Crash on running after install - _cpmorphology

Install on ubuntu 14.04 without serious issue.
On running, get the following:

Fourier:~/Documents/CellProfiler-release_2.1.0> python CellProfiler.py -b
Updating Java dependencies using Maven.
[debug] execute contextualize
[debug] execute contextualize
Uncaught exception in CellProfiler.py
Traceback (most recent call last):
File “CellProfiler.py”, line 168, in main
workspace_path = workspace_path)
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/cellprofilerapp.py”, line 37, in init
super(CellProfilerApp, self).init(*args, **kwargs)
File “/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/_core.py”, line 7981, in init
self._BootstrapApp()
File “/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/_core.py”, line 7555, in _BootstrapApp
return core.PyApp__BootstrapApp(*args, **kwargs)
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/cellprofilerapp.py”, line 67, in OnInit
from cellprofiler.gui.cpframe import CPFrame
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/gui/cpframe.py”, line 26, in
from cellprofiler.modules import get_data_tool_names, instantiate_module
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/modules/init.py”, line 21, in
import cellprofiler.cpmodule as cpm
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/cpmodule.py”, line 26, in
import cellprofiler.objects
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/objects.py”, line 19, in
from cellprofiler.cpmath.cpmorphology import all_connected_components
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/cpmath/cpmorphology.py”, line 20, in
import _cpmorphology
ImportError: No module named _cpmorphology
Failed to stop Ilastik
Failed to stop the JVM

See another post with similar inability to find _cpmorphology. Any ideas? thanks.

If you are installing from source, the -b switch will prevent CellProfiler from compiling _cpmorphology (and other c and cython modules). So just run it once like this:

[code]python CellProfiler.py --build-and-exit[/code]

and afterwards, use the -b switch and the --do-not-fetch switch to prevent it from compiling the c, cython and Java parts.

–Lee

Thanks for the reply. I did as stated, just for others also required editing the LD_LIBRARY_PATH to include $JAVA_HOME/jre/lib/amd64/:$JAVA_HOME/include and $JAVA_HOME/jre/lib/amd64/jamvm/", in addition to $JAVA_HOME as before.

The:
python CellProfiler.py --build-and-exit
command works, with a few warnings, but no errors.

However:
python CellProfiler.py -b --do-not-fetch
gives the following error:

java.lang.NoSuchMethodError: getContextClassLoader
Traceback (most recent call last):
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/utilities/jutil.py”, line 313, in start_thread
init_context_class_loader()
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/utilities/jutil.py”, line 794, in init_context_class_loader
"()Ljava/lang/ClassLoader;")
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/utilities/jutil.py”, line 881, in call
fn = make_call(o, method_name, sig)
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/utilities/jutil.py”, line 854, in make_call
raise JavaException(jexception)
JavaException: getContextClassLoader
Failed to create Java VM
Uncaught exception in CellProfiler.py
Traceback (most recent call last):
File “CellProfiler.py”, line 168, in main
workspace_path = workspace_path)
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/cellprofilerapp.py”, line 37, in init
super(CellProfilerApp, self).init(*args, **kwargs)
File “/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/_core.py”, line 7981, in init
self._BootstrapApp()
File “/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/_core.py”, line 7555, in _BootstrapApp
return core.PyApp__BootstrapApp(*args, **kwargs)
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/cellprofilerapp.py”, line 67, in OnInit
from cellprofiler.gui.cpframe import CPFrame
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/gui/cpframe.py”, line 26, in
from cellprofiler.modules import get_data_tool_names, instantiate_module
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/modules/init.py”, line 21, in
import cellprofiler.cpmodule as cpm
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/cpmodule.py”, line 28, in
import pipeline as cpp
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/pipeline.py”, line 59, in
from bioformats.omexml import OMEXML
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/bioformats/init.py”, line 187, in
start_cellprofiler_jvm()
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/bioformats/init.py”, line 157, in start_cellprofiler_jvm
jutil.start_vm(args, run_headless)
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/utilities/jutil.py”, line 362, in start_vm
raise RuntimeError(“Failed to start Java VM”)
RuntimeError: Failed to start Java VM
Failed to stop Ilastik

Any ideas?

Thanks.

What version of Java do you have installed ($JAVA_HOME/bin/java -version)? You’re hitting one of the first uses of the javabridge in that stack trace. It managed to do one thing right (get the current thread), but then fails trying to find a method that’s been in the JRE since 1998.

I can think of a few things to do to diagnose the problem, but the problem is pretty bizarre. The first is to print out the class signature for the offending class from the shell:

there should be two lines:

public java.lang.ClassLoader getContextClassLoader();
  Signature: ()Ljava/lang/ClassLoader;

The second thing is to run CellProfiler with debug logging like this:

You should see a very long line that starts with “Starting VM with arguments: u’–Djava.class.path=” I think you should send me the contents of that line. Perhaps there’s something wrong with the jars in your boot class path. Maybe there’s something wrong with the command line being fed into Java. That’s all I can think of right now - hopefully something will turn up.

Thanks for the response. Just FYI running ubuntu 14.04 LTS, standard kernel, nothing funky

Java:
java version "1.7.0_55"
OpenJDK Runtime Environment (IcedTea 2.4.7) (7u55-2.4.7-1ubuntu1)
OpenJDK 64-Bit Server VM (build 24.51-b03, mixed mode)

$JAVA_HOME/bin/javap -s java.lang.Thread

public java.lang.ClassLoader getContextClassLoader();
Signature: ()Ljava/lang/ClassLoader;

Yes this was present.

Debug mode gives:
Using /home/jtmaynes/Documents/CellProfiler-release_2.1.0/plugins as imagej plugin directory
Adding /home/jtmaynes/Documents/CellProfiler-release_2.1.0/plugins to class path
Skipping /home/jtmaynes/Documents/CellProfiler-release_2.1.0/plugins/loadimagesfromomero.py
JVM arguments: -Djava.class.path=/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/cellprofiler-java.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/netcdf-4.0.03.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/log4j-1.2.14.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/jcommander-1.27.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ome_plugins-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/lwf-stubs-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-tools-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/mdbtools-java-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-legacy-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/perf4j-0.9.13.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-swing-tools-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/jai_imageio-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-beans-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/commons-logging-1.1.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-swing-commands-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/eventbus-1.4.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-minimaven-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/itext-2.1.5.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/xml-apis-1.3.04.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-swing-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/bcmail-jdk14-138.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-commands-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/slf4j-api-1.5.10.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/miglayout-3.7.3.1-swing.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/markdownj-0.3.0-1.0.2b4.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-tx-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-context-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/scifio-devel-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-options-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/base64-2.3.8.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/rhino-1.7R4.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/specification-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/object-inspector-0.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/junit-4.8.2.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/xalan-2.7.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/slf4j-log4j12-1.5.10.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-1.49d.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/omero-client-4.3.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/forms-1.2.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/scifio-0.2.0.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ome-xml-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/aopalliance-1.0.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-swing-script-editor-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-updater-core-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/rsyntaxtextarea-2.0.4.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-text-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/testng-6.8.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-jdbc-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-scripting-java-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-common-awt-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/imglib2-ij-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ome-io-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-scripting-beanshell-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/jcommon-1.0.17.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/jsch-0.1.49.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-util-swing-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/jhotdraw-7.6.0.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ome-java-2.6.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/bcprov-jdk14-138.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/serializer-2.7.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-app-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/loci_plugins-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/jfreechart-1.0.14.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/javassist-3.16.1-GA.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-util-awt-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/imglib2-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-core-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-core-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/scifio-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-updater-ssh-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/sezpoz-1.9-imagej.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-platforms-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/imglib2-ops-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-orm-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-swing-updater-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/bsh-2.0b4.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/loci-legacy-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-expression-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/imglib2-algorithms-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-updater-webdav-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/xmlrpc-1.2-b1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/native-lib-loader-2.0-SNAPSHOT.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/commons-lang3-3.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/bio-formats-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/kryo-2.21-shaded.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-data-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/metakit-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-aop-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/scijava-common-1.4.0.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/poi-loci-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-asm-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-io-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/commons-httpclient-2.0-rc2.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/snakeyaml-1.6.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/turbojpeg-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/opencsv-2.3.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/blitz.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/common.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ice.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/model-psql.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/plugins -Dloci.bioformats.loaded=true -Xmx512m -Dplugins.dir=/home/jtmaynes/Documents/CellProfiler-release_2.1.0/plugins -Djava.util.prefs.PreferencesFactory=org.cellprofiler.headlesspreferences.HeadlessPreferencesFactory
Args = -Djava.class.path=/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/cellprofiler-java.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/netcdf-4.0.03.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/log4j-1.2.14.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/jcommander-1.27.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ome_plugins-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/lwf-stubs-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-tools-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/mdbtools-java-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-legacy-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/perf4j-0.9.13.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-swing-tools-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/jai_imageio-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-beans-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/commons-logging-1.1.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-swing-commands-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/eventbus-1.4.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-minimaven-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/itext-2.1.5.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/xml-apis-1.3.04.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-swing-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/bcmail-jdk14-138.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-commands-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/slf4j-api-1.5.10.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/miglayout-3.7.3.1-swing.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/markdownj-0.3.0-1.0.2b4.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-tx-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-context-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/scifio-devel-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-options-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/base64-2.3.8.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/rhino-1.7R4.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/specification-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/object-inspector-0.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/junit-4.8.2.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/xalan-2.7.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/slf4j-log4j12-1.5.10.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-1.49d.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/omero-client-4.3.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/forms-1.2.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/scifio-0.2.0.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ome-xml-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/aopalliance-1.0.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-swing-script-editor-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-updater-core-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/rsyntaxtextarea-2.0.4.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-text-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/testng-6.8.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-jdbc-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-scripting-java-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-common-awt-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/imglib2-ij-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ome-io-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-scripting-beanshell-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/jcommon-1.0.17.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/jsch-0.1.49.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-util-swing-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/jhotdraw-7.6.0.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ome-java-2.6.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/bcprov-jdk14-138.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/serializer-2.7.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-app-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/loci_plugins-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/jfreechart-1.0.14.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/javassist-3.16.1-GA.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-util-awt-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/imglib2-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-core-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-core-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/scifio-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-updater-ssh-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/sezpoz-1.9-imagej.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-platforms-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/imglib2-ops-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-orm-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-swing-updater-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/bsh-2.0b4.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/loci-legacy-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-expression-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/imglib2-algorithms-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-updater-webdav-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/xmlrpc-1.2-b1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/native-lib-loader-2.0-SNAPSHOT.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/commons-lang3-3.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/bio-formats-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/kryo-2.21-shaded.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-data-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/metakit-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-aop-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/scijava-common-1.4.0.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/poi-loci-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-asm-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-io-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/commons-httpclient-2.0-rc2.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/snakeyaml-1.6.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/turbojpeg-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/opencsv-2.3.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/blitz.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/common.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ice.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/model-psql.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/plugins
-Dloci.bioformats.loaded=true
-Xmx512m
-Dplugins.dir=/home/jtmaynes/Documents/CellProfiler-release_2.1.0/plugins
-Djava.util.prefs.PreferencesFactory=org.cellprofiler.headlesspreferences.HeadlessPreferencesFactory
Starting JVM monitor thread
Creating JVM object
JVM monitor thread started
Starting VM with arguments: ‘-Djava.class.path=/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/cellprofiler-java.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/netcdf-4.0.03.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/log4j-1.2.14.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/jcommander-1.27.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ome_plugins-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/lwf-stubs-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-tools-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/mdbtools-java-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-legacy-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/perf4j-0.9.13.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-swing-tools-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/jai_imageio-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-beans-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/commons-logging-1.1.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-swing-commands-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/eventbus-1.4.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-minimaven-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/itext-2.1.5.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/xml-apis-1.3.04.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-swing-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/bcmail-jdk14-138.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-commands-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/slf4j-api-1.5.10.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/miglayout-3.7.3.1-swing.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/markdownj-0.3.0-1.0.2b4.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-tx-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-context-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/scifio-devel-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-options-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/base64-2.3.8.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/rhino-1.7R4.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/specification-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/object-inspector-0.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/junit-4.8.2.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/xalan-2.7.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/slf4j-log4j12-1.5.10.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-1.49d.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/omero-client-4.3.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/forms-1.2.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/scifio-0.2.0.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ome-xml-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/aopalliance-1.0.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-swing-script-editor-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-updater-core-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/rsyntaxtextarea-2.0.4.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-text-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/testng-6.8.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-jdbc-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-scripting-java-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-common-awt-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/imglib2-ij-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ome-io-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-scripting-beanshell-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/jcommon-1.0.17.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/jsch-0.1.49.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-util-swing-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/jhotdraw-7.6.0.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ome-java-2.6.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/bcprov-jdk14-138.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/serializer-2.7.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-app-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/loci_plugins-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/jfreechart-1.0.14.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/javassist-3.16.1-GA.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-util-awt-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/imglib2-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-core-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-core-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/scifio-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-updater-ssh-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/sezpoz-1.9-imagej.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-platforms-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/imglib2-ops-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-orm-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-ui-swing-updater-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/bsh-2.0b4.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/loci-legacy-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-expression-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/imglib2-algorithms-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-updater-webdav-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/xmlrpc-1.2-b1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/native-lib-loader-2.0-SNAPSHOT.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/commons-lang3-3.1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/bio-formats-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/kryo-2.21-shaded.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-data-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/metakit-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-aop-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/scijava-common-1.4.0.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/poi-loci-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/spring-asm-3.0.1.RELEASE.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ij-io-2.0.0-beta-7.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/commons-httpclient-2.0-rc2.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/snakeyaml-1.6.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/turbojpeg-5.0.0-beta1.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/opencsv-2.3.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/blitz.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/common.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/ice.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/imagej/jars/model-psql.jar:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/plugins:/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/utilities/js.jar’, ‘-Dloci.bioformats.loaded=true’, ‘-Xmx512m’, ‘-Dplugins.dir=/home/jtmaynes/Documents/CellProfiler-release_2.1.0/plugins’, ‘-Djava.util.prefs.PreferencesFactory=org.cellprofiler.headlesspreferences.HeadlessPreferencesFactory’]
java.lang.NoSuchMethodError: getContextClassLoader
Traceback (most recent call last):
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/utilities/jutil.py”, line 313, in start_thread
init_context_class_loader()
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/utilities/jutil.py”, line 794, in init_context_class_loader
"()Ljava/lang/ClassLoader;")
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/utilities/jutil.py”, line 881, in call
fn = make_call(o, method_name, sig)
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/utilities/jutil.py”, line 854, in make_call
raise JavaException(jexception)
JavaException: getContextClassLoader
Failed to create Java VM
Signalling caller
Uncaught exception in CellProfiler.py
Traceback (most recent call last):
File “CellProfiler.py”, line 168, in main
workspace_path = workspace_path)
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/cellprofilerapp.py”, line 37, in init
super(CellProfilerApp, self).init(*args, **kwargs)
File “/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/_core.py”, line 7981, in init
self._BootstrapApp()
File “/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode/wx/_core.py”, line 7555, in _BootstrapApp
return core.PyApp__BootstrapApp(*args, **kwargs)
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/cellprofilerapp.py”, line 67, in OnInit
from cellprofiler.gui.cpframe import CPFrame
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/gui/cpframe.py”, line 26, in
from cellprofiler.modules import get_data_tool_names, instantiate_module
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/modules/init.py”, line 21, in
import cellprofiler.cpmodule as cpm
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/cpmodule.py”, line 28, in
import pipeline as cpp
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/pipeline.py”, line 59, in
from bioformats.omexml import OMEXML
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/bioformats/init.py”, line 187, in
start_cellprofiler_jvm()
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/bioformats/init.py”, line 157, in start_cellprofiler_jvm
jutil.start_vm(args, run_headless)
File “/home/jtmaynes/Documents/CellProfiler-release_2.1.0/cellprofiler/utilities/jutil.py”, line 362, in start_vm
raise RuntimeError(“Failed to start Java VM”)
RuntimeError: Failed to start Java VM
Failed to stop Ilastik

Thanks again.

I’ll see if I can recreate today. I’ve created a github issue for this: github.com/CellProfiler/CellPro … ssues/1163

I started a fresh Ubuntu 14.04 Server machine and ran the following. It seems to work.

apt-get install -y git python-h5py python-zmq python-matplotlib cython openjdk-7-jdk python-wxgtk2.8 python-scipy python-mysqldb python-vigra export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64 export LD_LIBRARY_PATH=/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server:/usr/lib/jvm/java-7-openjdk-amd64:/usr/lib/jvm/java-7-openjdk-amd64/include git clone git@github.com:CellProfiler/CellProfiler.git cd CellProfiler/ python CellProfiler.py

Did you do anything differently?

No, I was compiling, not using a git clone.

The compiling went without prob, few minor warnings, but gave the errors posted even if the suggestions were performed (i.e. running with -b and --do-not-fetch).

Your method with the git clone does however bring the interface up (hoorah)! I will test against some benchmarks to make sure it is actually working as well.

I do get the error:
ilastik import: failed to import the ilastik. Please follow the instructions on
"http://www.ilastik.org" to install ilastik
Traceback (most recent call last):
File “/home/jtmaynes/Documents/cell_profiler/CellProfiler/cellprofiler/modules/classifypixels.py”, line 82, in
from ilastik.core.dataMgr import DataMgr, DataItemImage
ImportError: No module named ilastik.core.dataMgr
ilastik import: failed to import the ilastik. Please follow the instructions on
"http://www.ilastik.org" to install ilastik
Traceback (most recent call last):
File “/home/jtmaynes/Documents/cell_profiler/CellProfiler/cellprofiler/modules/ilastik_pixel_classification.py”, line 81, in
import ilastik_main
ImportError: No module named ilastik_main
Version: 2014-07-14T17:07:03 b03b264 / 20140714170703

so I assume your git clone doesn’t come with ilastik. No problem, I don’t really use ilastik, as long as other components are also not affected.

Thanks again for your help.

Sincerely,
JTM