Salmon

2017-12-13 Thread Gert Wollny
Hi all, since in the build-tree there is also a version 0.8, and I had to give up fixing that version - there was some include "FrugalBooMap.hpp" missing, I've fixed the RC bug in an new branch: "version-7.2". Best, Gert

Re: Uploaded new version 1.6 of htslib, samtools & bcftools to experimental - any known issues with reverse dependencies

2017-12-13 Thread Mattia Rizzolo
On Tue, Dec 12, 2017 at 11:17:22PM +, John Marshall wrote: > But in short, upstream's guiding principle is this: API and ABI are > tightly related. If functions that are not declared within htslib/*.h > (therefore are not part of HTSlib's documented public API) are > changed, we do not consider

Re: Uploaded new version 1.6 of htslib, samtools & bcftools to experimental - any known issues with reverse dependencies

2017-12-13 Thread Andreas Tille
Hi Mattia, On Wed, Dec 13, 2017 at 12:53:48PM +0100, Mattia Rizzolo wrote: > > What is the argument in favour of considering clearly unsupported > > undocumented internal functions to be part of a library's interface > > just because symbols are visible — in the binary but not the headers? > > I'

Re: Uploaded new version 1.6 of htslib, samtools & bcftools to experimental - any known issues with reverse dependencies

2017-12-13 Thread Mattia Rizzolo
On Wed, Dec 13, 2017 at 01:03:21PM +0100, Andreas Tille wrote: > To come back to the initial discussion: You would agree that uploading > to unstable is fine? The reason why I've choosen experimental initially > was also that we have lots of packages depending from python-pysam which > sometimes

Re: Uploaded new version 1.6 of htslib, samtools & bcftools to experimental - any known issues with reverse dependencies

2017-12-13 Thread Andreas Tille
Hi Mattia, On Wed, Dec 13, 2017 at 04:40:46PM +0100, Mattia Rizzolo wrote: > > One thing: I noticed that in htslib's tracker page an important > multiarch issue is reported: libhts-dev is marked ma:same, but there is > a static library in a non-multiarch path. > The options to fix it are: > * don

Re: RFS: bowtie/1.2.1.1+dfsg-1

2017-12-13 Thread Dominique Belhachemi
On Sat, Oct 21, 2017 at 11:44 AM, Alex Mestiashvili < ames...@rsh2.donotuse.de> wrote: > On 10/20/2017 06:46 PM, Dominique Belhachemi wrote: > > On Thu, Oct 19, 2017 at 12:16 PM, Alex Mestiashvili < > > ames...@rsh2.donotuse.de> wrote: > > > >> Hello, > >> > >> I've worked a bit on bowtie in git [

Re: RFS: bowtie/1.2.1.1+dfsg-1

2017-12-13 Thread Andreas Tille
Hi Dominique, On Wed, Dec 13, 2017 at 01:37:11PM -0500, Dominique Belhachemi wrote: > > >> I've worked a bit on bowtie in git [0] and think that it is ready for > > >> upload. It also presumably closes #864439. One of the issues I run > > >> during package building is that bowtie unit tests fail o

Please ask upstream to use soversion (Was: CMake help needed to enable hdf5 for gatb-core)

2017-12-13 Thread Andreas Tille
Hi Olivier, thanks to Gert I made some progress. I noticed that upstream does not set a soversion. Please ask them to do so. I just invented soversion 0 in https://anonscm.debian.org/git/debian-med/gatb-core.git/tree/debian/patches/set_soversion.patch Kind regards Andreas. -- http