Re: Lets maintain libbpp-phyl-omics in Debian Med team

Hi Julien, some of the libbpp packages now arrived in unstable. It would be great if you could try to reprocude the failures in the test cases. It might be sensible to rebuild libbpp-seq in a clean Debian unstable chroot. The build shows: # For the moment ignore: # 3/7 Test #3:

Re: Lets maintain libbpp-phyl-omics in Debian Med team

Hi Julien, On Wed, Apr 13, 2016 at 11:55:26AM +0200, Julien Yann Dutheil wrote: > Thanks a lot. Just need to know what I should include upstream to > facilitate the packaging of the next versions. I guess the more I can > include the easier it should be for you, right? No, please include no

Re: Lets maintain libbpp-phyl-omics in Debian Med team

Hi Julien, On Wed, Apr 13, 2016 at 10:00:19AM +0200, Julien Yann Dutheil wrote: > > I have started to compile the libs with gcc 6. So far I get no issue if I > add (-std=c++98) to the compiler arguments (-std=gnu14 begin the default in > g++6, as far as I understood). We're currently porting the

Re: Lets maintain libbpp-phyl-omics in Debian Med team

Hi Julien, On Mon, Apr 11, 2016 at 12:19:29PM +0200, Julien Yann Dutheil wrote: > > On Mon, Apr 11, 2016 at 09:10:00AM +0200, Julien Yann Dutheil wrote: > > > I will look at the bug (and try to compile with gcc6 for a check of all > > > libs. As for bpp-seq, I think it is because it needs some

GIt tags on Github (Was: Lets maintain libbpp-phyl-omics in Debian Med team)

Hi Julien, On Mon, Apr 11, 2016 at 12:16:54PM +0200, Julien Yann Dutheil wrote: > Dear Andreas, > > On Mon, Apr 11, 2016 at 10:50 AM, Andreas Tille wrote: > > > Hi Julien, > > > > > > > Just a pragmatic question: If I would like to include these in the 2.2.0 > > > version,

Re: Lets maintain libbpp-phyl-omics in Debian Med team

Dear Andreas, On Mon, Apr 11, 2016 at 10:50 AM, Andreas Tille wrote: > Hi Julien, > > > > Just a pragmatic question: If I would like to include these in the 2.2.0 > > version, how can I do that with tags? I mean, we created a dedicated > branch > > for each stable version so

Re: Lets maintain libbpp-phyl-omics in Debian Med team

Hi Julien, On Mon, Apr 11, 2016 at 09:10:00AM +0200, Julien Yann Dutheil wrote: > I will look at the bug (and try to compile with gcc6 for a check of all > libs. As for bpp-seq, I think it is because it needs some input files that > should be in the test folder too (eg example.fasta, example.aln

Re: Lets maintain libbpp-phyl-omics in Debian Med team

Hi Julien, On Sat, Apr 09, 2016 at 12:19:07AM +0200, Andreas Tille wrote: > > I've started with libbpp-core[1] which is now conform to Debian Med > policy and fixes two open bugs. I have not yet closed "FTBFS with GCC > 6: cannot convert x to y" [2]. It would be great if you as upstream >

Re: Lets maintain libbpp-phyl-omics in Debian Med team

Hi Julien, On Thu, Apr 07, 2016 at 08:57:48AM +0200, Julien Yann Dutheil wrote: > > Sorry, no. You push a tag to github (or whatever repository you might > > use) and uscan will recognise a new version. It will download the > > according tarball and this tarball will be used as source tarball

Re: Lets maintain libbpp-phyl-omics in Debian Med team

Dear Julien, On Thu, Apr 07, 2016 at 08:57:48AM +0200, Julien Yann Dutheil wrote: > > Sorry, no. You push a tag to github (or whatever repository you might > > use) and uscan will recognise a new version. It will download the > > according tarball and this tarball will be used as source tarball

Re: Lets maintain libbpp-phyl-omics in Debian Med team

Dear Andreas, On Thu, Apr 7, 2016 at 6:18 AM, Andreas Tille wrote: > Hi Julien, > > > > > but I understand that you do that from the debian git > > repositories, right? So if I push a commit tagged 2.3.0 to > git.debian.org, > > then you will automatically create a new

Re: Lets maintain libbpp-phyl-omics in Debian Med team

Hi Julien, On Wed, Apr 06, 2016 at 10:00:03PM +0200, Julien Yann Dutheil wrote: > > Sorry, that's not team maintenance. The only sensible place to do the > > maintenance of the Debian packaging is on git.debian.org. We have > > developed a complex system of tools working with this repository

Re: Lets maintain libbpp-phyl-omics in Debian Med team

Hi Julien, On Wed, Apr 06, 2016 at 08:37:28PM +0200, Julien Yann Dutheil wrote: > > - We use our "central" git repository biopp.univ-montp2.fr/git/ to create > the debian ones. As I am still new to github, I would feel more comfortable > in using our good old repos (which I know to be up to

Re: Lets maintain libbpp-phyl-omics in Debian Med team

On 06/04/16 15:46, Andreas Tille wrote: As for the git repository, may I ask why you need to create one? Would that be a local debian copy of the one on github? Makes me think that it would be time to synchronize our local repos and the github one... The Debian *packaging* repository is

Re: Lets maintain libbpp-phyl-omics in Debian Med team

Hi Julien, On Wed, Apr 06, 2016 at 03:46:57PM +0200, Julien Yann Dutheil wrote: > Dear Andreas, Dear Loïc, > > I do not know how we did that, but we certainly did not do it on purpose :) You fast and helpful responses are a sign that it was not on purpose. ;-) > As far as I'm concerned, I'm

Lets maintain libbpp-phyl-omics in Debian Med team

Hi Loic and Julien, congratulations - you were the first who was flying below my radar about bioinformatics software inside Debian. You managed to inject a set of library packages (libbpp-core-dev, libbpp-phyl-dev, libbpp-phyl-omics-dev, libbpp-popgen-dev, libbpp-qt-dev, libbpp-raa-dev,