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

2016-04-08 Thread Andreas Tille
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 > could

Re: Does bwa really need to be limited to amd64?

2016-04-08 Thread Andreas Tille
On Fri, Apr 08, 2016 at 10:58:01PM -0700, Afif Elghraoui wrote: > > على الجمعـة 8 نيسـان 2016 ‫05:22، كتب Charles Plessy: > > > > In any case, for most bioinformatics software that is now developed on > > amd64, I > > would not trust output of the programs built successfully on other > > archit

Re: Does bwa really need to be limited to amd64?

2016-04-08 Thread Afif Elghraoui
على الجمعـة 8 نيسـان 2016 ‫05:22، كتب Charles Plessy: > BWA failed to build on i386 at version 0.7.5a-1 with the following error, > despite the -D_NO_SSE2 option: > > /usr/lib/gcc/i486-linux-gnu/4.7/include/emmintrin.h:32:3: error: #error > "SSE2 instruction set not enabled" > > https://b

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

2016-04-08 Thread Andreas Tille
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 fo

Re: Packaging parsnp and harvest-tools for Debian

2016-04-08 Thread Andreas Tille
Hi Todd, On Fri, Apr 08, 2016 at 07:11:28AM -0400, Todd Treangen wrote: > > >We intend to package parsnp[1] and when downloading the archive from > >Github[2] I realised that it contains some binaries we need to replace > >by Debian packaged binaries built from the according sources to enable a >

Re: Bug#820062: orthanc and orthanc-doc: error when trying to install together

2016-04-08 Thread Andreas Tille
On Fri, Apr 08, 2016 at 02:35:35PM +0200, Sébastien Jodogne wrote: > > > Indeed, I am currently running all my integration tests to be sure that > > > everything is OK. > > > > Hmmm, why not adding these tests as autopkgtest? > > Actually, running these integration tests requires a network connec

Re: Bug#820062: orthanc and orthanc-doc: error when trying to install together

2016-04-08 Thread Sébastien Jodogne
> > Indeed, I am currently running all my integration tests to be sure that > > everything is OK. > > Hmmm, why not adding these tests as autopkgtest? Actually, running these integration tests requires a network connection and a Docker infrastructure. They are much more involved than the unit te

Re: Bug#820062: orthanc and orthanc-doc: error when trying to install together

2016-04-08 Thread Andreas Tille
Hi Sébastien, [moving back to list to get the testing issue recorded ...] On Fri, Apr 08, 2016 at 02:00:23PM +0200, Sébastien Jodogne wrote: > > > Great! The option "-A" was exactly what I was not able to find by myself. > > > > ... but this should work now. :-) > > :) > > Indeed, I am current

Re: Does bwa really need to be limited to amd64?

2016-04-08 Thread Charles Plessy
Le Fri, Apr 08, 2016 at 01:04:15AM -0700, Afif Elghraoui a écrit : > > As I've mentioned before, I'm trying to get circlator into testing. I > requested of the release team to allow it to migrate despite it's being > uninstallable on i386 [1]. I was then asked if there was any way to fix > that, s

Does bwa really need to be limited to amd64?

2016-04-08 Thread Afif Elghraoui
Hi, all, As I've mentioned before, I'm trying to get circlator into testing. I requested of the release team to allow it to migrate despite it's being uninstallable on i386 [1]. I was then asked if there was any way to fix that, so I looked into the problematic dependencies. bwa is set to amd64 and