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

[Tobias Pietzsch]

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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