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Re: Package available (was Re: Micro Manager)

Hi Mark !

On Sat, Jan 7, 2012 at 1:35 PM, Mark Longair
<mark-debianlists@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:

> 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

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:

> 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 :)


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