After a quick look, there is a library issue (at least) 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). 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. Olivier On 05/03/2015 08:54 AM, Andreas Tille wrote: > Hi, > > I tried to upgrade to the latest fasqc version. When doing so I decided > to move from SVN to Git: > > Vcs-Git: git://anonscm.debian.org/debian-med/fastqc.git > > Upstream needs a new Build-Depends libjhdf5-java which I added. > However, I was not able to fix the build. When trying I considered > switching from the Makefile based build to ant (which sounds natural) > Unfortunately I did not succeeded in adapting build.xml. > > Any help would be appreciated > > 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