On 08/12/2015 08:43 PM, Tim Booth wrote: > Hi, > > After a fair amount of struggling I conclude that I do not have all the > code required to build this thing from source. > > The distribution of JHDF5 from > https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=26609113 > contains some Java source code and a bunch of pre-compiled JNI shared > libs, eg.: > > sis-jhdf5/lib/native/jhdf5/amd64-Linux/libjhdf5.so > > The source for this file is not to be found anywhere that I can see it. > One might assume (and the FAQ implies) that the file is equivalent > to /usr/lib/jni/libjhdf5.so provided by the exiting package libjhdf5-jni > but it isn't! Inspecting it with readelf shows it is full of symbols in > the ETH SIS namespace: > > tbooth@balisaur[sis-jhdf5] readelf -sW > ./sis-jhdf5/lib/native/jhdf5/amd64-Linux/libjhdf5.so | grep ch_systemsx | head > 19: 0000000000039a40 58 FUNC GLOBAL DEFAULT 10 > Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Scopy > 31: 000000000002e930 181 FUNC GLOBAL DEFAULT 10 > Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Dchdir_1ext > 35: 000000000003b590 918 FUNC GLOBAL DEFAULT 10 > Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Sget_1select_1bounds > 40: 00000000000387f0 45 FUNC GLOBAL DEFAULT 10 > Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pcreate_1xfer_1abort > 41: 0000000000038820 66 FUNC GLOBAL DEFAULT 10 > Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1char_1encoding > 46: 0000000000034500 203 FUNC GLOBAL DEFAULT 10 > Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Oopen > 47: 0000000000034ae0 363 FUNC GLOBAL DEFAULT 10 > Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pget_1version > 52: 0000000000035210 66 FUNC GLOBAL DEFAULT 10 > Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Pset_1layout > 65: 000000000003c560 126 FUNC GLOBAL DEFAULT 10 > Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Tget_1member_1name > 68: 0000000000032da0 58 FUNC GLOBAL DEFAULT 10 > Java_ch_systemsx_cisd_hdf5_hdf5lib_H5_H5Idec_1ref > ...and many more... > > So, this .so file is definitely specific to this library. It seems to > be a superset of a fork of the upstream NCSA code. The only contact > details I can find for the library are for Dr. Bernd Rinn who is the > head of the whole division, but I shall contact him personally and see > if he can pass the query on. I will have a look on my side. I think that I found some code some times ago, but this packaging is definitly quite hard. could you make what you made available (sis-hdf5, sis-base etc.) so that I avoid losing time doing the same thing to test compilation.
Olivier > > If Bernd can't help, then unless I've missed a trick we will have to > consider that this library and anything that depends on it (eg FastQC) > are not fully open source :-( > > Cheers, > > TIM > > On Wed, 2015-08-12 at 15:00 +0200, Andreas Tille wrote: >> Hi Tim, >> >> from my *very* naive point of view your considerations make sense. >> Olivier might have some more educated opinion (and perhaps some code?). >> >> I'll be available vor sponsering as usual. >> >> Thanks for your work on this >> >> Andreas. >> >> On Wed, Aug 12, 2015 at 11:44:19AM +0100, Tim Booth wrote: >>> Hi Andreas and Olivier, >>> >>> I'm going to have a crack at the FastQC update. I've been poking at the >>> HDF5 packages and here are my conclusions so far: >>> >>> --- >>> >>> We have 2 Free Java libraries for HDF5: >>> >>> 1) The "NCSA" lib distributed by hdfgroup.org with classes in namespace >>> ncsa.hdf.hdf5lib, packaged on Debian as libjhdf5-java. >>> >>> 2) The "CISD" aka. "SIS" lib distributed by ethz.ch with classes in the >>> namespace ch.systemsx, not currently packaged on Debian. >>> >>> The SIS library forks some Java code from the ncsa.hdf namespace, and >>> also needs to link against the NCSA native library (via JNI) at runtime. >>> >>> So, trying to package sis-jhdf5: >>> >>> wget >>> 'https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.1-r33502.zip?version=1&modificationDate=1424599261225&api=v2' >>> # The source is in a zip within the zip... >>> unzip sis-* >>> mkdir sis-jhdf5-14.12.1 >>> cd !$ >>> unzip ../sis-jhdf5/src/sis-jhdf5-src.zip >>> >>> For compilation to succeed, we also need sis-base, not to be confused >>> with the entirely separate project at sis.apache.org! >>> >>> wget >>> http://bs-svn01.ethz.ch/repos/cisd/libraries/trunk/sis-base/sis-base-src.zip >>> >>> The code also depends on their own args4j library, but only for the CLI >>> under ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java which we can >>> simply leave out just now. >>> >>> So - can we exclude the ncsa.hdf.hdf5lib.* classes from sis-jhdf5 and >>> compile it against the existing classes in /usr/share/java/jhdf5.jar? >>> My conclusion is not, because... >>> >>> The version of ncsa/hdf/hdf5lib/exceptions/HDF5Exception.java supplied >>> with the sis-jhdf5 code subclasses RuntimeException but the version in >>> libhdf5-java does not. The result is that the code here does not need >>> to declare the exceptions being thrown, and thus simply ignores them >>> all. One can go through and add all "throws" declarations (there are a >>> _lot_ of them!!), but then any client code using the library will also >>> break unless it is likewise patched or the code is modified to handle >>> the exceptions internally. I think we'd best just admit defeat here and >>> use the code supplied with sis-jhdf5. >>> >>> So, I'm going to try rolling two new packages, and see if that allows me >>> to compile the latest FastQC: >>> >>> libsis-base-java (should be simple) >>> libsis-jhdf5-java (depends on libsis-base-java + existing libjhdf5-jni) >>> >>> I'll report back on progress and commit to SVN as usual. Let me know if >>> you think I'm missing something. >>> >>> Cheers, >>> >>> TIM >>> >>> >>> On Thu, 2015-06-25 at 09:37 +0200, Andreas Tille wrote: >>>> Hi Olivier, >>>> >>>> any news about this hdf5lib packaging? >>>> >>>> Kind regards >>>> >>>> Andreas. >>>> >>>> On Tue, May 05, 2015 at 09:25:23AM +0200, Olivier Sallou wrote: >>>>> >>>>> 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 >>>>> >>>>> >>>> -- >>>> http://fam-tille.de >>>> >>>> >>> -- >>> Nothing is inherently mysterious - nothing that actually exists, that >>> is. If I am ignorant about a phenomenon, that is a fact about my state >>> of mind, not a fact about the phenomenon; to worship a phenomenon >>> because it seems so wonderfully mysterious, is to worship your own >>> ignorance. >>> >>> - Eliezer Yudkowsky >>> >>> > > -- > gpg key id: 4096R/326D8438 (keyring.debian.org) > Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
