Bug#778586: marked as done (ITP: r-bioc-ebseq -- R package for RNA-Seq Differential Expression Analysis)

2015-09-03 Thread Debian Bug Tracking System 
Your message dated Thu, 03 Sep 2015 10:00:26 +
with message-id 
and subject line Bug#778586: fixed in r-bioc-ebseq 1.6.0-1
has caused the Debian Bug report #778586,
regarding ITP: r-bioc-ebseq -- R package for RNA-Seq Differential Expression 
Analysis
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
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-- 
778586: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=778586
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Debian Med team 
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org

* Package name: r-bioc-ebseq
  Version : 1.6.0
  Upstream Author : Ning Leng 
* URL : https://www.biostat.wisc.edu/~kendzior/EBSEQ/
* License : Artistic-2.0
  Programming Lang: R
  Description : R package for RNA-Seq Differential Expression Analysis

r-bioc-ebseq is an R package for identifying genes and isoforms
differentially
 expressed (DE) across two or more biological conditions in an RNA-seq
 experiment.

EBSeq is an important program used in many bioinformatics pipelines. It is a
dependency of the Trinity RNASeq assembler (trinityrnaseq). This package
will
be group maintained by the Debian Med team.
~
--- End Message ---
--- Begin Message ---
Source: r-bioc-ebseq
Source-Version: 1.6.0-1

We believe that the bug you reported is fixed in the latest version of
r-bioc-ebseq, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 778...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Michael R. Crusoe  (supplier of updated r-bioc-ebseq package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


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Format: 1.8
Date: Mon, 16 Feb 2015 19:26:42 -0500
Source: r-bioc-ebseq
Binary: r-bioc-ebseq
Architecture: source all
Version: 1.6.0-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Description:
 r-bioc-ebseq - R package for RNA-Seq Differential Expression Analysis
Closes: 778586
Changes:
 r-bioc-ebseq (1.6.0-1) unstable; urgency=low
 .
   * Initial release (Closes: #778586)
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Re: Problems with libmtj-java and new version of beast-mcmc

2015-09-03 Thread olivier sallou 
Hi,
I have modified git repo to fix the build.xml file. With the f2jutil,
compil is ok for "missing" classes. There are still however other
dependencies issues (I have put them in changelog)

Olivier
Le mer. 2 sept. 2015 à 10:41, Olivier Sallou  a
écrit :

>
>
> - Mail transféré -
> > De: "Andreas Tille" 
> > À: "Olivier Sallou" , "Debian Med Packaging
> Team"
> > 
> > Envoyé: Mardi 1 Septembre 2015 13:51:17
> > Objet: Problems with libmtj-java and new version of beast-mcmc
> >
> > Hi Olivier,
> >
> > I have updated beast-mcmc to latest upstream version (in
> > testing/unstable as well as jessie-backports).  A local user stumbled
> upon
> > a problem that is connected to the Debian packaged version of libmtj-java
> > that does not contain all classes as the lib/mtj.jar[1] from upstream.
> > The latter provides classes in
> >
> >org/netlib/util
> >
> > which are part of the Debian package libnetlib-java in
> > /usr/share/java/netlib-java.jar.  Unfortunately it seems that the Beast
> > upstream found a newer version of netlib-java to include into mtj.jar
> > than we have packaged for Debian.
> >
> >Exception in thread "Thread-1" java.lang.NoClassDefFoundError:
> >org/netlib/util/intW
> >
> > Unfortunately I was not able to reproduce this problem with the example
> > data sets inside Beast - feel free to ping me in private to reproduce
> > this issue.
> >
> > The class org/netlib/util/intW is not part of the netlib version we have
> > packaged for Debian.  However, if I try to upgrade libnetlib-java for
> > Debian (we are lagging several versions behind upstream since it was
> > moved to Github[2]) I'm running into two types of trouble:
> >
> >1. The latest version also does not have org/netlib/util/intW
> >2. I would need to change the packaging of libnetlib-java
> >   from ant to maven (and I was not very lucky with this in
> >   the past.
> >
> > Any idea how we could provide org/netlib/util/intW?
> >
> > Kind regards
> >
> >   Andreas.
> >
> > [1] https://github.com/beast-dev/beast-mcmc/blob/master/lib/mtj.jar
> > [2] https://github.com/fommil/netlib-java
> >
> > --
> > http://fam-tille.de
> >
>

Re: Problems with libmtj-java and new version of beast-mcmc

2015-09-03 Thread olivier sallou 
Le jeu. 3 sept. 2015 à 20:57, Andreas Tille  a écrit :

> On Thu, Sep 03, 2015 at 06:01:49PM +, olivier sallou wrote:
> > > >
> > > > Yes, I pushed to the git repositroy
> > >
> > > To beast-mcmc?  I can not see any changes.  Libmtj-java is in svn and
> > >
> >
> > to libjmt-java which is in git.
> > In svn it is said that package switched to git under java team.
>
> Stupid me - I did the move myself ... ;-)
>
> Do you want me to work on the todo list (which looks a bit scary to me -
> but I might try to have a look).
>

Nope, for the moment I will continue.
But will take time. It needs intensive patching because netlib-java classes
do not use the same namespace than embeded/used library.
So patches are *easy* but many files to patch with different class
namespaces

There is also a dependency not available in debian.   I will check but it
seems they use a small part of something really bigger. I may patch the
code to remove this dependency.

I will let you know when I get something.



>
> Kind regards
>
>   Andreas.
>
> --
> http://fam-tille.de
>

Re: Forbid parallel build with DEB_BUILD_OPTIONS

2015-09-03 Thread Dmitry Smirnov 
On Monday 31 August 2015 11:57:44 Corentin Desfarges wrote:
> Concerning the issue 797475 [1], is there any way to forbid parallel build
> for my package ?

Correct way to do that would be to pass "--max-parallel=1" to "dh" (or 
perhaps only to `dh_auto_build`). Sometimes you may get away with value 2 or 
higher. Please do not set DEB_BUILD_OPTIONS from "debian/rules" -- it is 
wrong.

-- 
Cheers,
 Dmitry Smirnov.

---

Perhaps is is better to be irresponsible and right, than to be responsible
and wrong.
-- Winston Churchill


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