Source of seqstat.jar is missing in PGAP

2017-01-18 Thread Andreas Tille
Hi Zhao Yongbing, I'm writing you on behalf of the Debian Med team which is a group inside Debian with the objective to package free software in life sciences and medicine for official Debian. You can see a list of the current software in the field of biology which might interest you on our so

Re: Bug#848236: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)

2017-01-18 Thread Andreas Tille
On Wed, Jan 18, 2017 at 02:21:04PM -0500, Lincoln Stein wrote: > Yes, I'll remove it immediately and apply the patches to bio::graphics as > well. Fine. Do you intend to do a micro release (say 2.56.1) after this change or should I remove the file here locally for the time beeing? Both would be

Re: Bug#848236: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)

2017-01-18 Thread Andreas Tille
On Wed, Jan 18, 2017 at 05:39:05PM +0100, gregor herrmann wrote: > > > > > > https://anonscm.debian.org/cgit/debian-med/gbrowse.git/tree/debian/patches > > Oh, cool, adding the (build)-dep is really enough, no patching > required. Nice. Yes, we needed this for another package ... > For

Re: Bug#848236: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)

2017-01-18 Thread gregor herrmann
On Wed, 18 Jan 2017 17:27:21 +0100, Andreas Tille wrote: > > Cool. In Debian terminology this means a new "Build-Depends" and after > > adding > > libbio-coordinate-perl package to this the tests succeeded. Thanks a lot > > for > > your help and patience! > > > > I now need to sort out some

Re: Bug#848236: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)

2017-01-18 Thread Andreas Tille
[droping debian-perl list from CC] On Wed, Jan 18, 2017 at 02:30:32PM +0100, Andreas Tille wrote: > Hi Lincoln, > > On Wed, Jan 18, 2017 at 07:07:55AM -0500, Lincoln Stein wrote: > > > > There appears to be a new dependency on libbio-coordinate. Probably best to > > add a "use Bio::Coordinate"

Re: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)

2017-01-18 Thread gregor herrmann
On Wed, 18 Jan 2017 14:00:47 +, Lincoln Stein wrote: > Glad to be of help. No source changes to bio::graphics needed then? Probably that too :) I'll take a look later today. Thanks for your efforts and your enormous help! Cheers, gregor -- .''`. https://info.comodo.priv.at/ - Debian

Autopkgtest for falcon (Was: New version of fast5 does not build)

2017-01-18 Thread Andreas Tille
Hi again, On Wed, Jan 18, 2017 at 11:34:44AM +0100, Andreas Tille wrote: > Hi Afif, > > On Wed, Jan 18, 2017 at 01:33:55AM -0800, Afif Elghraoui wrote: > > > > falcon's new release fails autopkgtest, which I have not gotten around to > > debugging, so I have not uploaded it. > > I'll have a

Re: Remaining issue with gbrowse - any help (Was: Urgent call to BioPerl users (Was: Bug#848236: src:gbrowse: ...)

2017-01-18 Thread Andreas Tille
Hi Lincoln, On Wed, Jan 18, 2017 at 07:07:55AM -0500, Lincoln Stein wrote: > > There appears to be a new dependency on libbio-coordinate. Probably best to > add a "use Bio::Coordinate" and the dependency to Bio::Graphics. Then the > problem will disappear. Cool. In Debian terminology this

New version of mriconvert

2017-01-18 Thread Andreas Tille
Hi Steve, after fixing the watch file of mriconvert I realised that there is a new version. I've commited a state in SVN that I'd regard as ready for upload. I'm hesitating a bit since I have no idea about this program and in the upstream source a whole directory tree (utf8proc-v1.1.6) was

Re: New version of fast5 does not build

2017-01-18 Thread Andreas Tille
Hi Afif, On Wed, Jan 18, 2017 at 01:33:55AM -0800, Afif Elghraoui wrote: > > > >I guess it should be not to hard to fix the clean target but I'm > >wondering whether you might intend to continue on this. > > This new version, if I remember correctly, has made the example program into > a

Re: New version of fast5 does not build

2017-01-18 Thread Afif Elghraoui
Hi, Andreas, On الأربعاء 18 كانون الثاني 2017 00:50, Andreas Tille wrote: Hi Afif, I'm currently trying to update all our packages to latest upstream (according to developers dashboard[1]) since January 25 might be the last one to get new versions inzo next stable release. I was stumbling

New version of fast5 does not build

2017-01-18 Thread Andreas Tille
Hi Afif, I'm currently trying to update all our packages to latest upstream (according to developers dashboard[1]) since January 25 might be the last one to get new versions inzo next stable release. I was stumbling upon fast5 which you commited to Git. The Build fails with: I: pybuild