Hi Mark ! On Sat, Jan 7, 2012 at 1:35 PM, Mark Longair <mark-debianli...@longair.net> wrote: ... > 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.)
That's awesome ! > 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 This package is a real nightmare ! Thanks for simplifying the dependencies, I was not able to do that. > 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 Cool. I'll import that into the debian-med svn if this is ok with you: svn.debian.org/svn/debian-med/trunk/packages/netcdf-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. ok > 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 This is bogus. I was confused with this statement too. The java binding is BSD AFAIK. However you do not have access to the source code the C library. I believe I put some notes about that in the debian java package for javaimageio. I initiially work on this java-imageio package for the bio-formats package. > 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 It is in non-free. > 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 cool. If this is ok with you I'll import this into debian-med svn at: svn.debian.org/svn/debian-med/trunk/packages/bio-formats > 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. Definitely ! Thanks very much. I was getting afraid of the number of dependencies for bio-formats, so you simplified this to the bare minimum, this is great ! I'll work on bio-formats again this week. Feel free to ping me if things are not moving as fast as you like :) -- Mathieu -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CA+7wUswUgJrL=h2czzab6ebq8kylomwwp2q_auu9ectkq-d...@mail.gmail.com