Re: Missing files in libjhdf5-java (Was: Help needed to update to latest fastqc)
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@irisa.fr> -----
>
> Date: Tue, 05 May 2015 09:25:23 +0200
> From: Olivier Sallou <olivier.sallou@irisa.fr>
> To: debian-med@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)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
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