Re: python-pbcore 1.2.2

2015-08-12 Thread Andreas Tille
Hi, On Tue, Aug 11, 2015 at 07:45:02PM -0700, Afif Elghraoui wrote: > Hi, team, > I have prepared an update to this package, but had to drop the > (apparently nonfunctional) Python 3 version that I created the first > time. Python 3 is not supported upstream yet, but is planned in the > future [1]

Re: python-pbcore 1.2.2

2015-08-12 Thread Afif Elghraoui
On الأربعاء 12 آب 2015 00:37, Andreas Tille wrote: > Hi, > > On Tue, Aug 11, 2015 at 07:45:02PM -0700, Afif Elghraoui wrote: >> Hi, team, >> I have prepared an update to this package, but had to drop the >> (apparently nonfunctional) Python 3 version that I created the first >> time. Python 3 is

DebianMed policy error

2015-08-12 Thread olivier sallou
Hi, there is an error in DebianMed policy page [0]: *svn-buildpackage* --svn-tag-only => --svn-only-tag [0] http://debian-med.alioth.debian.org/docs/policy.html Olivier

Re: DebianMed policy error

2015-08-12 Thread Charles Plessy
Le Wed, Aug 12, 2015 at 09:12:34AM +, olivier sallou a écrit : > > there is an error in DebianMed policy page [0]: > > *svn-buildpackage* --svn-tag-only > => --svn-only-tag Bonjour Olivier, I just realised that svn-buildpackage accepts both (according to its manpage). Have a nice day, Cha

Re: DebianMed policy error

2015-08-12 Thread Sascha Steinbiss
Hi, Btw, in the same paragraph, I think it should additionally be '--svn-noautodch' instead of '--svn-no-autodch': [vagrant@debian-8:~] $ svn-buildpackage --help | grep autodch --svn-noautodch Don't add a new Debian changelog entry when done Cheers Sascha On 12/08/2015 10:12, olivier sal

Re: DebianMed policy error

2015-08-12 Thread Andreas Tille
Hi, if anybody spots an error - the policy is in SVN and can be fixed by anybody. You can use make publish to push it online easily. Kind regards Andreas. On Wed, Aug 12, 2015 at 10:25:55AM +0100, Sascha Steinbiss wrote: > Hi, > > Btw, in the same paragraph, I think it should addi

Re: Help needed to update to latest fastqc

2015-08-12 Thread Tim Booth
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: --- We have 2 Free Java libraries for HDF5: 1) The "NCSA" lib distributed by hdfgroup.org with classes in namespace ncsa.hdf.hdf5lib, packaged on De

Re: Help needed to update to latest fastqc

2015-08-12 Thread Andreas Tille
Hi Tim, from my *very* naive point of view your considerations make sense. Olivier might have some more educated opinion (and perhaps some code?). I'll be available vor sponsering as usual. Thanks for your work on this Andreas. On Wed, Aug 12, 2015 at 11:44:19AM +0100, Tim Booth wrote: >

Re: Help needed to update to latest fastqc

2015-08-12 Thread Tim Booth
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 source code and a bunch of pre-compiled JNI shared libs, eg.

Wgsim stays in samtools.

2015-08-12 Thread Charles Plessy
Hello everyone, in conclusion, wgsim stays in samtools, where it will only get bug fixes, but no further developments. https://github.com/samtools/samtools/issues/429#issuecomment-129412846 Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Ts

Please update from ITK v3 to v4 [Re: RM: insighttoolkit -- ROM; Obsoleted by insighttoolkit4]

2015-08-12 Thread Steve M. Robbins
Hi, Previously on debian-med, I proposed that ITK v3 be dropped from the archive [1]. The only respondent agreed with that. So I filed for removal [2] and received notice that several packages still depend on ITK v3 (e.g. on libinsighttoolkit3-dev). Could those package maintainers update to

Re: Please update from ITK v3 to v4 [Re: RM: insighttoolkit -- ROM; Obsoleted by insighttoolkit4]

2015-08-12 Thread Dmitry Smirnov
On Wednesday 12 August 2015 22:01:36 Steve M. Robbins wrote: > Could those package maintainers update to v4, please? First ITK-4 needs to be re-build for GCC-5 transition. At the moment "ginkgocadx" FTBFS in "unstable" (but not in "testing") due to libstdc++6 : Breaks: libinsighttoolkit4.7 (<

Re: gcc-5 transition of GDCM

2015-08-12 Thread michkapopoff
> On August 5, 2015 03:29:30 PM Sébastien Jodogne wrote: > >>> I will try hard to get the script into VCS tonight and then I will welcome >>> help in testing the builds on dependent packages. >> >> Great! Let me know when things are ready. > > OK. The gccxml package is updated with a wrapper ar