Unable to start ImageJ on Ubuntu 16.04.2 (fresh install)

linux
ubuntu
java
Tags: #<Tag:0x00007fd53ff396b8> #<Tag:0x00007fd53ff39500> #<Tag:0x00007fd53ff393c0>

#1

Hi,
I have recently updated by system to Ubuntu 16.04.2 and had to re-install after some other troubles.
On the first install, ImageJ was running fine using both the Java included with it or Oracle Java 8. On my new install, and although I cannot think of anything different from the previous install… I got the following error regardless of the Java I point to in the config file:

Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
Segmentation fault (core dumped)

The parameters in the cfg file are:

.
jre/bin/java
-Xmx5000m -cp ij.jar ij.ImageJ

ImageJ is in my home folder.
I have no idea how to solve this…
Thank you in advance for your help.
Rv


Crash on centos7 after latest kernel update
Java HotSpot(TM) 64-Bit Server VM problems
Installing Fiji on RHEL7 Machine
#2

Seconded - some recent update (not sure if it was Ubuntu or Fiji that did it) broke the launcher. The workaround I found is to do:
ImageJ-linux64 --system

You might need to export JAVA_HOME=/usr/lib/... for the appropriate JDK.


Fiji won't launch: "Segmentation fault"
Installing Fiji on RHEL7 Machine
#3

Hi Rv,

Can you check what kernel you are using? I ran into the exact same problem today in Ubuntu 16.04 after updating to 4.4.0-81. After booting with kernel 4.4.0-79 (and presumably any earlier kernels) ImageJ / FIJI are working without a problem.

Edit: mabruce’s suggestion of launching with the --system option works for me with 4.4.0-81


#4

I can confirm that kernel 4.4.0-81 is running on my system after an update last night.


#5

Hi,
I am running kernel 4.8.0-56-generic.
Cheers,
Rv


#6

What do you mean by [quote=“mabruce, post:2, topic:5757”]
ImageJ-linux64 --system
[/quote]
Where shall I put that line? in the cfg file? Can you explain?
Sorry for the naive questions… I am a rookie with ImageJ and java…
Thanks,
Rv


#7

I start Fiji from the command line usually, and it launches when I add the --system flag.


#8

I have the same issue and using --system flag solves it. I wonder, if there is going to be a permanent solution.
For people with less experience in command line:
Simply navigate to the folder Fiji.app.
Right click on an empty space (no files selected). And open terminal.
Type “./ImageJ-linux64 --system” and hit enter.

Alternatively, open the terminal and navigate to Fiji.app.
Type “./ImageJ-linux64 --system” and hit enter.


#9

There is never a permanent solution. At any time, updates can (and in this case did) break people’s systems.

More investigation is needed to determine the scope of this problem. If it is a general bug in the Linux kernel (or Ubuntu flavor thereof), which affects more people than just ImageJ users, I expect it will be fixed relatively quickly upstream. But if it is a bizarre interaction with the ImageJ launcher specifically, maybe not.

We are planning to migrate to a different JavaFX-based launcher eventually (see imagej/imagej-launcher#33 for technical details). You can generate an alpha build of this new launcher as follows:

git clone git://github.com/imagej/imagej
cd imagej
mvn -Pdist
cd target/jfx/native

And there should be a platform-specific application bundle in there, including native launcher. You can also look in target/jfx/native-nojre for a version of the app without an embedded Java runtime.

Note that I did not test this on Linux recently. I am not sure, but it may ask you to install additional utilities in order to successfully generate things.

Also note that while this process generates a standalone version of ImageJ2, the app may still have quirks. I am telling you this now mainly so you can test whether it works successfully, or also core dumps.


#10

Just to let you know, my recent upgrade from Debian 8 to Debian 9 also killed the launcher. The --system flag also did the trick.


#11

For those launching from the icon, try editing ImageJ.desktop in the Fiji.app folder. You might also find similar variants in the ~/.local/share/applications/ folder.


#12

@mabruce @amichaut @SarenT @rvboutin @James_Minto If you get a chance, could you please try generating the new JavaFX ImageJ bundle as described above, and check whether that launches successfully in an affected kernel?


#13

Can report that ./ImageJ --system fixes the launch issue on Scientific Linux 7.3 (RHEL-based) too.

uname -r
3.10.0-514.21.2.el7.x86_64

#15

I just tried it. I got the following error after the compilation:

[INFO] Compiling 3 source files to /home/amichaut/imagej/target/classes
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR :
[INFO] -------------------------------------------------------------
[ERROR] No compiler is provided in this environment. Perhaps you are running on a JRE rather than a JDK?
[INFO] 1 error
[INFO] -------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 02:11 min
[INFO] Finished at: 2017-06-21T12:05:39-04:00
[INFO] Final Memory: 43M/1144M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.6.0:compile (default-compile) on project imagej: Compilation failure
[ERROR] No compiler is provided in this environment. Perhaps you are running on a JRE rather than a JDK?
[ERROR]
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException

I didn’t have mvn before, I just installed it a few minutes ago, so maybe the error is related to my mvn installation. I don’t know anything about java, JDK, JRE. So I don’t really get the error.


#16

Try sudo apt-get install openjdk-8-jdk before running mvn. Otherwise you won’t have a Java compiler.


#18

Did it and I get a new error:

[ERROR] Could not connect to existing ImageJ instance. If problem persists, please delete file: /tmp/ImageJ-amichaut-_0-7.stub
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.53 sec - in net.imagej.app.MainTest
Running net.imagej.app.ToplevelImageJAppTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 sec - in net.imagej.app.ToplevelImageJAppTest

Results :

Tests run: 5, Failures: 0, Errors: 0, Skipped: 0

[INFO] 
[INFO] --- maven-jar-plugin:2.6:jar (default-jar) @ imagej ---
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (default) @ imagej ---
[INFO] Building jar: /home/amichaut/imagej/target/imagej-2.0.0-rc-62-SNAPSHOT-sources.jar
[INFO] 
[INFO] >>> javafx-maven-plugin:8.6.0:native (dist-with-jre) > :jar @ imagej >>>
[INFO] 
[INFO] >>> javafx-maven-plugin:8.6.0:jar (jar) > [jfxjar]package @ imagej >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-rules) @ imagej ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.12:regex-property (sanitize-version) @ imagej ---
[INFO] 
[INFO] --- buildnumber-maven-plugin:1.4:create (default) @ imagej ---
[INFO] 
[INFO] --- scijava-maven-plugin:1.0.0:set-rootdir (set-rootdir) @ imagej ---
[INFO] 
[INFO] --- maven-resources-plugin:3.0.2:resources (default-resources) @ imagej ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/amichaut/imagej/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ imagej ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-resources-plugin:3.0.2:testResources (default-testResources) @ imagej ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/amichaut/imagej/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.6.0:testCompile (default-testCompile) @ imagej ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ imagej ---
[INFO] Skipping execution of surefire because it has already been run for this configuration
[INFO] 
[INFO] --- maven-jar-plugin:2.6:jar (default-jar) @ imagej ---
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (default) @ imagej ---
[INFO] Building jar: /home/amichaut/imagej/target/imagej-2.0.0-rc-62-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-jar-plugin:2.6:test-jar (default) @ imagej ---
[INFO] 
[INFO] <<< javafx-maven-plugin:8.6.0:jar (jar) < [jfxjar]package @ imagej <<<
[INFO] 
[INFO] 
[INFO] --- javafx-maven-plugin:8.6.0:jar (jar) @ imagej ---
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 11.404 s
[INFO] Finished at: 2017-06-21T13:39:53-04:00
[INFO] Final Memory: 39M/1326M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal com.zenjava:javafx-maven-plugin:8.6.0:jar (jar) on project imagej: Execution jar of goal com.zenjava:javafx-maven-plugin:8.6.0:jar failed: Plugin com.zenjava:javafx-maven-plugin:8.6.0 or one of its dependencies could not be resolved: Could not find artifact javafx-packager:javafx-packager:jar:1.8.0_20 at specified path /usr/lib/jvm/java-8-openjdk-amd64/jre/../lib/ant-javafx.jar -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal com.zenjava:javafx-maven-plugin:8.6.0:jar (jar) on project imagej: Execution jar of goal com.zenjava:javafx-maven-plugin:8.6.0:jar failed: Plugin com.zenjava:javafx-maven-plugin:8.6.0 or one of its dependencies could not be resolved: Could not find artifact javafx-packager:javafx-packager:jar:1.8.0_20 at specified path /usr/lib/jvm/java-8-openjdk-amd64/jre/../lib/ant-javafx.jar
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:213)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:154)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:146)
	at org.apache.maven.lifecycle.internal.MojoExecutor.executeForkedExecutions(MojoExecutor.java:353)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:198)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:154)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:146)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:117)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:81)
	at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
	at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:309)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:194)
	at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:107)
	at org.apache.maven.cli.MavenCli.execute(MavenCli.java:993)
	at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:345)
	at org.apache.maven.cli.MavenCli.main(MavenCli.java:191)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
	at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
	at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
Caused by: org.apache.maven.plugin.PluginExecutionException: Execution jar of goal com.zenjava:javafx-maven-plugin:8.6.0:jar failed: Plugin com.zenjava:javafx-maven-plugin:8.6.0 or one of its dependencies could not be resolved: Could not find artifact javafx-packager:javafx-packager:jar:1.8.0_20 at specified path /usr/lib/jvm/java-8-openjdk-amd64/jre/../lib/ant-javafx.jar
	at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:106)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:208)
	... 24 more
Caused by: org.apache.maven.plugin.PluginResolutionException: Plugin com.zenjava:javafx-maven-plugin:8.6.0 or one of its dependencies could not be resolved: Could not find artifact javafx-packager:javafx-packager:jar:1.8.0_20 at specified path /usr/lib/jvm/java-8-openjdk-amd64/jre/../lib/ant-javafx.jar
	at org.apache.maven.plugin.internal.DefaultPluginDependenciesResolver.resolveInternal(DefaultPluginDependenciesResolver.java:218)
	at org.apache.maven.plugin.internal.DefaultPluginDependenciesResolver.resolve(DefaultPluginDependenciesResolver.java:149)
	at org.apache.maven.plugin.internal.DefaultMavenPluginManager.createPluginRealm(DefaultMavenPluginManager.java:402)
	at org.apache.maven.plugin.internal.DefaultMavenPluginManager.setupPluginRealm(DefaultMavenPluginManager.java:374)
	at org.apache.maven.plugin.DefaultBuildPluginManager.getPluginRealm(DefaultBuildPluginManager.java:231)
	at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:102)
	... 25 more
Caused by: org.eclipse.aether.resolution.ArtifactResolutionException: Could not find artifact javafx-packager:javafx-packager:jar:1.8.0_20 at specified path /usr/lib/jvm/java-8-openjdk-amd64/jre/../lib/ant-javafx.jar
	at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:453)
	at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifacts(DefaultArtifactResolver.java:255)
	at org.eclipse.aether.internal.impl.DefaultRepositorySystem.resolveDependencies(DefaultRepositorySystem.java:376)
	at org.apache.maven.plugin.internal.DefaultPluginDependenciesResolver.resolveInternal(DefaultPluginDependenciesResolver.java:210)
	... 30 more
Caused by: org.eclipse.aether.transfer.ArtifactNotFoundException: Could not find artifact javafx-packager:javafx-packager:jar:1.8.0_20 at specified path /usr/lib/jvm/java-8-openjdk-amd64/jre/../lib/ant-javafx.jar
	at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:295)
	... 33 more
[ERROR] 
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/PluginResolutionException

Do you need I run it with -X flag to get the full debug?


#19

I got it to compile (after installing the necessary JavaFX package). However, it seg faults immediately. Tried installing from the deb created by Maven, but that seg faults too.

Edit: I did some digging with gdb. Segfault is caused in libjvm.so (from the JRE packaged by JavaFX build I assume). I copied my JRE into the native-nojre build, same segfault. With no JRE copied into the -nojre build, it returns:

ImageJ Failed to locate JNI_CreateJavaVM
ImageJ Failed to launch JVM

#20

Sorry, I wasn’t clear enough. I meant an update/fix for users, without experience in terminals or have difficulties finding this page. I will try it, whenever I get the chance.


#21

It compiled for me, but the native launcher immediately gives a segmentation fault, the native-nojre gives:

ImageJ Failed to locate JNI_CreateJavaVM
ImageJ Failed to launch JVM

Should there be some details on which jre to use in ImageJ.cfg? Contents of ImageJ.cfg for the native launcher are:

[Application]
app.name=ImageJ
app.mainjar=ImageJ.jar
app.version=2.0.0
app.preferences.id=ImageJ
app.mainclass=net/imagej/Main
app.classpath=lib/imagej-common-0.24.4.jar:lib/imglib2-4.2.1.jar:lib/imglib2-roi-0.4.6.jar:lib/trove4j-3.0.3.jar:lib/udunits-4.3.18.jar:lib/imagej-notebook-0.2.2.jar:lib/imagej-ops-0.38.0.jar:lib/imglib2-algorithm-0.8.0.jar:lib/jama-1.0.3.jar:lib/ojalgo-43.0.jar:lib/imglib2-algorithm-fft-0.1.4.jar:lib/mines-jtk-20151125.jar:lib/imglib2-realtransform-2.0.0-beta-37.jar:lib/jitk-tps-2.1.1.jar:lib/ejml-0.24.jar:lib/log4j-1.2.17.jar:lib/mpicbg-1.1.1.jar:lib/opencsv-3.9.jar:lib/commons-beanutils-1.9.3.jar:lib/commons-logging-1.2.jar:lib/commons-collections-3.2.2.jar:lib/parsington-1.0.1.jar:lib/scripting-javascript-0.4.4.jar:lib/commons-math3-3.6.1.jar:lib/imagej-updater-0.8.3.jar:lib/scifio-0.32.0.jar:lib/scifio-jai-imageio-1.1.1.jar:lib/mapdb-1.0.3.jar:lib/scijava-common-2.64.0.jar:lib/gentyref-1.1.0.jar:lib/eventbus-1.4.jar:lib/imagej-legacy-0.25.0.jar:lib/ij1-patcher-0.12.6.jar:lib/ij-1.51n.jar:lib/imglib2-ij-2.0.0-beta-37.jar:lib/scijava-ui-awt-0.1.6.jar:lib/scijava-ui-swing-0.9.2.jar:lib/swing-checkbox-tree-1.0.2.jar:lib/jdatepicker-1.3.2.jar:lib/javassist-3.22.0-CR1.jar:lib/imagej-deprecated-0.1.2.jar:lib/imagej-plugins-commands-0.7.1.jar:lib/object-inspector-0.1.jar:lib/base64-2.3.8.jar:lib/imagej-plugins-tools-0.3.1.jar:lib/imagej-plugins-uploader-ssh-0.3.2.jar:lib/jsch-0.1.54.jar:lib/imagej-plugins-uploader-webdav-0.2.2.jar:lib/imagej-scripting-0.6.0.jar:lib/scripting-beanshell-0.3.2.jar:lib/bsh-2.0b6.jar:lib/scripting-clojure-0.1.6.jar:lib/clojure-1.8.0.jar:lib/scripting-groovy-0.2.6.jar:lib/groovy-2.4.8.jar:lib/ivy-2.2.0.jar:lib/scripting-java-0.4.1.jar:lib/minimaven-2.2.1.jar:lib/scripting-jruby-0.2.5.jar:lib/jruby-core-1.7.12.jar:lib/asm-4.0.jar:lib/asm-commons-4.0.jar:lib/asm-tree-4.0.jar:lib/asm-analysis-4.0.jar:lib/asm-util-4.0.jar:lib/joni-2.1.1.jar:lib/jnr-netdb-1.1.2.jar:lib/jnr-enxio-0.4.jar:lib/jnr-x86asm-1.0.2.jar:lib/jnr-unixsocket-0.3.jar:lib/jnr-posix-3.0.1.jar:lib/bytelist-1.0.11.jar:lib/jnr-constants-0.8.5.jar:lib/jcodings-1.0.10.jar:lib/jnr-ffi-1.0.7.jar:lib/jffi-1.2.7.jar:lib/jffi-1.2.7-native.jar:lib/snakeyaml-1.13.jar:lib/jzlib-1.1.3.jar:lib/invokebinder-1.2.jar:lib/nailgun-server-0.9.1.jar:lib/yecht-1.0.jar:lib/joda-time-2.9.9.jar:lib/options-1.1.jar:lib/jruby-stdlib-1.7.12.jar:lib/scripting-jython-0.4.1.jar:lib/jython-shaded-2.7.0.jar:lib/scripting-renjin-0.2.2.jar:lib/renjin-script-engine-0.8.1906.jar:lib/renjin-core-0.8.1906.jar:lib/commons-math-2.2.jar:lib/gcc-runtime-0.8.1906.jar:lib/netlib-java-0.9.3-renjin-patched-2.jar:lib/lapack-0.8.jar:lib/f2jutil-0.8.jar:lib/xerbla-0.8.jar:lib/blas-0.8.jar:lib/commons-vfs2-2.0.jar:lib/maven-scm-api-1.4.jar:lib/plexus-utils-1.5.6.jar:lib/maven-scm-provider-svnexe-1.4.jar:lib/maven-scm-provider-svn-commons-1.4.jar:lib/regexp-1.3.jar:lib/commons-compress-1.4.1.jar:lib/xz-1.0.jar:lib/jtransforms-2.4.jar:lib/jung-api-2.0.1.jar:lib/collections-generic-4.01.jar:lib/jung-graph-impl-2.0.1.jar:lib/guava-21.0.jar:lib/codemodel-2.6.jar:lib/stats-0.8.1906.jar:lib/renjin-appl-0.8.1906.jar:lib/renjin-gnur-runtime-0.8.1906.jar:lib/methods-0.8.1906.jar:lib/datasets-0.8.1906.jar:lib/utils-0.8.1906.jar:lib/grDevices-0.8.1906.jar:lib/graphics-0.8.1906.jar:lib/scripting-scala-0.2.1.jar:lib/scala-compiler-2.12.1.jar:lib/scala-library-2.12.1.jar:lib/scala-reflect-2.12.1.jar:lib/scala-xml_2.12-1.0.6.jar:lib/imagej-ui-swing-0.21.2.jar:lib/miglayout-3.7.4-swing.jar:lib/jfreechart-1.0.19.jar:lib/jcommon-1.0.24.jar:lib/jhotdraw-7.6.0.jar:lib/imagej-ui-awt-0.3.1.jar:lib/scijava-plugins-commands-0.2.3.jar:lib/scijava-plugins-platforms-0.3.0.jar:lib/scijava-plugins-text-markdown-0.1.3.jar:lib/markdownj-0.3.0-1.0.2b4.jar:lib/scijava-plugins-text-plain-0.1.3.jar:lib/commons-lang3-3.5.jar:lib/script-editor-0.1.4.jar:lib/rsyntaxtextarea-2.6.1.jar:lib/languagesupport-2.6.0.jar:lib/autocomplete-2.6.1.jar:lib/rhino-1.7.6.jar
app.runtime=$APPDIR/runtime
app.identifier=ImageJ

[JVMOptions]

[JVMUserOptions]

[ArgOptions]

#22

@mabruce @James_Minto Thank you for testing! It is unfortunate that the JavaFX launcher also has this problem. It sounds like a new bug in the Linux kernel.

@SarenT Of course we want to fix it. But this may be a tough one.

I don’t think it will matter. It seems clear that the native launcher (both the current one and the new JavaFX one) are linking to the JVM shared library and calling a function which segfaults. The fix probably needs to be upstream from ImageJ. But more investigation is needed.