integrate it and fa

status on picard-tools and issue with libsnappy-java

I copy below the answer from upstream team. They will not go to latest snappy version. Seems it was quite difficult to integrate it and faced issues. The problem is snappy-java 1.0.4 breaks its API and is not compatible with version 1.0.3 used by picard-tools. At runtime, picard-tools tries to de

Re: Ping: Help for non-technical task needed (Was: License of colt [colt_1.2.0~dfsg-1_amd64.changes REJECTED)

Le 8/10/12 2:18 PM, Andreas Tille a écrit : > Hi Olivier (or whoever else might lurk un FB) > > On Wed, Aug 01, 2012 at 11:07:53AM +0200, Olivier Sallou wrote: >>> Perhaps I'm wrong but I found the following: >>> >>> >>> http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libcolt-java/t

netlib-java not moving to testing

Hi, package netlib-java remains in unstable and has not moved to testing due to: libnetlib-java/i386 unsatisfiable Depends: f2j f2j, in non-free, is available as binary only on amd64. But I wonder why package does not move to testing if amd64 is available. Any idea of I should do to get it in tes

Re: use of json.org in biojava3-ws

Le 5/30/12 9:33 AM, Alexandre Rossi a écrit : > Hi, > >> I've already seen this library, but it is not a compatible API. >> I gonna ask to biojava team if they would go to using such library >> instead of org.json one... > For what it's worth, from the work I've begun doing on GWT, which had > t

Re: use of json.org in biojava3-ws

Le 5/29/12 6:30 PM, Steffen Möller a écrit : > On 05/29/2012 02:23 PM, Mehdi Dogguy wrote: >> On 29/05/12 14:17, Andreas Tille wrote: >>> On Tue, May 29, 2012 at 02:03:27PM +0200, Niels Thykier wrote: On 2012-05-29 13:59, Olivier Sallou wrote: > Hi, biojava3 makes use of json.org library

pdb2pqr

Hi all, I tried to get pdb2pqr to build and upload it. However, new version does not build at all (failure at install time). I think I will need Manuel help to get the package ready. I see that Makefile.in contains lots of options (@with_propka@,...), and as I do not know the program, I do not kno

Re: [Debichem-devel] Where to maintain pdb2pqr

Le 5/18/12 5:56 PM, Andreas Tille a écrit : > On Fri, May 18, 2012 at 12:16:04PM +0200, Michael Banck wrote: >> I believe it is best kept at team maintenance, either in the debian-med >> or the debichem repository, I do not particularly care which one, and as >> it is already in debian-med, it mi

Re: Where to maintain pdb2pqr

Le 5/16/12 9:38 AM, Andreas Tille a écrit : > Hi, > > I just noticed that pdb2pqr has set > > Maintainer: DebiChem Team > Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/pdb2pqr/trunk/ > > I do not mind what team finally cares for this package but having one > team set as maintainer

please update in alioth my login

Hi, I have now the DD status (thanks for those that help me), could you please update in alioth my login from osallou-guest to osallou in your respective projects? Thanks Olivier -- gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438

Bug#657832: ITP: mmtk -- Python molecular modelling toolkit

Package: wnpp Severity: wishlist Owner: Olivier Sallou X-Debbugs-Cc: debian-med@lists.debian.org * Package name: mmtk Version : 2.6.1 Upstream Author : Konrad Hinsen * URL : https://sourcesup.cru.fr/projects/mmtk/ * License : CeCILL C Programming Lang: C, P

Need someone to upload Chado

Hi, I have finished the Chado package, ready in SVN for a first upload and a volunteer to do so. There are several Lintian warnings raised. I added some explanation in Debian.source, especially regarding warning on non trap errors in postinst step (which are trapped in fact, but differently). Tes