Mathieu Malaterre <[email protected]> wrote: > > Hi Mark, > > On Thu, Nov 3, 2011 at 5:14 PM, Mark Longair > <[email protected]> wrote: > [...] [..] >> * The Fiji source tree contains a number of binary jar files >> without corresponding source. The bio-formats submodule is >> particularly concerning, since it's an important library in >> general for biological image processing, and the source tree >> currently bundles 24 jar files which should be external >> dependencies. > > Tell me about it ;) see: > http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=641448 > > Any help is welcome :) [..]
Hi Mathieu, I did some work on bio-formats packaging at a Fiji hackathon at the end of last year, and have a pretty good package of it now, with a few qualifications. (There were OME and Bio-Formats developers around at that event to help.) The most difficult dependency is NetCDF Java, which I see you also have an ITP for: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=641447 NetCDF Java itself also bundles a huge number of jar files in the source distribution, but to build the core of NetCDF you actually need relatively few dependencies. I made a package that builds just the core of NetCDF (i.e. the makeCore ant target) and only relies on Debian-packaged dependencies. (The NetCDF core is all that bio-formats requires, I believe.) That repository is here: https://github.com/mhl/libnetcdf-java The first commit on master is just the original upstream source (including the bundled jars) and the subsequent commits remove those and add the debian subdirectory. The bio-formats package can then use that as a dependency. I've got the point where the bio-formats jar targets that can be successfully built are: jar-autogen generate JAR file for LOCI autogen jar-common generate JAR file for LOCI common library jar-formats generate JAR file for Bio-Formats jar-jai generate JAR file for JAI Image I/O Tools library jar-loci-plugins generate JAR file for LOCI Plugins for ImageJ jar-lwf-stubs generate JAR file for LWF stubs jar-mdbtools generate JAR file for MDB Tools Java library jar-metakit generate JAR file for Metakit Java library jar-ome-xml generate JAR file for OME-XML Java library jar-poi-loci generate JAR file for Apache POI library jar-scifio generate JAR file for SciFIO ... while those that still aren't built, due to dependency problems, are: jar-ome-editor generate JAR file for OME Metadata Editor jar-ome-io generate JAR file for OME I/O jar-ome-notes generate JAR file for OME Notes jar-ome-plugins generate JAR file for OME Plugins for ImageJ jar-tests generate JAR file for LOCI testing framework The former group rely on jar files that are built by some part of the Open Microscopy Environment project. Although it would be great to have these, I don't think they should hold up an initial release of bio-formats. The testing framework is a similar case, I think. The remaining problematic jar file, which I am still including in the source archive of bio-formats, is clibwrapper_jiio.jar. This is a strange case - I can't find the source for these classes anywhere. It is distributed as part of jai-imageio-core [1], which, despite being BSD-licensed, only contains a sourceless jar file of clibwrapper_jiio.jar, and there's no corresponding source elsewhere in the repository. (There are also native libraries in there that seem to be missing source - those are, I think, the libraries called via JNI from clibwrapper_jiio.jar.) [1] http://java.net/projects/jai-imageio-core/ ITP: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=641276 bio-formats actually contains its own fork of jar-imageio-core, but the clibwrapper_jiio.jar in bio-formats is identical to one in earlier revisions of the upstream jar-imageio-core repository. So, I guess that the most sensible solution is for jar-imageio-core to be packaged and put into non-free and for bio-formats to depend on that to provide clibwrapper_jiio.jar. Hopefuly at some point someone can figure out where the source is for the jclib4jai component of jai-imageio-core (the compoment that contains all these problematic files). The repository with my Debian packaging of bio-formats is here: https://github.com/mhl/libbio-formats-java Or the generated packages for both libbio-formats-java and libnetcdf-core-java are here: http://fiji.sc/~longair/bio-formats-debian-packages/all/ I hope that's of some use. best regards, mark -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/[email protected]
