[Cleaned up the CC list] Roger,
On Thu, Aug 2, 2012 at 5:44 PM, Roger Leigh <[email protected]> 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(-) -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". 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