Hi Andreas, the migration of JHDF5 to HDF5 1.10 is ongoing and mostly depend on me having a block of time I can spend on it. Your analysis of the work that needs to be done is right from what I can see. The plan is to switch to using the JNI library from the HDF group wherever possible (it may still be necessary to have a small JNI library though as some calls appear to be missing).
I will keep you updated. Kind regards, Bernd On 11/22/2016 03:31 PM, Andreas Tille wrote: > Hi Bernd, > > I'm hereby forwarding the main parts of the discussion of the bug report > which might contain hints what to do to make jhdf5 compliant with hdf5 > version 1.10. > > It would be nice if you could give us a hint if you were able to fix this. > > Kind regards > > Andreas. > > On Tue, Nov 15, 2016 at 12:37:20AM +0100, Gilles Filippini wrote: >>>>> Thank you for this upload. Have you tested the build against hdf5-1.10 >>>>> in experimental? >>>> >>>> Hmmm, sorry, no - I just made sure that the *sid* pbuilder environment >>>> is instaling hdf5-1.10. >>> >>> Ah. The fact that HDF5 1.8.16 builds libhdf5-10 might be confusing. HDF5 >>> 1.10 builds libhdf5-100 and is still in experimental. >>> >>>> If this is not sufficient please reopen ... >>>> and please give some helping hint if the package might not build >>>> properly. Otherwise I have no idea what to do - patches are very >>>> welcome. >>> >>> There are at least 3 majors changes brought by HDF5 1.10: >>> 1- The widely used hid_t datatype is now uint64_t (instead of int) >>> 2- The java wrapper library is now part of the HDF5 source tree >>> 3- HDF5Exception is now a checked exception. >>> >>> (2) and (3) might be worked out with a new upload of hdf5, to ship the >>> java wrapper library packages, patched to define HDF5Exception as an >>> unchecked exception. I'd rather wait after the transition. >>> >>> (1) Involves patching libsis-jhdf5-java. >> >> I've spent some time trying to figure it out, and I'm afraid this is a >> huge task I can't afford working on. >> >>> The best option would be a new upstream release. Do you know their >>> schedule wrt HDF5 1.10? >> >> If there is a risk that libsis-jhdf5-java won't be ready for stretch, >> then we could easily avoid the fastqc removal by disabling the fast5 >> file format support. It should be easy enough for anyone to convert >> fast5 files to fastq using e.g. poretools. >> What do you think?
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