[ImageJ-devel] [VIGRA] Avian VM and Bio-Formats

[Mark Hiner]

Hello again Ullrich,

 I believe the SCIFIO test failure is fixed on the latest master (commit
877bf5<https://github.com/scifio/scifio/commit/877bf58fa27f4aaca09e5caf92a56c5c30d670d9>).
Note to self: don't rely on annotations in src/test/java.

 Sorry for the inconvenience, but thanks again for bringing it up.

- Mark


On Thu, Dec 5, 2013 at 2:06 PM, Tobias Pietzsch <pietzsch at mpi-cbg.de> wrote:

> Hi Ulli,
>
> > When I try to compile Tobias' code (branch 'buffer'), I get
> >
> > [WARNING] The POM for
> com.github.maven-nar:nar-maven-plugin:jar:3.0.0-rc-3-SNAPSHOT is missing,
> no dependency information available
> > [ERROR] The build could not read 1 project -> [Help 1]
>
>
> my bad, I set a version of the nar-maven-plugin that cannot be obtained
> from the public maven repository but must be build locally.
> I reverted to version 3.0.0-rc-2. It should work now. Can you try again?
> best regards,
> Tobias
>
> On Dec 5, 2013, at 7:15 PM, Ullrich Koethe <
> ullrich.koethe at iwr.uni-heidelberg.de> wrote:
>
> > Hi Johannes and Tobias,
> >
> > following your instructions, I now installed all dependencies on Linux
> (64-bit Ubuntu, gcc 4.7.3). Here is what I got:
> >
> > In scifio, maven compiles, but then complains
> >
> >   Failed tests:   testDefaultEnabled(io.scif.filters.utests.FilterTest)
> >
> > In vigra-imglib2 (branch 'wip'), 'mvn install' compiles and produces a
> number of compiler warnings which seem to be uncritical on first glance,
> but are confusingly flagged as "[ERROR]" in the maven output.
> >
> > When I finally run './avian-run.sh', I get the following output
> >
> > java.io.EOFException
> >  at java.util.zip.InflaterInputStream.read (line 54)
> >  at java.util.zip.ZipFile$1.read (line 120)
> >  at java.util.zip.ZipFile$1.read (line 114)
> >  at java.util.zip.InflaterInputStream.read (line 39)
> >  at java.util.zip.ZipFile$1.read (line 106)
> >  at java.util.Properties$InputStreamParser.readCharacter (line 192)
> >  at java.util.Properties$Parser.parse (line 106)
> >  at java.util.Properties.load (line 21)
> >  at net.imglib2.vigra.NarHelper.loadLibrary (line 41)
> >  at net.imglib2.vigra.VigraImg3DUnsignedByte.<clinit> (line 23)
> >  at net.imglib2.vigra.VigraImgFactory3DUnsignedByte.create (line 19)
> >  at net.imglib2.vigra.VigraImgFactory3DUnsignedByte.create (line 14)
> >  at io.scif.img.ImgOpener.openImg (line 301)
> >  at io.scif.img.ImgOpener.openImg (line 217)
> >  at io.scif.img.ImgOpener.openImg (line 200)
> >  at Example.main (line 34)
> >  at Example.main (line 22)
> > java.lang.ExceptionInInitializerError
> >  at net.imglib2.vigra.VigraImgFactory3DUnsignedByte.create (line 19)
> >  at net.imglib2.vigra.VigraImgFactory3DUnsignedByte.create (line 14)
> >  at io.scif.img.ImgOpener.openImg (line 301)
> >  at io.scif.img.ImgOpener.openImg (line 217)
> >  at io.scif.img.ImgOpener.openImg (line 200)
> >  at Example.main (line 34)
> >  at Example.main (line 22)
> > caused by: java.lang.UnsatisfiedLinkError: Could not find native library
> >  at net.imglib2.vigra.NarHelper.loadLibrary (line 78)
> >  at net.imglib2.vigra.VigraImg3DUnsignedByte.<clinit> (line 23)
> >  at net.imglib2.vigra.VigraImgFactory3DUnsignedByte.create (line 19)
> >  at net.imglib2.vigra.VigraImgFactory3DUnsignedByte.create (line 14)
> >  at io.scif.img.ImgOpener.openImg (line 301)
> >  at io.scif.img.ImgOpener.openImg (line 217)
> >  at io.scif.img.ImgOpener.openImg (line 200)
> >  at Example.main (line 34)
> >  at Example.main (line 22)
> >
> > No image is created. The input image I used is attached.
> >
> > When I try to compile Tobias' code (branch 'buffer'), I get
> >
> > [WARNING] The POM for
> com.github.maven-nar:nar-maven-plugin:jar:3.0.0-rc-3-SNAPSHOT is missing,
> no dependency information available
> > [ERROR] The build could not read 1 project -> [Help 1]
> > [ERROR]
> > [ERROR]   The project net.imglib2.vigra:vigra-imglib2:1.0.0-SNAPSHOT
> (/home/ukoethe/src/vigra-imglib2/pom.xml) has 2 errors
> > [ERROR]     Unresolveable build extension: Plugin
> com.github.maven-nar:nar-maven-plugin:3.0.0-rc-3-SNAPSHOT or one of its
> dependencies could not be resolved: Failure to find
> com.github.maven-nar:nar-maven-plugin:jar:3.0.0-rc-3-SNAPSHOT in
> http://mvnplugins.fusesource.org/repo/release was cached in the local
> repository, resolution will not be reattempted until the update interval of
> mvnplugins.fusesource.org has elapsed or updates are forced -> [Help 2]
> >
> > Best regards
> > Ulli
> > <img.pgm>
>
>
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