Bug#842815: Re-opening: Please support HDF5 1.10
pini a écrit le 04/12/2016 à 12:42 : > Hi, > > On Wed, 23 Nov 2016 08:06:27 +0100 Andreas Tille > wrote: >> Hi Bernd, >> >> On Wed, Nov 23, 2016 at 06:54:21AM +0100, Bernd Rinn wrote: >>> 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). >> >> Thanks for your feedback. >> >>> I will keep you updated. >> >> This would be very helpful. Just to let you know: If you want to have >> JHDF5 distributed with the next stable Debian release the deadline for a >> fix would be about Christmas since there is a freeze at 5.1.2017 and the >> package needs 10 days from beeing uploaded to make it into the pool >> called "testing" where all release candidates are residing. >> >> Kind regards and thanks for your cooperation > > The hdf5 package now in Debian experimental builds the java wrapper > library shipped with hdf5-1.10: libhdf5-java, libhdf5-jni. HDF5-1.10 transition is done and libhdf5-java and libhdf5-jni are now in unstable. Thanks, _g. signature.asc Description: OpenPGP digital signature
Bug#842815: Re-opening: Please support HDF5 1.10
Hi, On Wed, 23 Nov 2016 08:06:27 +0100 Andreas Tille wrote: > Hi Bernd, > > On Wed, Nov 23, 2016 at 06:54:21AM +0100, Bernd Rinn wrote: > > 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). > > Thanks for your feedback. > > > I will keep you updated. > > This would be very helpful. Just to let you know: If you want to have > JHDF5 distributed with the next stable Debian release the deadline for a > fix would be about Christmas since there is a freeze at 5.1.2017 and the > package needs 10 days from beeing uploaded to make it into the pool > called "testing" where all release candidates are residing. > > Kind regards and thanks for your cooperation The hdf5 package now in Debian experimental builds the java wrapper library shipped with hdf5-1.10: libhdf5-java, libhdf5-jni. Thanks, _g.
Bug#842815: Re-opening: Please support HDF5 1.10
Hi Bernd, On Wed, Nov 23, 2016 at 06:54:21AM +0100, Bernd Rinn wrote: > 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). Thanks for your feedback. > I will keep you updated. This would be very helpful. Just to let you know: If you want to have JHDF5 distributed with the next stable Debian release the deadline for a fix would be about Christmas since there is a freeze at 5.1.2017 and the package needs 10 days from beeing uploaded to make it into the pool called "testing" where all release candidates are residing. Kind regards and thanks for your cooperation Andreas. -- http://fam-tille.de
Bug#842815: Re-opening: Please support HDF5 1.10
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? smime.p7s Description: S/MIME Cryptographic Signature
Bug#842815: Re-opening: Please support HDF5 1.10
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? -- http://fam-tille.de
