[Debian-med-packaging] Please fix more bugs to make sure we can keep the usual quality - ${drink} offered

[Andreas Tille]

Hi,

two drinks are just given

On Tue, Sep 04, 2018 at 09:35:02PM +0200, Andreas Tille wrote:
> Hi folks,
> 
> I've just created the monthly team statistics and stumbled upon our bugs
> closing statistics[1].  Despite I'm fighting very hard the number of our
> open bugs (also RC critical ones) is growing (slowly but anyway).  So we
> need to do more and I specifically like to encourage people who are
> listed as Uploaders to some packages to feel dedicated to those packages
> (if somebody can't really remember I can do an UDD query to generate a
> list).  Despite I have quite some one bug per day rate and basically
> collected packages from all those maintainers that became MIA the help
> that is given by some active bug fixers is not sufficient to bear the
> workload.
> 
> To give some motivation for those who have no idea what to do I try to
> give a list of issues that urgently needs fixing.  I'd offer a ${drink}
> at next meeting for anybody who contributes to the solution of the named
> bugs until 1st of October.
> 
> #906811 blasr
>   needs fixing pbbam_0.18.0+dfsg-1 first.  I asked for help (and I
>   really need it) here:
>    https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-August/064944.html

That's not yet fully solved (see another dedicated mail) but Fabian
Kloetzl brought me back on track which qualified at least for a
$softdring ;-) but Fabian deserves in any case for picking up #908459
and fixing it very quickly.
 
> #902132 falcon
>   I commited the latest upstream version that looks promising to fix that
>   issue but it does not build.  The issue looks not *that* complicated
>   (build system needs adapting to make sure the test suite will write
>    to some writable location) but it just needs to be done.
> 
> #907819 jellyfish
>   The bug is actually fixed in Git.  However I also tried to get the latest
>   upstream version build which fails due some issues with the Python module
>   and I have currently no idea how to fix this.
> 
> #906371 jmodeltest
>   Here is a link by Olivier given (who is always very helpful - thanks a lot
>   Olivier) but may be some Java educated team member want to pick up this
>     https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=906371#27
>   and finalises the package
> 
> #897795 librcsb-core-wrapper
>   My comment in the changelog in Git says:
>     While the gcc-8 bug is fixed the build system is somehow messed
>     up.  No idea how to fix this for the moment
>   Anybody volunteering for this? 
> 
> #896531 & #901455 libsbml
>   Bug #896531 was easy and is fixed in Git.  The other bug has hints on
>   this thread on this mailing list
>     https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-May/062662.html
>   which is basically: Remove the Java docs.
>   I've started with this but failed.  This package is complex and
>   definitely needs way more love than I could spent.  We should also
>   check for a new upstream and we also should provide a Python3 package
>   (see #847013). 
> 
> #842815 libsis-base-java / libsis-jhdf5-java
>   Upstream has finally solved the issue of libsis-jhdf5-java but the
>   new upstream version needs libsis-base-java.  Both have changed the
>   build system to gradle.  I would really LOVE if somebody would spent
>   some time into this.  We have interesting dependencies from these
>   packages (inside the archive and pending upload to new)
> 
> #906156 python-skbio
>   I have injected the last upstream version and packaged its new dependency
>   python3-hdmedians but the package has several errors in the test suite.
>   Pretty please investigate.
> 
> #897867 spades
>   I've injectes a new upstream version which fixes the bug.  Unfortunately
>   something has changed in the build system throwing exception:
>     IOError: [Errno 2] No such file or directory: '/build/spades-3.12.0+dfsg/install_spades/bin/VERSION'
>   My gut feeling is that this is a pretty simple and stupid error but
>   I did not manage to solve this small riddle

Thanks to Alexandre Mestiashvili.

> #897877 trinityrnaseq
>   New upstream fixes the FTBFS bug but depends from salmon > 0.9
>   Any volunteer to upgrade salmon which is not very simple since it
>   needs heavy (but more clever! - just ask me if you want to give it
>   a try) editing of cmake files
> 
> There are *lots* of other probably more simple bugs.  Closing *any* bug
> helps to enhance our quality.  I have heard that people are concerned
> about the rise of bioconda cutting from our "market share".  I
> personally think that there is only a small subset of applications we
> share with bioconda and both projects have good chances to evolve in
> parallel and healthy.  However, I'm afraid way more that we will loose
> in terms of quality and thus the acceptance of Debian Med will become
> smaller for internal reasons.  So everybody who is interested in keeping
> Debian Med healthy and who has profitted from the project so far is
> kindly invited to give back something and fix at least one bug per
> month.  If anybody manages to contribute to the solution of one of the
> named bugs above until 1st of October I offer a ${drink} at the next
> meeting (Sprint, DebConf, or ???).
> 
> If you have no idea how to start I have another statistics for you:  My
> "contributions" to the debian-mentors at lists.debian.org[2] are basically
> **asking** questions about things I just don't know.  I'm also asking a
> lot on debian-java at lists.debian.org and debian-python at lists.debian.org
> (as well as debian-perl but the bugs above do not seem to be connected
> to any perl issue).  So don't be shy, use the Debian channels, there is
> also IRC (which I'm rarely using).  Try to investigate the issues and
> help to make Debian Med the first choice for free software in life
> sciences.
> 
> If you have further questions its possibly best to answer in the
> according bug repoort.

Thanks a lot to Alexandre and Fabian.  Any other bug fixers?

Kind regards

        Andreas.

 
> Kind regards
> 
>         Andreas.
> 
> [1] http://blends.debian.net/liststats/bugs_debian-med.png
> [2] http://blends.debian.net/liststats/authorstat_debian-mentors.png

-- 
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