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

[Ullrich Koethe]

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
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