{"action":"created","issue":{"url":"https://api.github.com/repos/ClearVolume/ClearVolume/issues/24","labels_url":"https://api.github.com/repos/ClearVolume/ClearVolume/issues/24/labels{/name}","comments_url":"https://api.github.com/repos/ClearVolume/ClearVolume/issues/24/comments","events_url":"https://api.github.com/repos/ClearVolume/ClearVolume/issues/24/events","html_url":"https://github.com/ClearVolume/ClearVolume/issues/24","id":82051164,"number":24,"title":"ClearVolume crashes","user":{"login":"ctrueden","id":556626,"avatar_url":"https://avatars.githubusercontent.com/u/556626?v=3","gravatar_id":"","url":"https://api.github.com/users/ctrueden","html_url":"https://github.com/ctrueden","followers_url":"https://api.github.com/users/ctrueden/followers","following_url":"https://api.github.com/users/ctrueden/following{/other_user}","gists_url":"https://api.github.com/users/ctrueden/gists{/gist_id}","starred_url":"https://api.github.com/users/ctrueden/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ctrueden/subscriptions","organizations_url":"https://api.github.com/users/ctrueden/orgs","repos_url":"https://api.github.com/users/ctrueden/repos","events_url":"https://api.github.com/users/ctrueden/events{/privacy}","received_events_url":"https://api.github.com/users/ctrueden/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/ClearVolume/ClearVolume/labels/ready","name":"ready","color":"ededed"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":6,"created_at":"2015-05-28T17:50:48Z","updated_at":"2015-06-02T04:17:00Z","closed_at":null,"body":"From @acardona:\r\n> When opening the ClearVolume Network Client the whole JVM segfaults:\r\n> ```\r\n> #\r\n> # A fatal error has been detected by the Java Runtime Environment:\r\n> #\r\n> #  SIGSEGV (0xb) at pc=0x00007f28a2d62d80, pid=27327, tid=139811869296384\r\n> #\r\n> # JRE version: Java(TM) SE Runtime Environment (7.0_67-b01) (build 1.7.0_67-b01)\r\n> # Java VM: Java HotSpot(TM) 64-Bit Server VM (24.65-b04 mixed mode linux-amd64 compressed oops)\r\n> # Problematic frame:\r\n> # C  [ld-linux-x86-64.so.2+0x9d80]  _dl_rtld_di_serinfo+0x670\r\n> #\r\n> # Failed to write core dump. Core dumps have been disabled. To enable core dumping, try \"ulimit -c unlimited\" before starting Java again\r\n> #\r\n> # An error report file with more information is saved as:\r\n> # /home/albert/Programming/fiji-linux64-20091014/Fiji.app/hs_err_pid27327.log\r\n> #\r\n> # If you would like to submit a bug report, please visit:\r\n> #   http://bugreport.sun.com/bugreport/crash.jsp\r\n> #\r\n> Aborted\r\n> ```\r\n> \r\n> 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:\r\n> ```\r\n> (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%)\r\n>  \r\n> java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.NullPointerException\r\n> \tat net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:271)\r\n> \tat net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:162)\r\n> \tat ij.IJ.runPlugIn(IJ.java)\r\n> \tat ij.Executer.runCommand(Executer.java:131)\r\n> \tat ij.Executer.run(Executer.java:64)\r\n> \tat java.lang.Thread.run(Thread.java:745)\r\n> Caused by: java.util.concurrent.ExecutionException: java.lang.NullPointerException\r\n> \tat java.util.concurrent.FutureTask.report(FutureTask.java:122)\r\n> \tat java.util.concurrent.FutureTask.get(FutureTask.java:188)\r\n> \tat net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:267)\r\n> \t... 5 more\r\n> Caused by: java.lang.NullPointerException\r\n> \tat net.imagej.legacy.translate.ImagePlusDatasetConverter.populateInputCandidates(ImagePlusDatasetConverter.java:126)\r\n> \tat org.scijava.convert.DefaultConvertService.getCompatibleInputs(DefaultConvertService.java:111)\r\n> \tat org.scijava.widget.AbstractInputHarvester.getObjects(AbstractInputHarvester.java:153)\r\n> \tat org.scijava.widget.AbstractInputHarvester.addInput(AbstractInputHarvester.java:128)\r\n> \tat org.scijava.widget.AbstractInputHarvester.buildPanel(AbstractInputHarvester.java:94)\r\n> \tat org.scijava.widget.AbstractInputHarvester.harvest(AbstractInputHarvester.java:75)\r\n> \tat org.scijava.ui.AbstractInputHarvesterPlugin.process(AbstractInputHarvesterPlugin.java:76)\r\n> \tat org.scijava.module.ModuleRunner.preProcess(ModuleRunner.java:104)\r\n> \tat org.scijava.module.ModuleRunner.run(ModuleRunner.java:156)\r\n> \tat org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)\r\n> \tat org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)\r\n> \tat org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:181)\r\n> \tat java.util.concurrent.FutureTask.run(FutureTask.java:262)\r\n> \tat java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)\r\n> \tat java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)\r\n> \t... 1 more\r\n> ```\r\n> \r\n> And the exception in the case of an RGB image stack being open:\r\n> ```\r\n> (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%)\r\n>  \r\n> java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.NullPointerException\r\n> \tat net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:271)\r\n> \tat net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:162)\r\n> \tat ij.IJ.runPlugIn(IJ.java)\r\n> \tat ij.Executer.runCommand(Executer.java:131)\r\n> \tat ij.Executer.run(Executer.java:64)\r\n> \tat java.lang.Thread.run(Thread.java:745)\r\n> Caused by: java.util.concurrent.ExecutionException: java.lang.NullPointerException\r\n> \tat java.util.concurrent.FutureTask.report(FutureTask.java:122)\r\n> \tat java.util.concurrent.FutureTask.get(FutureTask.java:188)\r\n> \tat net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:267)\r\n> \t... 5 more\r\n> Caused by: java.lang.NullPointerException\r\n> \tat de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initClearVolumeUnsignedShortArrayImg(ImgLib2ClearVolume.java:264)\r\n> \tat de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initRealImgs(ImgLib2ClearVolume.java:418)\r\n> \tat de.mpicbg.jug.clearvolume.gui.ClearVolumeManager.run(ClearVolumeManager.java:156)\r\n> \tat de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.launchClearVolumeManager(GenericClearVolumeGui.java:208)\r\n> \tat de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.<init>(GenericClearVolumeGui.java:135)\r\n> \tat de.mpicbg.jug.plugins.ClearVolumePlugin.run(ClearVolumePlugin.java:80)\r\n> \tat org.scijava.command.CommandModule.run(CommandModule.java:201)\r\n> \tat org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)\r\n> \tat org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)\r\n> \tat org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)\r\n> \tat org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:181)\r\n> \tat java.util.concurrent.FutureTask.run(FutureTask.java:262)\r\n> \tat java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)\r\n> \tat java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)\r\n> ```\r\n> \r\n> ```\r\n> Information about your version of Java:\r\n>   os.arch => amd64\r\n>   os.name => Linux\r\n>   os.version => 3.13.11-031311ckt16-generic\r\n>   java.version => 1.7.0_67\r\n>   java.vendor => Oracle Corporation\r\n>   java.runtime.name => Java(TM) SE Runtime Environment\r\n>   java.runtime.version => 1.7.0_67-b01\r\n>   java.vm.name => Java HotSpot(TM) 64-Bit Server VM\r\n>   java.vm.version => 24.65-b04\r\n>   java.vm.vendor => Oracle Corporation\r\n>   java.vm.info => mixed mode\r\n>   java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment\r\n>   java.specification.name => Java Platform API Specification\r\n>   java.specification.version => 1.7\r\n>   sun.cpu.endian => little\r\n>   sun.desktop => gnome\r\n>   file.separator => /\r\n> \r\n> The up-to-date check says: REMIND_LATER\r\n> \r\n> Information relevant to JAVA_HOME related problems:\r\n> \r\n>   JAVA_HOME is set to: /home/albert/Programming/fiji-linux64-20091014/Fiji.app/java/linux-amd64/jdk1.7.0_67//jre\r\n>   imagej.dir => /home/albert/Programming/fiji-linux64-20091014/Fiji.app\r\n> \r\n> Information about the version of each plugin:\r\n> \r\n> Activated update sites:\r\n> ImageJ: http://update.imagej.net/ (last check:20150522062918)\r\n> Fiji: http://fiji.sc/update/ (last check:20150528120151)\r\n> ClearVolume: http://sites.imagej.net/ClearVolume/ (last check:20150527195605)\r\n> FFMPEG: http://fiji.sc/~schindelin/ffmpeg-plugins/ (last check:20130606112449)\r\n> MOSAIC ToolSuite: http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite/ (last check:20150227140151)\r\n> \r\n> Files not up-to-date:\r\n>   1581bc4d (MODIFIED) 20120131124042 Contents/MacOS/ImageJ-macosx\r\n>   75db148f (MODIFIED) 20120131124042 Contents/MacOS/ImageJ-tiger\r\n>   1ad3be0d (LOCAL_ONLY) 20090930112722 jars/jpedalSTD.jar\r\n>   32a5cb57 (LOCAL_ONLY) 20090910082726 macros/StartupMacros.txt\r\n>   dc7fce6b (LOCAL_ONLY) 20111014094119 plugins/Motion_Deblur.jar\r\n>   32738eb1 (LOCAL_ONLY) 20120511160900 plugins/SAT-lib-Drosophila-3rd-instar.clj\r\n>   3335decb (LOCAL_ONLY) 20101016092738 plugins/T2-NIT.jar\r\n>   063de9b3 (LOCAL_ONLY) 20150526100515 plugins/dynamic_vision_sensor-like.py\r\n>   7c95e931 (LOCAL_ONLY) 20140420121925 plugins/test_haskell_splitAt.py\r\n>   7f241f66 (LOCAL_ONLY) 20100603001850 plugins/tests/Example_Cursors.class\r\n>   a47f6af3 (LOCAL_ONLY) 20130425143259 plugins/tests/crop-file.py\r\n>   d3260180 (LOCAL_ONLY) 20090910082729 scripts/Record_Desktop.py\r\n>   0ea7f8fc (LOCAL_ONLY) 20090910082729 scripts/Record_Window.py\r\n> ```\r\n\r\nThe original bug report is [Fiji BugZilla #1076](http://fiji.sc/bugzilla/show_bug.cgi?id=1076)."},"comment":{"url":"https://api.github.com/repos/ClearVolume/ClearVolume/issues/comments/107797950","html_url":"https://github.com/ClearVolume/ClearVolume/issues/24#issuecomment-107797950","issue_url":"https://api.github.com/repos/ClearVolume/ClearVolume/issues/24","id":107797950,"user":{"login":"royerloic","id":1870994,"avatar_url":"https://avatars.githubusercontent.com/u/1870994?v=3","gravatar_id":"","url":"https://api.github.com/users/royerloic","html_url":"https://github.com/royerloic","followers_url":"https://api.github.com/users/royerloic/followers","following_url":"https://api.github.com/users/royerloic/following{/other_user}","gists_url":"https://api.github.com/users/royerloic/gists{/gist_id}","starred_url":"https://api.github.com/users/royerloic/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/royerloic/subscriptions","organizations_url":"https://api.github.com/users/royerloic/orgs","repos_url":"https://api.github.com/users/royerloic/repos","events_url":"https://api.github.com/users/royerloic/events{/privacy}","received_events_url":"https://api.github.com/users/royerloic/received_events","type":"User","site_admin":false},"created_at":"2015-06-02T04:17:00Z","updated_at":"2015-06-02T04:17:00Z","body":"Ok thanks! I think we are getting closer. It could be that we are packaging the wrong linux binaries - which makes no sense since we don't even ship the 32bit libs only the 64bit ones. Could you check if there is any JOGL jars installed somewhere in you JDK/JRE like in the ext folder?\r\nWe are going to do more testing under linux to figure out what's going on. Now we have a good lead on the cause. Thanks!"}}