<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 - ClearVolume crashes"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1076">1076</a>
</td>
</tr>
<tr>
<th>Summary</th>
<td>ClearVolume crashes
</td>
</tr>
<tr>
<th>Product</th>
<td>Fiji
</td>
</tr>
<tr>
<th>Version</th>
<td>unspecified
</td>
</tr>
<tr>
<th>Hardware</th>
<td>PC
</td>
</tr>
<tr>
<th>OS</th>
<td>Linux
</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>sapristi@gmail.com
</td>
</tr>
<tr>
<th>CC</th>
<td>sapristi@gmail.com
</td>
</tr></table>
<p>
<div>
<pre>When opening the ClearVolume Network Client the whole JVM segfaults:
#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00007f28a2d62d80, pid=27327, tid=139811869296384
#
# JRE version: Java(TM) SE Runtime Environment (7.0_67-b01) (build
1.7.0_67-b01)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (24.65-b04 mixed mode linux-amd64
compressed oops)
# Problematic frame:
# C [ld-linux-x86-64.so.2+0x9d80] _dl_rtld_di_serinfo+0x670
#
# Failed to write core dump. Core dumps have been disabled. To enable core
dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /home/albert/Programming/fiji-linux64-20091014/Fiji.app/hs_err_pid27327.log
#
# If you would like to submit a bug report, please visit:
# <a href="http://bugreport.sun.com/bugreport/crash.jsp">http://bugreport.sun.com/bugreport/crash.jsp</a>
#
Aborted
Additionally, when using the "Open in ClearVolume", it fails with an exception
if no images are open, and it throws an exception if an RGB stack is open,
leaving the splash screen looping forever. Eventually the whole of Fiji
freezes. The exception in the case of no images:
(Fiji Is Just) ImageJ 2.0.0-rc-30/1.49s; Java 1.7.0_67 [64-bit]; Linux
3.13.11-031311ckt16-generic; 59MB of 4096MB (1%)
java.lang.RuntimeException: java.util.concurrent.ExecutionException:
java.lang.NullPointerException
at
net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:271)
at
net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:162)
at ij.IJ.runPlugIn(IJ.java)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.concurrent.ExecutionException:
java.lang.NullPointerException
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:188)
at
net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:267)
... 5 more
Caused by: java.lang.NullPointerException
at
net.imagej.legacy.translate.ImagePlusDatasetConverter.populateInputCandidates(ImagePlusDatasetConverter.java:126)
at
org.scijava.convert.DefaultConvertService.getCompatibleInputs(DefaultConvertService.java:111)
at
org.scijava.widget.AbstractInputHarvester.getObjects(AbstractInputHarvester.java:153)
at
org.scijava.widget.AbstractInputHarvester.addInput(AbstractInputHarvester.java:128)
at
org.scijava.widget.AbstractInputHarvester.buildPanel(AbstractInputHarvester.java:94)
at
org.scijava.widget.AbstractInputHarvester.harvest(AbstractInputHarvester.java:75)
at
org.scijava.ui.AbstractInputHarvesterPlugin.process(AbstractInputHarvesterPlugin.java:76)
at org.scijava.module.ModuleRunner.preProcess(ModuleRunner.java:104)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:156)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
at
org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:181)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
... 1 more
And the exception in the case of an RGB image stack being open:
(Fiji Is Just) ImageJ 2.0.0-rc-30/1.49s; Java 1.7.0_67 [64-bit]; Linux
3.13.11-031311ckt16-generic; 75MB of 4096MB (1%)
java.lang.RuntimeException: java.util.concurrent.ExecutionException:
java.lang.NullPointerException
at
net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:271)
at
net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:162)
at ij.IJ.runPlugIn(IJ.java)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.concurrent.ExecutionException:
java.lang.NullPointerException
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:188)
at
net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:267)
... 5 more
Caused by: java.lang.NullPointerException
at
de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initClearVolumeUnsignedShortArrayImg(ImgLib2ClearVolume.java:264)
at
de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initRealImgs(ImgLib2ClearVolume.java:418)
at
de.mpicbg.jug.clearvolume.gui.ClearVolumeManager.run(ClearVolumeManager.java:156)
at
de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.launchClearVolumeManager(GenericClearVolumeGui.java:208)
at
de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.<init>(GenericClearVolumeGui.java:135)
at de.mpicbg.jug.plugins.ClearVolumePlugin.run(ClearVolumePlugin.java:80)
at org.scijava.command.CommandModule.run(CommandModule.java:201)
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$2.call(DefaultThreadService.java:181)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
Information about your version of Java:
os.arch => amd64
os.name => Linux
os.version => 3.13.11-031311ckt16-generic
java.version => 1.7.0_67
java.vendor => Oracle Corporation
java.runtime.name => Java(TM) SE Runtime Environment
java.runtime.version => 1.7.0_67-b01
java.vm.name => Java HotSpot(TM) 64-Bit Server VM
java.vm.version => 24.65-b04
java.vm.vendor => Oracle Corporation
java.vm.info => mixed mode
java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
java.specification.name => Java Platform API Specification
java.specification.version => 1.7
sun.cpu.endian => little
sun.desktop => gnome
file.separator => /
The up-to-date check says: REMIND_LATER
Information relevant to JAVA_HOME related problems:
JAVA_HOME is set to:
/home/albert/Programming/fiji-linux64-20091014/Fiji.app/java/linux-amd64/jdk1.7.0_67//jre
imagej.dir => /home/albert/Programming/fiji-linux64-20091014/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:20150522062918)
Fiji: <a href="http://fiji.sc/update/">http://fiji.sc/update/</a> (last check:20150528120151)
ClearVolume: <a href="http://sites.imagej.net/ClearVolume/">http://sites.imagej.net/ClearVolume/</a> (last check:20150527195605)
FFMPEG: <a href="http://fiji.sc/~schindelin/ffmpeg-plugins/">http://fiji.sc/~schindelin/ffmpeg-plugins/</a> (last check:20130606112449)
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:20150227140151)
Files not up-to-date:
1581bc4d (MODIFIED) 20120131124042 Contents/MacOS/ImageJ-macosx
75db148f (MODIFIED) 20120131124042 Contents/MacOS/ImageJ-tiger
1ad3be0d (LOCAL_ONLY) 20090930112722 jars/jpedalSTD.jar
32a5cb57 (LOCAL_ONLY) 20090910082726 macros/StartupMacros.txt
dc7fce6b (LOCAL_ONLY) 20111014094119 plugins/Motion_Deblur.jar
32738eb1 (LOCAL_ONLY) 20120511160900
plugins/SAT-lib-Drosophila-3rd-instar.clj
3335decb (LOCAL_ONLY) 20101016092738 plugins/T2-NIT.jar
063de9b3 (LOCAL_ONLY) 20150526100515 plugins/dynamic_vision_sensor-like.py
7c95e931 (LOCAL_ONLY) 20140420121925 plugins/test_haskell_splitAt.py
7f241f66 (LOCAL_ONLY) 20100603001850 plugins/tests/Example_Cursors.class
a47f6af3 (LOCAL_ONLY) 20130425143259 plugins/tests/crop-file.py
d3260180 (LOCAL_ONLY) 20090910082729 scripts/Record_Desktop.py
0ea7f8fc (LOCAL_ONLY) 20090910082729 scripts/Record_Window.py</pre>
</div>
</p>
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