<html>
<head>
<base href="http://fiji.sc/bugzilla/" />
</head>
<body><table border="1" cellspacing="0" cellpadding="8">
<tr>
<th>Bug ID</th>
<td><a class="bz_bug_link
bz_status_NEW "
title="NEW - Exception when trying to run Cookbook > Deconvolution > Diffraction PSF 3D"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1078">1078</a>
</td>
</tr>
<tr>
<th>Summary</th>
<td>Exception when trying to run Cookbook > Deconvolution > Diffraction PSF 3D
</td>
</tr>
<tr>
<th>Product</th>
<td>Fiji
</td>
</tr>
<tr>
<th>Version</th>
<td>unspecified
</td>
</tr>
<tr>
<th>Hardware</th>
<td>Macintosh
</td>
</tr>
<tr>
<th>OS</th>
<td>Mac OS
</td>
</tr>
<tr>
<th>Status</th>
<td>NEW
</td>
</tr>
<tr>
<th>Severity</th>
<td>normal
</td>
</tr>
<tr>
<th>Priority</th>
<td>P4
</td>
</tr>
<tr>
<th>Component</th>
<td>Plugins
</td>
</tr>
<tr>
<th>Assignee</th>
<td>imagej-bugs@imagej.net
</td>
</tr>
<tr>
<th>Reporter</th>
<td>graemeball@googlemail.com
</td>
</tr>
<tr>
<th>CC</th>
<td>graemeball@googlemail.com
</td>
</tr></table>
<p>
<div>
<pre>Exception when trying to run Cookbook > Deconvolution > Diffraction PSF 3D
In case the stack trace is not attached automatically from the console, here it
is:
javax.xml.transform.TransformerException: java.io.FileNotFoundException:
file:/var/folders/kz/js9r4l5159n2x4jzrvkz72dh000cc9/T/java1008253920954071734/pom.xml
(No such file or directory)
at
org.apache.xalan.transformer.TransformerIdentityImpl.createResultContentHandler(TransformerIdentityImpl.java:245)
at
org.apache.xalan.transformer.TransformerIdentityImpl.transform(TransformerIdentityImpl.java:278)
at
org.scijava.plugins.scripting.java.JavaEngine.fakePOM(JavaEngine.java:744)
at
org.scijava.plugins.scripting.java.JavaEngine.writeTemporaryProject(JavaEngine.java:631)
at
org.scijava.plugins.scripting.java.JavaEngine.getMavenProject(JavaEngine.java:532)
at
org.scijava.plugins.scripting.java.JavaEngine.access$600(JavaEngine.java:95)
at
org.scijava.plugins.scripting.java.JavaEngine$Builder.<init>(JavaEngine.java:410)
at
org.scijava.plugins.scripting.java.JavaEngine$Builder.<init>(JavaEngine.java:372)
at
org.scijava.plugins.scripting.java.JavaEngine.compile(JavaEngine.java:198)
at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:135)
at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:173)
at org.scijava.script.ScriptModule.run(ScriptModule.java:174)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
at
org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:181)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
at java.lang.Thread.run(Thread.java:695)
Caused by: java.io.FileNotFoundException:
file:/var/folders/kz/js9r4l5159n2x4jzrvkz72dh000cc9/T/java1008253920954071734/pom.xml
(No such file or directory)
at java.io.FileOutputStream.open(Native Method)
at java.io.FileOutputStream.<init>(FileOutputStream.java:194)
at java.io.FileOutputStream.<init>(FileOutputStream.java:84)
at
org.apache.xalan.transformer.TransformerIdentityImpl.createResultContentHandler(TransformerIdentityImpl.java:235)
... 20 more
---------
java.io.FileNotFoundException:
file:/var/folders/kz/js9r4l5159n2x4jzrvkz72dh000cc9/T/java1008253920954071734/pom.xml
(No such file or directory)
at java.io.FileOutputStream.open(Native Method)
at java.io.FileOutputStream.<init>(FileOutputStream.java:194)
at java.io.FileOutputStream.<init>(FileOutputStream.java:84)
at
org.apache.xalan.transformer.TransformerIdentityImpl.createResultContentHandler(TransformerIdentityImpl.java:235)
at
org.apache.xalan.transformer.TransformerIdentityImpl.transform(TransformerIdentityImpl.java:278)
at
org.scijava.plugins.scripting.java.JavaEngine.fakePOM(JavaEngine.java:744)
at
org.scijava.plugins.scripting.java.JavaEngine.writeTemporaryProject(JavaEngine.java:631)
at
org.scijava.plugins.scripting.java.JavaEngine.getMavenProject(JavaEngine.java:532)
at
org.scijava.plugins.scripting.java.JavaEngine.access$600(JavaEngine.java:95)
at
org.scijava.plugins.scripting.java.JavaEngine$Builder.<init>(JavaEngine.java:410)
at
org.scijava.plugins.scripting.java.JavaEngine$Builder.<init>(JavaEngine.java:372)
at
org.scijava.plugins.scripting.java.JavaEngine.compile(JavaEngine.java:198)
at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:135)
at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:173)
at org.scijava.script.ScriptModule.run(ScriptModule.java:174)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
at
org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:181)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
at java.lang.Thread.run(Thread.java:695)
Information about your version of Java:
os.arch => x86_64
os.name => Mac OS X
os.version => 10.9.5
java.version => 1.6.0_65
java.vendor => Apple Inc.
java.runtime.name => Java(TM) SE Runtime Environment
java.runtime.version => 1.6.0_65-b14-462-11M4609
java.vm.name => Java HotSpot(TM) 64-Bit Server VM
java.vm.version => 20.65-b04-462
java.vm.vendor => Apple Inc.
java.vm.info => mixed mode
java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
java.specification.name => Java Platform API Specification
java.specification.version => 1.6
sun.cpu.endian => little
sun.desktop => null
file.separator => /
The up-to-date check says: REMIND_LATER
Information relevant to JAVA_HOME related problems:
JAVA_HOME is set to: null
imagej.dir => /Applications/Fiji.app
Information about the version of each plugin:
Activated update sites:
ImageJ: <a href="http://update.imagej.net/">http://update.imagej.net/</a> (last check:20150501194914)
Fiji: <a href="http://fiji.sc/update/">http://fiji.sc/update/</a> (last check:20150509234919)
3D ImageJ Suite: <a href="http://sites.imagej.net/Tboudier/">http://sites.imagej.net/Tboudier/</a> (last check:20150513055927)
Cookbook: <a href="http://sites.imagej.net/Cookbook/">http://sites.imagej.net/Cookbook/</a> (last check:20150302220629)
MOSAIC ToolSuite:
<a href="http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite/">http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite/</a> (last
check:20150227190151)
Files not up-to-date:
4aa5c2f5 (MODIFIED) 20150424135216 Contents/Info.plist
14b8544b (MODIFIED) 20150512145526 jars/imagej-updater-0.7.4.jar
4ccabde3 (MODIFIED) 20150526192326 jars/imagej-updater-0.7.5.jar
1ad3be0d (LOCAL_ONLY) 20150109125307 jars/jpedalSTD.jar
e7f9b16f (LOCAL_ONLY) 20150317134408 macros/BatchMacro.ijm
726548fe (LOCAL_ONLY) 20150429005317 macros/Plot_Multicolor4.3.txt
404c9259 (LOCAL_ONLY) 20150526173649 plugins/ICTN_.jar
6f7ce779 (LOCAL_ONLY) 20150429005205 plugins/Macros/Plot_Multicolor4.3.txt
ec17890b (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/JHotDraw.jar
91ece67d (LOCAL_ONLY) 20140123090208
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/JWlz.jar
36cb5c0a (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/TableLayout.jar
c3a86bd0 (LOCAL_ONLY) 20140123090208
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/assumeng.jar
7c4005e7 (LOCAL_ONLY) 20050801102630
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/axis-wsdl4j.jar
364315a9 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/axis.jar
3370a633 (LOCAL_ONLY) 20070427143948
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/axis2-saaj.jar
0af1624e (LOCAL_ONLY) 20140714161754
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/backport-util-concurrent.jar
07f50124 (LOCAL_ONLY) 20150427193612
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/blitz-javadoc.jar
ab21bcc1 (LOCAL_ONLY) 20150427193542
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/blitz-sources.jar
63fdcaa4 (LOCAL_ONLY) 20150427193618
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/blitz.jar
189f61fa (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/bufr.jar
94e35e33 (LOCAL_ONLY) 20150427193306
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/common-javadoc.jar
3646964f (LOCAL_ONLY) 20150427193302
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/common-sources.jar
c0f30819 (LOCAL_ONLY) 20150427193306
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/common.jar
940245e0 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-codec.jar
64d8a654 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-collections.jar
86ab9004 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-digester.jar
9e9eb622 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-discovery.jar
d59d3e4c (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-io.jar
f6139801 (LOCAL_ONLY) 20100225002342
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-lang.jar
fa9b8239 (LOCAL_ONLY) 20141210140056
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-logging.jar
60a83b54 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-validator.jar
abf211c5 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ehcache-core.jar
e33cecc2 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/grib.jar
2cd0d04c (LOCAL_ONLY) 20141125101518
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/guava.jar
85c28658 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/hibernate-jpa-2.0-api.jar
0c6e277e (LOCAL_ONLY) 20141210140056
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/httpclient.jar
9f61e37d (LOCAL_ONLY) 20141210140056
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/httpcore.jar
d216e98a (LOCAL_ONLY) 20141210140056
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/httpmime.jar
1911c9e1 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ice-glacier2.jar
b1d709fb (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ice-grid.jar
c49b8fa2 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ice-storm.jar
53aa5393 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ice.jar
84b54b46 (LOCAL_ONLY) 20150218193626
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ij.jar
6ce638fb (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ini4j.jar
f1b65457 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/java-getopt.jar
c827227f (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/java-image-scaling.jar
e72f9b2b (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/jaxrpc.jar
07f15e96 (LOCAL_ONLY) 20140724163642
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/jcommon.jar
c4eeeb8f (LOCAL_ONLY) 20140731133446
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/jfreechart.jar
5defc8da (LOCAL_ONLY) 20150320195720
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/jhdf5.jar
df7a0b63 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/jna.jar
4c09d41c (LOCAL_ONLY) 20140123090208
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/joda-time.jar
4a754817 (LOCAL_ONLY) 20140929140200
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/kryo.jar
b47bd885 (LOCAL_ONLY) 20150427193148
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/lwf-stubs.jar
ab8ff4ee (LOCAL_ONLY) 20150218193636
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/metadata-extractor.jar
16b765c2 (LOCAL_ONLY) 20140929140200
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/minlog.jar
c74b45b0 (LOCAL_ONLY) 20150427193258
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/model-psql-javadoc.jar
0436d2f4 (LOCAL_ONLY) 20150427193246
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/model-psql-sources.jar
6267f51d (LOCAL_ONLY) 20150427193258
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/model-psql.jar
66de339f (LOCAL_ONLY) 20140905201058
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/native-lib-loader.jar
a51a31db (LOCAL_ONLY) 20140123090208
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/netcdf.jar
aff28c0e (LOCAL_ONLY) 20140929140200
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/objenesis.jar
18382f06 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ome-java.jar
7af6ddeb (LOCAL_ONLY) 20140123090208
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/perf4j.jar
b3056152 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/platform.jar
4ef2cfd3 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/poi.jar
eedc0cd9 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/serializer.jar
5085d943 (LOCAL_ONLY) 20140321125832
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/slf4j-api.jar
228d9879 (LOCAL_ONLY) 20150427193144
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/specification.jar
ba32bfdf (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/swingx.jar
c8694e76 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/xalan.jar
93f166fd (LOCAL_ONLY) 20150218193636
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/xercesImpl.jar
a5c15945 (LOCAL_ONLY) 20150218193636
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/xmpcore.jar
d428b86d (LOCAL_ONLY) 20150427194034
plugins/OMERO.insight-ij-5.1.1-ice35-b43/omero_ij.jar
0e8ddb6d (LOCAL_ONLY) 20130914180736 plugins/ParallelFFTJ/arpack-combo.jar
1a08e201 (LOCAL_ONLY) 20130914180736 plugins/ParallelFFTJ/csparsej.jar
924b8d62 (LOCAL_ONLY) 20130914180736 plugins/ParallelFFTJ/jplasma.jar
fca468e8 (LOCAL_ONLY) 20130914180736 plugins/ParallelFFTJ/jtransforms.jar
14ccf036 (LOCAL_ONLY) 20130914180736
plugins/ParallelFFTJ/licenses/parallelcolt.LICENSE.txt
c6c2bb4d (LOCAL_ONLY) 20130914180736
plugins/ParallelFFTJ/licenses/parallelfftj.LICENSE.txt
89cb5823 (LOCAL_ONLY) 20130914180736 plugins/ParallelFFTJ/netlib-java.jar
25802519 (LOCAL_ONLY) 20130914180736 plugins/ParallelFFTJ/optimization.jar
3a6c661d (LOCAL_ONLY) 20130914180736
plugins/ParallelFFTJ/parallel_fftj-1.4.jar
87fc836e (LOCAL_ONLY) 20130914180736
plugins/ParallelFFTJ/parallelcolt-0.9.4.jar
c58cb4bf 20150525222659 plugins/SIMcheck-0.9.9-SNAPSHOT-javadoc.jar
bd5d5c61 20150525222659 plugins/SIMcheck-0.9.9-SNAPSHOT-sources.jar
514d26dc (LOCAL_ONLY) 20150527125150 plugins/SIMcheck_-0.9.9.jar
f57ea4b0 20150525222659 plugins/SIMcheck_0.9.9-SNAPSHOT.jar
034d1e63 (LOCAL_ONLY) 20150422123024 plugins/Temporal_plugins-1.0.0.jar</pre>
</div>
</p>
<hr>
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