[ome-users] Hamamatsu export kCGErrorFailure

Wed Nov 27 09:35:37 GMT 2013

(Sending again for the benefit of the mailing list…)  

Hi Andreas,

I believe the issue you are seeing is a symptom of your Xgrid configuration. If you are not using Xgrid with authentication enabled, then jobs run under user “nobody” by default. Unfortunately, user “nobody” does not have access to the window server, which is required for a variety of different graphics processing routines. The simplest fix would be to set up a dedicated “xgrid” user on your Xgrid nodes and use password or kerberos-based authentication between the Xgrid controller and the nodes.
Cheers,

Josh

On Tuesday, November 26, 2013 at 16:47, Andreas Heindl wrote:

> Dear Melissa,
> I upgraded to the latest version which didn't solve the problem.  
> However, on Linux (Ubuntu, 64bit) it works fine.
> On our XServe (Java[1]) it still crashed with the error beneath:
>  
> 012A-2013-11-18_15.06.56.ndpi
> Reading IFDs
> Populating metadata
> Populating OME metadata
> [Hamamatsu NDPI] -> ./012A-2013-11-18_15.06.56/Tile0.jpg [JPEG]
> Mon Nov 25 16:39:42 yy1.local java[37867] <Error>: kCGErrorFailure:
> Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are
> logged.
> Exception in thread "main" java.lang.InternalError: Can't connect to
> window server - not enough permissions.
> at java.lang.ClassLoader$NativeLibrary.load(Native Method)
> at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1833)
> at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1730)
> at java.lang.Runtime.loadLibrary0(Runtime.java:823)
> at java.lang.System.loadLibrary(System.java:1044)
> at sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:50)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.awt.Toolkit.loadLibraries(Toolkit.java:1605)
> at java.awt.Toolkit.<clinit>(Toolkit.java:1627)
> at loci.formats.codec.JPEGTileDecoder.initialize(JPEGTileDecoder.java:136)
> at loci.formats.in.NDPIReader.setupService(NDPIReader.java:365)
> at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:114)
> at loci.formats.FormatReader.openBytes(FormatReader.java:781)
> at loci.formats.ImageReader.openBytes(ImageReader.java:400)
> at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:544)
> at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:486)
> at loci.formats.tools.ImageConverter.main(ImageConverter.java:672)
>  
>  
>  
>  
> [1]
> java version "1.6.0_65"
> Java(TM) SE Runtime Environment (build 1.6.0_65-b14-462-10M4609)
> Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-462, mixed mode)
>  
>  
>  
> On 25/11/13 18:34, Melissa Linkert wrote:
> > Hi Andreas,
> >  
> > > I recently noticed a new error message while extracting tiles from a
> > > ndpi (Hamamatsu) file. I'm using the most recent (stable)
> > > loci/bftools versions. Unfortunately, I couldn't find anything
> > > related to that error on google thus I hope you have an hint for me.
> > > It's running on a MacOSX XServe and the error message is attached
> > > here[1].
> >  
> >  
> > Are you using the 4.4.9 version of Bio-Formats? If so, I would very
> > much recommend that you try the 5.0.0-beta1 version instead:
> >  
> > http://downloads.openmicroscopy.org/bio-formats/5.0.0-beta1/
> >  
> > If 5.0.0-beta1 also produces an error message, please let us know.
> >  
> > Regards,
> > -Melissa
> >  
> > On Mon, Nov 25, 2013 at 04:46:33PM +0000, Andreas Heindl wrote:
> > > Dear all,
> > >  
> > > I recently noticed a new error message while extracting tiles from a
> > > ndpi (Hamamatsu) file. I'm using the most recent (stable)
> > > loci/bftools versions. Unfortunately, I couldn't find anything
> > > related to that error on google thus I hope you have an hint for me.
> > > It's running on a MacOSX XServe and the error message is attached
> > > here[1].
> > >  
> > > Thanks a lot and regards,
> > > Andreas
> > >  
> > >  
> > > [1]
> > >  
> > > 012A-2013-11-18_15.06.56.ndpi
> > > Reading IFDs
> > > Populating metadata
> > > Populating OME metadata
> > > [Hamamatsu NDPI] -> ./012A-2013-11-18_15.06.56/Tile0.jpg [JPEG]
> > > Mon Nov 25 16:39:42 yy1.local java[37867] <Error>: kCGErrorFailure:
> > > Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are
> > > logged.
> > > Exception in thread "main" java.lang.InternalError: Can't connect to
> > > window server - not enough permissions.
> > > at java.lang.ClassLoader$NativeLibrary.load(Native Method)
> > > at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1833)
> > > at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1730)
> > > at java.lang.Runtime.loadLibrary0(Runtime.java:823)
> > > at java.lang.System.loadLibrary(System.java:1044)
> > > at sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:50)
> > > at java.security.AccessController.doPrivileged(Native Method)
> > > at java.awt.Toolkit.loadLibraries(Toolkit.java:1605)
> > > at java.awt.Toolkit.<clinit>(Toolkit.java:1627)
> > > at loci.formats.codec.JPEGTileDecoder.initialize(JPEGTileDecoder.java:136)
> > > at loci.formats.in.NDPIReader.setupService(NDPIReader.java:365)
> > > at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:114)
> > > at loci.formats.FormatReader.openBytes(FormatReader.java:781)
> > > at loci.formats.ImageReader.openBytes(ImageReader.java:400)
> > > at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:544)
> > > at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:486)
> > > at loci.formats.tools.ImageConverter.main(ImageConverter.java:672)
> > >  
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