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
[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>
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
OK, thanks Yuri.
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.
Any progress on this? Looks like there's a newer version available.
Created attachment 238321 [details] patch Hi Jason, While trying to update the port to 3.9.1 I encountered an error. Just reported it to https://cytoscape.org/bug-report.html This website promised that they will respond in several days. Thanks, Yuri ----error---- [ERROR] [ERROR] Some problems were encountered while processing the POMs: [FATAL] Non-resolvable parent POM for org.cytoscape.app-developer:cytoscape:3.9.0: Could not transfer artifact org.cytoscape:parent:pom:3.9.0 from/to maven-default-http-blocker (http://0.0.0.0/): Blocked mirror for repositories: [cytoscape_snapshots (http://nrnb-nexus.ucsd.edu/repository/cytoscape_snapshots/, default, snapshots), cytoscape_releases (http://nrnb-nexus.ucsd.edu/repository/cytoscape_releases/, default, releases)] and 'parent.relativePath' points at wrong local POM @ line 4, column 10 [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.cytoscape:jobs-api:jar -> duplicate declaration of version ${project.version} @ line 191, column 15 @ [ERROR] The build could not read 1 project -> [Help 1] [ERROR] [ERROR] The project org.cytoscape.app-developer:cytoscape:3.9.0 (/disk-samsung/freebsd-ports/biology/cytoscape/work/cytoscape-3.9.1/app-developer/pom.xml) has 1 error [ERROR] Non-resolvable parent POM for org.cytoscape.app-developer:cytoscape:3.9.0: Could not transfer artifact org.cytoscape:parent:pom:3.9.0 from/to maven-default-http-blocker (http://0.0.0.0/): Blocked mirror for repositories: [cytoscape_snapshots (http://nrnb-nexus.ucsd.edu/repository/cytoscape_snapshots/, default, snapshots), cytoscape_releases (http://nrnb-nexus.ucsd.edu/repository/cytoscape_releases/, default, releases)] and 'parent.relativePath' points at wrong local POM @ line 4, column 10 -> [Help 2] [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/ProjectBuildingException [ERROR] [Help 2] http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException *** Error code 1
I resolved the previous issue by using maven-3.6.3 But the latest version now fails with another error. Updating the URL of the bug report. ----------------------------------- [INFO] Reactor Summary: [INFO] [INFO] Basic Cytoscape POM Configuration 3.8.2 ............ SUCCESS [ 4.602 s] [INFO] Cytoscape API Parent Project POM 3.8.2 ............. SUCCESS [ 21.404 s] [INFO] Cytoscape Documentation Taglets 3.8.2 .............. FAILURE [ 1.300 s] [INFO] Cytoscape Event API (event-api) 3.8.2 .............. FAILURE [ 0.413 s] [INFO] Cytoscape Model API (model-api) 3.8.2 .............. SKIPPED [INFO] Cytoscape Service API (service-api) 3.8.2 .......... FAILURE [ 0.200 s] [INFO] Cytoscape View Model API (viewmodel-api) 3.8.2 ..... SKIPPED [INFO] Cytoscape CI API (ci-api) 3.8.2 .................... SUCCESS [ 9.123 s] [INFO] Cytoscape Work API (work-api) 3.8.2 ................ FAILURE [ 0.646 s] [INFO] Cytoscape Presentation API (presentation-api) 3.8.2 SKIPPED [INFO] Cytoscape Application API (application-api) 3.8.2 .. SKIPPED [INFO] Cytoscape Property API (property-api) 3.8.2 ........ SKIPPED [INFO] Cytoscape VizMap API (vizmap-api) 3.8.2 ............ SKIPPED [INFO] Cytoscape Session API (session-api) 3.8.2 .......... SKIPPED [INFO] Cytoscape Filter API (filter-api) 3.8.2 ............ SKIPPED [INFO] Cytoscape IO API (io-api) 3.8.2 .................... SKIPPED [INFO] Cytoscape Core Task API (core-task-api) 3.8.2 ...... SKIPPED [INFO] Cytoscape Equations API (equations-api) 3.8.2 ...... SKIPPED [INFO] Cytoscape Layout API (layout-api) 3.8.2 ............ SKIPPED [INFO] Cytoscape Groups API (group-api) 3.8.2 ............. SKIPPED [INFO] Cytoscape Groups API (jobs-api) 3.8.2 .............. SKIPPED [INFO] Cytoscape Webservice API (webservice-api) 3.8.2 .... SKIPPED [INFO] Cytoscape Data Source API (datasource-api) 3.8.2 ... SKIPPED [INFO] Cytoscape Command Executor API (command-executor-api) 3.8.2 SKIPPED [INFO] Cytoscape Util API (util-api) 3.8.2 ................ SKIPPED [INFO] Cytoscape App API (app-api) 3.8.2 .................. SKIPPED [INFO] Cytoscape Work Swing API (work-swing-api) 3.8.2 .... SKIPPED [INFO] Cytoscape Swing Utility API (swing-util-api) 3.8.2 . SKIPPED [INFO] Cytoscape Swing Application API (swing-application-api) 3.8.2 SKIPPED [INFO] Cytoscape VizMap GUI API (vizmap-gui-api) 3.8.2 .... SKIPPED [INFO] Cytoscape Webservice Swing API (webservice-swing-api) 3.8.2 SKIPPED [INFO] Cytoscape Swing App API (swing-app-api) 3.8.2 ...... SKIPPED [INFO] Cytoscape API (api-bundle) 3.8.2 ................... SKIPPED [INFO] Cytoscape Implementation Parent Project POM 3.8.2 .. SKIPPED [INFO] Cytoscape Equations Impl (equations-impl) 3.8.2 .... SKIPPED [INFO] Cytoscape Model Impl Parent (model-impl-parent) 3.8.2 SKIPPED [INFO] Cytoscape Model Impl (model-impl) 3.8.2 ............ SKIPPED [INFO] Cytoscape Command Executor Impl (command-executor-impl) 3.8.2 SKIPPED [INFO] Cytoscape View Model Impl Parent (viewmodel-impl-parent) 3.8.2 SKIPPED [INFO] Cytoscape View Model Impl (viewmodel-impl) 3.8.2 ... SKIPPED [INFO] Cytoscape Ding Impl Parent (ding-impl) 3.8.2 ....... SKIPPED [INFO] Cytoscape Ding View/Presentation Impl (ding-presentation-impl) 3.8.2 SKIPPED [INFO] Cytoscape Groups Impl (group-impl) 3.8.2 ........... SKIPPED [INFO] Cytoscape Event Impl Parent (event-impl-parent) 3.8.2 SKIPPED [INFO] Cytoscape Event Impl (event-impl) 3.8.2 ............ SKIPPED [INFO] Cytoscape Filters Impl (filter-impl) 3.8.2 ......... SKIPPED [INFO] Cytoscape Filters 2 Impl (filter2-impl) 3.8.2 ...... SKIPPED [INFO] Cytoscape IO Impl Parent (io-impl-parent) 3.8.2 .... SKIPPED [INFO] Cytoscape IO Impl (io-impl) 3.8.2 .................. SKIPPED [INFO] Cytoscape Layout Impl (layout-impl) 3.8.2 .......... SKIPPED [INFO] Cytoscape Ding View/Presentation Impl Performance (ding-impl-performance-debug) 3.8.2 SKIPPED [INFO] Cytoscape Editor Impl (editor-impl) 3.8.2 .......... SKIPPED [INFO] Cytoscape Equation Functions Impl (equations-functions-impl) 3.8.2 SKIPPED [INFO] Cytoscape GraphML Impl (graphml-impl) 3.8.2 ........ SKIPPED [INFO] Cytoscape IO Impl Performance (io-impl-performance) 3.8.2 SKIPPED [INFO] Cytoscape Jobs Impl (jobs-impl) 3.8.2 .............. SKIPPED [INFO] Cytoscape Layout Algorithms Impl (layout-cytoscape-impl) 3.8.2 SKIPPED [INFO] Cytoscape JGraph Layout Impl (layout-jgraph-impl) 3.8.2 SKIPPED [INFO] Cytoscape Prefuse Layout Impl (layout-prefuse-impl) 3.8.2 SKIPPED [INFO] Cytoscape Linkout Impl (linkout-impl) 3.8.2 ........ SKIPPED [INFO] Cytoscape Log Swing Impl (log-swing-impl) 3.8.2 .... SKIPPED [INFO] Cytoscape Manual Layout Impl (manual-layout-impl) 3.8.2 SKIPPED [INFO] Cytoscape Model Impl Performance Debug (model-impl-performance-debug) 3.8.2 SKIPPED [INFO] Cytoscape Model Impl Table Performance Debug (model-impl-table-performance-debug) 3.8.2 SKIPPED [INFO] Cytoscape App Impl (app-impl) 3.8.2 ................ SKIPPED [INFO] Cytoscape Presentation Impl (presentation-impl) 3.8.2 SKIPPED [INFO] Cytoscape Property Impl (property-impl) 3.8.2 ...... SKIPPED [INFO] Cytoscape Search Impl (search-impl) 3.8.2 .......... SKIPPED [INFO] Cytoscape Session Impl (session-impl) 3.8.2 ........ SKIPPED [INFO] Cytoscape Swing Utility Impl (swing-util-impl) 3.8.2 SKIPPED [INFO] Cytoscape Swing Application Impl (swing-application-impl) 3.8.2 SKIPPED [INFO] Cytoscape Table Browser Impl (table-browser-impl) 3.8.2 SKIPPED [INFO] Cytoscape Table Import Impl (table-import-impl) 3.8.2 SKIPPED [INFO] Cytoscape VizMap GUI Core Impl (vizmap-gui-core-impl) 3.8.2 SKIPPED [INFO] Cytoscape VizMap GUI Impl (vizmap-gui-impl) 3.8.2 .. SKIPPED [INFO] Cytoscape VizMap Impl Parent (vizmap-impl-parent) 3.8.2 SKIPPED [INFO] Cytoscape VizMap Impl (vizmap-impl) 3.8.2 .......... SKIPPED [INFO] Cytoscape Webservice Impl (webservice-impl) 3.8.2 .. SKIPPED [INFO] org.cytoscape.work-headless-impl 3.8.2 ............. SKIPPED [INFO] org.cytoscape.work-impl 3.8.2 ...................... SKIPPED [INFO] Cytoscape Work Swing Impl Parent (work-swing-impl-parent) 3.8.2 SKIPPED [INFO] Cytoscape Work Swing Impl (work-swing-impl) 3.8.2 .. SKIPPED [INFO] Cytoscape Application Impl (application-impl) 3.8.2 SKIPPED [INFO] Cytoscape Datasource Impl (datasource-impl) 3.8.2 .. SKIPPED [INFO] Cytoscape Support Parent Project POM 3.8.2 ......... SUCCESS [ 0.022 s] [INFO] Cytoscape Launch Framework 3.8.2 ................... SUCCESS [ 0.016 s] [INFO] CommandLine Provider 3.8.2 ......................... FAILURE [ 0.012 s] [INFO] Cytoscape GUI Command Line Parser Impl (gui-cmdline-parser-impl) 3.8.2 SKIPPED [INFO] Cytoscape Edge Bundler Impl (edge-bundler-impl) 3.8.2 SKIPPED [INFO] Cytoscape Scripting Impl (scripting-impl) 3.8.2 .... SKIPPED [INFO] Cytoscape Core Task Impl (core-task-impl) 3.8.2 .... SKIPPED [INFO] Cytoscape Utils org.cytoscape.util-impl 3.8.2 ...... SKIPPED [INFO] Cytoscape Headless Application Impl (headless-application-impl) 3.8.2 SKIPPED [INFO] org.cytoscape.cy-commons-cli 3.8.2 ................. FAILURE [ 0.020 s] [INFO] Cytoscape Headless Command Line Parser Impl (headless-cmdline-parser-impl) 3.8.2 SKIPPED [INFO] Cytoscape 3 App Archetypes Parent 3.8.2 ............ SUCCESS [ 0.492 s] [INFO] Cytoscape 3 Archetype - Creates an App providing public API 3.8.2 SUCCESS [ 0.818 s] [INFO] Cytoscape 3 Archetype - Creates an App with a Task 3.8.2 SUCCESS [ 0.378 s] [INFO] Cytoscape 3 Archetype - Creates a CyAction (menu item) for desktop application 3.8.2 SUCCESS [ 0.392 s] [INFO] Cytoscape 3 Archetype - Creates a Meta-App to install multiple related apps 3.8.2 SUCCESS [ 0.454 s] [INFO] org.cytoscape.integration-test-support 3.8.2 ....... FAILURE [ 0.080 s] [INFO] Launcher 3.8.2 ..................................... SKIPPED [INFO] StartLevel Assembly 3.8.2 .......................... SUCCESS [ 1.335 s] [INFO] Tasks for Testing 3.8.2 ............................ SKIPPED [INFO] Cytoscape Desktop Application Distribution 3.8.2 ... SUCCESS [ 0.056 s] [INFO] Cytoscape Third-Party Dependencies (third-party) 3.8.2 SUCCESS [01:02 min] [INFO] SplashScreen Launcher 3.8.2 ........................ SKIPPED [INFO] Cytoscape Launcher 3.8.2 ........................... FAILURE [ 0.104 s] [INFO] Splash Updater 3.8.2 ............................... SKIPPED [INFO] Cytoscape Command Line Provider Implementation 3.8.2 SKIPPED [INFO] Cytoscape Diagnostics 3.8.2 ........................ SKIPPED [INFO] Cytoscape Branding 3.8.2 ........................... SUCCESS [ 1.026 s] [INFO] Cytoscape Application Implementation Metadata 3.8.2 SUCCESS [ 0.689 s] [INFO] Cytoscape GUI-Distribution Integration Test (integration-test) 3.8.2 SKIPPED [INFO] Cytoscape Feature Repository 3.8.2 ................. SUCCESS [ 0.336 s] [INFO] Cytoscape Karaf Distribution 3.8.2 ................. SUCCESS [ 58.569 s] [INFO] Distribution 3.9.0 ................................. SUCCESS [ 12.264 s] [INFO] Cytoscape Project POM 3.9.1-SNAPSHOT ............... SUCCESS [ 0.359 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 03:10 min [INFO] Finished at: 2022-11-24T13:47:22-08:00 [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project taglets: Fatal error compiling: invalid flag: --release -> [Help 1] [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project event-api: Fatal error compiling: invalid flag: --release -> [Help 1] [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project service-api: Fatal error compiling: invalid flag: --release -> [Help 1] [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project work-api: Fatal error compiling: invalid flag: --release -> [Help 1] [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project cmdline: Fatal error compiling: invalid flag: --release -> [Help 1] [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project cy-commons-cli: Fatal error compiling: invalid flag: --release -> [Help 1] [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project integration-test-support: Fatal error compiling: invalid flag: --release -> [Help 1] [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project karaf-launcher: Fatal error compiling: invalid flag: --release -> [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/MojoExecutionException [ERROR] [ERROR] After correcting the problems, you can resume the build with the command [ERROR] mvn <args> -rf :taglets *** Error code 1
Thanks for checking. FYI, this is not important to me. I was just browsing PRs and noticed how old this one was, so I sent a ping.
(In reply to Jason W. Bacon from comment #8) Thanks for pinging.