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

[Johannes Schindelin]

Hi Ulli,

On Thu, 5 Dec 2013, Ullrich Koethe wrote:

> 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)

Hopefully you will not need to compile SCIFIO yourself anymore soon (I
require https://github.com/scifio/scifio/pull/98 or something similar to
be merged for that).

> 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.

Which ones? (Please just paste such errors when you encounter them, of
course I could reproduce, if only I had more time!)

> 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

I will make that error message more informative. Thanks for testing.

Hopefully I will be able to set aside time to work on this project next
week.

Ciao,
Dscho