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

[Olivier Sallou]

On 05/05/2015 10:21 AM, Andreas Tille wrote:
> 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?
I do not know if https://svncisd.ethz.ch/repos/cisd/jhdf5 is the same
"source" as package in Debian.
>
> 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

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