Bug 247337 - biology/cytoscape fails to start
Summary: biology/cytoscape fails to start
Status: New
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: i386 Any
: --- Affects Only Me
Assignee: Yuri Victorovich
URL:
Keywords:
Depends on:
Blocks:
 
Reported: 2020-06-17 09:22 UTC by chris
Modified: 2020-06-17 20:39 UTC (History)
1 user (show)

See Also:
bugzilla: maintainer-feedback? (yuri)


Attachments

Note You need to log in before you can comment on or make changes to this bug.
Description chris 2020-06-17 09:22:33 UTC
Can anybody tell me how exactly does one start cytoscape? If I run the command "cytoscape" from the shell all I get is a splash screen followed by a cytoscape command prompt, i.e. with no gui interface.

Thanks
Comment 1 chris 2020-06-17 09:24:59 UTC
[Desktop]$ cytoscape
*** Missing Cytoscape.vmoptions, falling back to using defaults!
karaf.base: /usr/local/share/cytoscape/gui-distribution/assembly/target/cytoscape/framework
JAVA_HOME: /usr/local/openjdk8
FelixStartLevel WARN [org.ops4j.pax.url.mvn.internal.AetherBasedResolver] - Error resolving artifactorg.cytoscape.distribution:diagnostics-impl:jar:3.6.1:Could not find artifact org.cytoscape.distribution:diagnostics-impl:jar:3.6.1
shaded.org.eclipse.aether.resolution.ArtifactResolutionException: Could not find artifact org.cytoscape.distribution:diagnostics-impl:jar:3.6.1
	at shaded.org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:444)
	at shaded.org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifacts(DefaultArtifactResolver.java:246)
	at shaded.org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifact(DefaultArtifactResolver.java:223)
	at shaded.org.eclipse.aether.internal.impl.DefaultRepositorySystem.resolveArtifact(DefaultRepositorySystem.java:294)
	at org.ops4j.pax.url.mvn.internal.AetherBasedResolver.resolve(AetherBasedResolver.java:476)
	at org.ops4j.pax.url.mvn.internal.AetherBasedResolver.resolve(AetherBasedResolver.java:433)
	at org.ops4j.pax.url.mvn.internal.AetherBasedResolver.resolve(AetherBasedResolver.java:411)
	at org.ops4j.pax.url.mvn.internal.AetherBasedResolver.resolve(AetherBasedResolver.java:386)
	at org.ops4j.pax.url.mvn.internal.Connection.getInputStream(Connection.java:124)
	at java.net.URL.openStream(URL.java:1068)
	at org.apache.karaf.features.internal.BundleManager.getInputStreamForBundle(BundleManager.java:185)
	at org.apache.karaf.features.internal.BundleManager.doInstallBundleIfNeeded(BundleManager.java:95)
	at org.apache.karaf.features.internal.BundleManager.installBundleIfNeeded(BundleManager.java:89)
	at org.apache.karaf.features.internal.FeaturesServiceImpl.doInstallFeature(FeaturesServiceImpl.java:556)
	at org.apache.karaf.features.internal.FeaturesServiceImpl.installFeatures(FeaturesServiceImpl.java:419)
	at org.apache.karaf.features.internal.BootFeaturesInstaller.installBootFeatures(BootFeaturesInstaller.java:92)
	at org.apache.karaf.features.internal.BootFeaturesInstaller.start(BootFeaturesInstaller.java:76)
	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.apache.aries.blueprint.utils.ReflectionUtils.invoke(ReflectionUtils.java:297)
	at org.apache.aries.blueprint.container.BeanRecipe.invoke(BeanRecipe.java:958)
	at org.apache.aries.blueprint.container.BeanRecipe.runBeanProcInit(BeanRecipe.java:712)
	at org.apache.aries.blueprint.container.BeanRecipe.internalCreate2(BeanRecipe.java:824)
	at org.apache.aries.blueprint.container.BeanRecipe.internalCreate(BeanRecipe.java:787)
	at org.apache.aries.blueprint.di.AbstractRecipe$1.call(AbstractRecipe.java:79)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at org.apache.aries.blueprint.di.AbstractRecipe.create(AbstractRecipe.java:88)
	at org.apache.aries.blueprint.container.BlueprintRepository.createInstances(BlueprintRepository.java:245)
	at org.apache.aries.blueprint.container.BlueprintRepository.createAll(BlueprintRepository.java:183)
	at org.apache.aries.blueprint.container.BlueprintContainerImpl.instantiateEagerComponents(BlueprintContainerImpl.java:682)
	at org.apache.aries.blueprint.container.BlueprintContainerImpl.doRun(BlueprintContainerImpl.java:377)
	at org.apache.aries.blueprint.container.BlueprintContainerImpl.run(BlueprintContainerImpl.java:269)
	at org.apache.aries.blueprint.container.BlueprintExtender.createContainer(BlueprintExtender.java:294)
	at org.apache.aries.blueprint.container.BlueprintExtender.createContainer(BlueprintExtender.java:263)
	at org.apache.aries.blueprint.container.BlueprintExtender.modifiedBundle(BlueprintExtender.java:253)
	at org.apache.aries.util.tracker.hook.BundleHookBundleTracker$Tracked.customizerModified(BundleHookBundleTracker.java:500)
	at org.apache.aries.util.tracker.hook.BundleHookBundleTracker$Tracked.customizerModified(BundleHookBundleTracker.java:433)
	at org.apache.aries.util.tracker.hook.BundleHookBundleTracker$AbstractTracked.track(BundleHookBundleTracker.java:725)
	at org.apache.aries.util.tracker.hook.BundleHookBundleTracker$Tracked.bundleChanged(BundleHookBundleTracker.java:463)
	at org.apache.aries.util.tracker.hook.BundleHookBundleTracker$BundleEventHook.event(BundleHookBundleTracker.java:422)
	at org.apache.felix.framework.util.SecureAction.invokeBundleEventHook(SecureAction.java:1103)
	at org.apache.felix.framework.util.EventDispatcher.createWhitelistFromHooks(EventDispatcher.java:695)
	at org.apache.felix.framework.util.EventDispatcher.fireBundleEvent(EventDispatcher.java:483)
	at org.apache.felix.framework.Felix.fireBundleEvent(Felix.java:4403)
	at org.apache.felix.framework.Felix.startBundle(Felix.java:2092)
	at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)
	at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)
	at java.lang.Thread.run(Thread.java:748)
Caused by: shaded.org.eclipse.aether.transfer.ArtifactNotFoundException: Could not find artifact org.cytoscape.distribution:diagnostics-impl:jar:3.6.1
	at shaded.org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolve(DefaultArtifactResolver.java:434)
	... 49 more
             _                                    
   ___ _   _| |_  ___  ___  ___  __ _ _ __   ___  
  / __| | | | __|/ _ \/ __|/ __|/ _` | '_ \ / _ \ 
 | (__| |_| | |_| (_) \__ \ (__| (_| | |_) |  __/ 
  \___|\__, |\__|\___/|___/\___|\__,_| .__/ \___| 
       |___/                         |_|          

Cytoscape 3.6.1

Hit '<tab>' for a list of available commands
   and '[cmd] --help' for help on a specific command.
Hit '<ctrl-d>' or 'osgi:shutdown' to shutdown Cytoscape.

Cytoscape 3.6.1>
Comment 2 Yuri Victorovich freebsd_committer 2020-06-17 09:51:46 UTC
Thanks for your report.

It seems that the older version of Cytoscape doesn't work any more. JDK might have changed.

I'll try to update to 3.8.0 and see it it would work.


Yuri
Comment 3 chris 2020-06-17 12:09:32 UTC
OK, thanks Yuri.
Comment 4 Yuri Victorovich freebsd_committer 2020-06-17 20:39:01 UTC
I looked into updating it to the latest version. However, their main repository has one version, and the dependent repositories have an older version. This is confusing, I asked them to clarify this. No answer so far.