Missing files in libjhdf5-java (Was: Help needed to update to latest fastqc)

[Andreas Tille]

Hi Sylvestre,

Olivier claimed below that some files are missing in the Debian packaged
libjhdf5-java.  I have checked the jhdf packaging and realised that we
are lagging behind upstream.  I took the freedom to add a "Team upload"
entry to d/changelog and updated debian/watch to point to the new
download location.  I also moved to machine readable copyright and used
Files-Excluded to get rid of the bundled *.jar files.  Moreover I used
`cme fix dpkg-control` to normalise the d/control file and update to
latest Standard-Version.

I hope that this might help to upgrade to the latest upsteam version
which might be interesting to package.  Unfortunately I can not find
find any ch/... files and thus I wonder where Olivier might have found
these.  Olivier, are you refering to some older jhdf version?

Kind regards

        Andreas.

----- Forwarded message from Olivier Sallou <olivier.sallou at irisa.fr> -----

Date: Tue, 05 May 2015 09:25:23 +0200
From: Olivier Sallou <olivier.sallou at irisa.fr>
To: debian-med at lists.debian.org
Subject: Re: Help needed to update to latest fastqc



On 05/04/2015 10:52 PM, Andreas Tille wrote:
> Hi Olivier,
>
> On Mon, May 04, 2015 at 06:41:10PM +0200, Olivier Sallou wrote:
>> File fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java imports
>> HDFS5Factory from ch.systemsx.cisd.hdf5
>>
>> but jhdf5.jar only contains files like:  ncsa/hdf/hdf5lib/... and no
>> HDF5Factory
>>
>> this jhdf5 is not the correctl lib (or an other one is needed).
> I guess its this one:
>
>     https://svncisd.ethz.ch/doc/hdf5/hdf5-8.10/ch/systemsx/cisd/hdf5/package-summary.html
seems that original code source is the same
(https://svncisd.ethz.ch/repos/cisd/jhdf5/trunk/source/java/)
(/ncsa/...) but that /ch/...  has not been included for a reason
>  
>> In addition, in debian/patches/build.xml is missing commons-math3.jar to
>> be added in pathelement for classpath.
>>
>> for duplicate classes, I don't yet, but hdf5 first need to be resolved.
> If I do not hear from you I'll try the URL above tomorrow (if nobody
> else might beat me which would for sure welcome as always).
>
> Kind regards
>
>       Andreas.
>

-- 
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
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