Starting Cytoscape with JAVA 9

[diyoyo]

Hi, 

I have had trouble starting Cytoscape using Java 9. Surprisingly, I get the following error:

 

I have tried decreasing the -Xmx in the cytoscape config, but it does not work. 

Everything works fine using jre1.8.0_144.

Any idea?

Thanks.

[Barry Demchak]

Hi –

 

Cytoscape does not support Java 9. Please use Java 8.

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[diyoyo]

Hi, 

I have seen that the 3.7.0 snapshot had been released and according to the roadmap, I guess it supports Java 9 now, doesn't it?

So I tried, and had to follow this suggestion : https://stackoverflow.com/questions/45917401/tomcat-7-0-73-doesnt-work-with-java-9 

In the end, I removed two lines of the karaf.bat to make it kind of start, but now I am stuck on the splashscreen with this message:

karaf.base: D:\PortableApps\PortableApps\Cytoscape_v3.7.0\framework\bin\..

WARNING: An illegal reflective access operation has occurred

WARNING: Illegal reflective access by org.apache.felix.framework.ext.ClassPathEx

tenderFactory$DefaultClassLoaderExtender (file:/D:/PortableApps/PortableApps/Cyt

oscape_v3.7.0/framework/system/org/apache/felix/org.apache.felix.framework/5.6.1

0/org.apache.felix.framework-5.6.10.jar) to method java.net.URLClassLoader.addUR

L(java.net.URL)

WARNING: Please consider reporting this to the maintainers of org.apache.felix.f

ramework.ext.ClassPathExtenderFactory$DefaultClassLoaderExtender

WARNING: Use --illegal-access=warn to enable warnings of further illegal reflect

ive access operations

WARNING: All illegal access operations will be denied in a future release

Is there any trick?

Thanks 

[David Otasek]

I haven't run into anything like this yet, but will test the windows execution again. What lines were removed from the .bat file?

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[David Otasek]

Also, how are you getting the snapshot build?

[diyoyo]

I am getting the snapshots here: http://code.cytoscape.org/jenkins/job/cytoscape-3-gui-distribution/lastSuccessfulBuild/org.cytoscape.distribution$cytoscape/

as mentioned here (Nighly builds) from here: http://cytoscape.org/download-platforms.html

I removed the two lines after $CLASSPATH definition, about "ext" and "endorsed". I forgot to make a backup first, but if I remember well, it was around line 417 from karaf.bat.

When I switched back the snapshot 3.7.0 to the JRE1.8.0_152, it worked well, even without these two lines.

[diyoyo]

So you confirm that it should work with Java9, right?

[diyoyo]

I have also tried with Mac and Java 9.0.4, and I get this error on the splashscreen (without removing any line or anything) : 

Exception in thread "main" java.lang.NoClassDefFoundError: com/apple/eawt/OpenFilesHandler

at org.cytoscape.launcher.internal.Launcher.main(Launcher.java:60)

Caused by: java.lang.ClassNotFoundException: com.apple.eawt.OpenFilesHandler

at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:582)

at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:185)

at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:496)

... 1 more

[David Otasek]

I can confirm; it should work with Java 9. I will try to replicate on a Windows machine myself, but at present I'm working on Linux. Has anyone else in the group run with Java 9 on Windows?

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[David Otasek]

I set up a machine to test on, and can replicate the issue.

There are instances of this issue and similar on the Karaf forums; the version of Karaf we're using for 3.7 is still a release candidate, and hasn't been made final. I will try to get a bug report to them quickly so they can offer us solutions or make fixes.

[David Otasek]

To confirm, these are the offending lines from the karaf.bat file:

-Djava.endorsed.dirs="%JAVA_HOME%\jre\lib\endorsed;%JAVA_HOME%\lib\endorsed;%KARAF_HOME%\lib\endorsed" ^
                -Djava.ext.dirs="%JAVA_HOME%\jre\lib\ext;%JAVA_HOME%\lib\ext;%KARAF_HOME%\lib\ext"

 

[David Otasek]

After a look at the karaf.bat script, and the nature of some of the karaf forum posts regarding similar errors, it looks like the script is executing thinking that Java 8 is still being run. 

Earlier in Karaf development, they had a similar problem compiling under Java 9, and the fix came rather quickly, and had to do with the logic they were using to identify Java versions.

I made them aware of the bug here, if you're interested in keeping track: https://issues.apache.org/jira/browse/KARAF-5611

[diyoyo]

Hi, 

even though the bug is marked as resolved, the problem is still present using the latest nightlies.

I haven't tried again, but it seems like the bug I previously reported for Mac is completely different from the karaf one, isn't it?

Cheers,

Y