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 - > > Date: Tue, 05 May 2015 09:25:23 +0200 > From: Olivier Sallou > 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 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/554893e1.2030...@irisa.fr
Missing files in libjhdf5-java (Was: Help needed to update to latest fastqc)
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 - Date: Tue, 05 May 2015 09:25:23 +0200 From: Olivier Sallou 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 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/55487063.1090...@irisa.fr - End forwarded message - -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150505082120.gb...@an3as.eu
