[ome-users] Hamamatsu export kCGErrorFailure

Tue Nov 26 14:47:34 GMT 2013

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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>>
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The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.