Avian VM and Bio-Formats

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Re: [VIGRA] Avian VM and Bio-Formats

Ullrich Koethe
Hi Tobias,

>> 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?

Yes, it works. Thank you very much!

Ulli

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Re: [VIGRA] Avian VM and Bio-Formats

Ullrich Koethe
In reply to this post by dscho
Hi Johannes,

 >> 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!)
 >

These warnings are related to VIGRA itself, so there is no need for you
to act on them. I merely complained about the fact that warnings are
flagged as [ERROR] by maven. In fact, that's not quite precise: The
actual warning is correctly flagged as [WARNING], but the preceding
diagnostic lines which merely provide template instantiation context
(i.e. the call stack leading up to the warning) are flagged as [ERROR].
It would be much better to flag them as [CONTEXT] or similar.

[ERROR] In file included from
/home/ukoethe/src/vigra-imglib2/src/main/cxx/VigraImg3DUnsignedByte.cxx:2:0:
...
[ERROR]
/home/ukoethe/src/vigra-imglib2/src/main/cxx/VigraImg3DUnsignedByte.cxx:54:45:
   required from here
[WARNING]
/home/ukoethe/vigra-git/vigra/include/vigra/multi_array.hxx:3194:55:
warning: conversion to 'int' from 'vigra::MultiArrayView<2u, unsigned
char, vigra::StridedArrayTag>::difference_type_1 {aka long int}' may
alter its value [-Wconversion]

In the meantime, the error message produced by ./avian-run.sh changed.
But it looks like the same problem as before.

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: library not found:
/home/ukoethe/src/vigra-imglib2/target/nar/vigra-imglib2-1.0.0-SNAPSHOT-amd64-Linux-gpp-jni/lib/amd64-Linux-gpp/jni/libvigra-imglib2-1.0.0-SNAPSHOT.so
   at java.lang.Runtime.load
   at java.lang.Runtime.load (line 32)
   at java.lang.System.load (line 117)
   at net.imglib2.vigra.NarHelper.loadLibrary (line 75)
   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)

The library it complains about exists:

 >> ls -l
/home/ukoethe/src/vigra-imglib2/target/nar/vigra-imglib2-1.0.0-SNAPSHOT-amd64-Linux-gpp-jni/lib/amd64-Linux-gpp/jni/libvigra-imglib2-1.0.0-SNAPSHOT.so

-rwxr-xr-x 1 ukoethe ukoethe 122627 Dec  9 14:51
/home/ukoethe/src/vigra-imglib2/target/nar/vigra-imglib2-1.0.0-SNAPSHOT-amd64-Linux-gpp-jni/lib/amd64-Linux-gpp/jni/libvigra-imglib2-1.0.0-SNAPSHOT.so

Best regards
Ulli

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Re: [VIGRA] Avian VM and Bio-Formats

Ullrich Koethe
In reply to this post by dscho
Hi Johannes,

>> When I finally run './avian-run.sh', I get the following output
>>
>> java.io.EOFException
>> caused by: java.lang.UnsatisfiedLinkError: Could not find native library
>

I solved the problem - it was just a omission in the LD_LIBRARY_PATH.
'./avian-run.sh' now works and produced the desired output.

Best regards
Ulli

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