bioformats (re-resume work)
[Cleaned up the CC list]
Roger,
On Thu, Aug 2, 2012 at 5:44 PM, Roger Leigh <r.leigh@dundee.ac.uk> wrote:
[...]
> With this and my patch for the missing build-deps, it sort-of works.
>
> Please find attached a proposed patch for removing the non-free
> jai-imageio dependency. Note that we're in the process of testing this
> to make sure there are no regressions in any of the format readers, but
> it builds fine at least. This is also available from git at
>
> http://github.com/rleigh-dundee/bioformats/tree/codeclib
> git://github.com/rleigh-dundee/bioformats.git (branch codeclib)
>
> With this patch applied, bioformats will now build. However, there are
> two problems which will still need attention:
>
> 1) The following jars are still required:
>
> jar/ome-java-deprecated.jar
> jar/ome-java.jar
> jar/omero_client.jar
>
> None of these are non-free; they are part of the OMERO build
> AFAICT. However, they do represent a nasty circular dependency
> between bioformats and omero. That's something that I think we'll
> need to address if building without embedded jars is going to be
> possible, which I think is quite an important thing to achieve.
>
> 2) Even with the above jars, the build fails due to perf4j being
> missing. It looks like this is missing from Debian at present,
> unless I'm just not finding it.
>
> So hopefully this represents some sort of forward progress, since
> non-free jars are now eliminated completely, despite this exposing some
> additional complications with the circular dependencies which need
> addressing. The missing perf4j, if not in Debian, just needs packaging
> and adding to the build-deps.
Thanks a bunch ! The patch looks a bit scary to me (*). I do not feel
very confortable with such a big patch to maintain in the long term.
Since upstream seems to be interested in having bio-formats in debian,
wouldn't it be better is this patch was somehow applied upstream ?
As for perf4j, it looks like no-one work on it:
http://lists.debian.org/debian-java/2011/09/msg00056.html
If this package is important, I can start working on this while the
large patch issue can be discussed. Thanks again for your help !
(*)
$ xzcat bioformats-codeclib-removal.patch.xz | diffstat
/dev/null
|binary
b/ant/toplevel.properties
| 4
b/build.xml
| 7
b/components/forks/jai/build.properties
| 2
b/components/forks/jai/pom.xml
| 8
b/components/forks/jai/src/com/sun/media/imageioimpl/common/PackageUtil.java
| 42
b/components/forks/jai/src/com/sun/media/imageioimpl/plugins/jpeg2000/J2KImageReaderSpi.java
| 2
b/components/forks/jai/src/com/sun/media/imageioimpl/plugins/jpeg2000/J2KImageWriterSpi.java
| 2
b/components/forks/jai/src/com/sun/media/imageioimpl/plugins/tiff/TIFFImageReader.java
| 34
b/components/forks/jai/src/com/sun/media/imageioimpl/plugins/tiff/TIFFImageWriter.java
| 42
b/scan-deps.pl
| 15
components/forks/jai/src/com/sun/media/imageioimpl/plugins/clib/CLibImageReader.java
| 802 --
components/forks/jai/src/com/sun/media/imageioimpl/plugins/clib/CLibImageWriter.java
| 854 --
components/forks/jai/src/com/sun/media/imageioimpl/plugins/jpeg/CLibJPEGImageReader.java
| 388 -
components/forks/jai/src/com/sun/media/imageioimpl/plugins/jpeg/CLibJPEGImageReaderSpi.java
| 205
components/forks/jai/src/com/sun/media/imageioimpl/plugins/jpeg/CLibJPEGImageWriter.java
| 383 -
components/forks/jai/src/com/sun/media/imageioimpl/plugins/jpeg/CLibJPEGImageWriterSpi.java
| 215
components/forks/jai/src/com/sun/media/imageioimpl/plugins/jpeg/CLibJPEGMetadata.java
| 1695 -----
components/forks/jai/src/com/sun/media/imageioimpl/plugins/jpeg2000/J2KImageReaderCodecLib.java
| 507 -
components/forks/jai/src/com/sun/media/imageioimpl/plugins/jpeg2000/J2KImageReaderCodecLibSpi.java
| 207
components/forks/jai/src/com/sun/media/imageioimpl/plugins/jpeg2000/J2KImageWriterCodecLib.java
| 915 ---
components/forks/jai/src/com/sun/media/imageioimpl/plugins/jpeg2000/J2KImageWriterCodecLibSpi.java
| 180
components/forks/jai/src/com/sun/media/imageioimpl/plugins/jpeg2000/J2KRenderedImageCodecLib.java
| 1056 ---
components/forks/jai/src/com/sun/media/imageioimpl/plugins/jpeg2000/MediaLibAccessor.java
| 1258 ----
components/forks/jai/src/com/sun/media/imageioimpl/plugins/png/CLibPNGImageReader.java
| 285
components/forks/jai/src/com/sun/media/imageioimpl/plugins/png/CLibPNGImageReaderSpi.java
| 185
components/forks/jai/src/com/sun/media/imageioimpl/plugins/png/CLibPNGImageWriter.java
| 448 -
components/forks/jai/src/com/sun/media/imageioimpl/plugins/png/CLibPNGImageWriterSpi.java
| 209
components/forks/jai/src/com/sun/media/imageioimpl/plugins/png/CLibPNGMetadata.java
| 2944 ----------
components/forks/jai/src/com/sun/media/imageioimpl/plugins/png/CLibPNGMetadataFormat.java
| 556 -
components/forks/jai/src/com/sun/media/imageioimpl/plugins/png/CLibPNGMetadataFormatResources.java
| 277
components/forks/jai/src/com/sun/media/imageioimpl/plugins/tiff/TIFFCodecLibFaxDecompressor.java
| 244
components/forks/jai/src/com/sun/media/imageioimpl/plugins/tiff/TIFFCodecLibRLECompressor.java
| 181
components/forks/jai/src/com/sun/media/imageioimpl/plugins/tiff/TIFFCodecLibT4Compressor.java
| 198
components/forks/jai/src/com/sun/media/imageioimpl/plugins/tiff/TIFFCodecLibT6Compressor.java
| 181
35 files changed, 2 insertions(+), 14529 deletions(-)
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