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

[Mark Hiner]

Hi Ullrich,

 I found this issue a while ago on my Windows 8 (64-bit) laptop, but
stopped looking at it after a brief investigation, since the test was
passing on our Win7 VM (and every other system I've tried it on).

 Anyway, Curtis and I are trying to reproduce on other systems right now to
figure out what's going on.

 Which Java version are you using?

The issue can be found here:
https://github.com/scifio/scifio/issues/79

Thanks for bringing it to our attention!

- Mark


On Thu, Dec 5, 2013 at 12:15 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
>
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>
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