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. 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 [email protected] > > > > with a subject of "unsubscribe". Trouble? Contact > > > > [email protected] > > > > Archive: https://lists.debian.org/[email protected] > > > > > > > > > > > > > > -- > > > 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 > > > > > -- 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
