BioArchLinux/Packages

[BUG] cytoscape: can't start

I-Love-BioArchLinux opened this issue · 13 comments

I-Love-BioArchLinux commented

Log of the bug

Can't start cytoscape

$ cytoscape
karaf: JAVA_HOME not set; results may vary
Error: LinkageError occurred while loading main class org.cytoscape.launcher.internal.Launcher
        java.lang.UnsupportedClassVersionError: org/cytoscape/launcher/internal/Launcher has been compiled by a more recent version of the Java Runtime (class file version 61.0), this version of the Java Runtime only recognizes class file versions up to 55.0

Desktop (please complete the following information):

  • Desktop Enviroment: kde
  • Linux Kernel: 6.3.6-arch1-1
  • Package Version: 3.10.0-1
starsareintherose commented

What's your java version

Deleted user commented

What's your java version

java-20-openjdk

starsareintherose commented

Java-runtime=11 is needed

Deleted user commented 
$ archlinux-java status
Available Java environments:
  java-11-openjdk (default)
  java-17-openjdk
  java-20-openjdk
  java-8-openjdk
$ cytoscape
karaf: JAVA_HOME not set; results may vary
Error: LinkageError occurred while loading main class org.cytoscape.launcher.internal.Launcher
        java.lang.UnsupportedClassVersionError: org/cytoscape/launcher/internal/Launcher has been compiled by a more recent version of the Java Runtime (class file version 61.0), this version of the Java Runtime only recognizes class file versions up to 55.0

still

starsareintherose commented

what about java 17?

starsareintherose commented

compile error here

[INFO] 
[INFO] ------------------------------------------------------------------------
[INFO] Skipping Distribution
[INFO] This project has been banned from the build due to previous failures.
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] -----------------------< org.cytoscape:project >------------------------
[INFO] Building Cytoscape Project POM 3.11.0-SNAPSHOT                  [22/122]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-install-plugin:2.4:install (default-install) @ project ---
[INFO] Installing /home/guoyi/Downloads/cytoscape-3.10.0/cytoscape/pom.xml to /home/guoyi/.m2/repository/org/cytoscape/project/3.11.0-SNAPSHOT/project-3.11.0-SNAPSHOT.pom
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Cytoscape Project POM 3.11.0-SNAPSHOT:
[INFO] 
[INFO] Basic Cytoscape POM Configuration .................. SUCCESS [  0.279 s]
[INFO] Cytoscape API Parent Project POM ................... FAILURE [  4.278 s]
[INFO] Cytoscape Documentation Taglets .................... SKIPPED
[INFO] Cytoscape Event API (event-api) .................... SKIPPED
[INFO] Cytoscape Model API (model-api) .................... SKIPPED
[INFO] Cytoscape Service API (service-api) ................ SKIPPED
[INFO] Cytoscape View Model API (viewmodel-api) ........... SKIPPED
[INFO] Cytoscape CI API (ci-api) .......................... SKIPPED
[INFO] Cytoscape Work API (work-api) ...................... SKIPPED
[INFO] Cytoscape Util API (util-api) ...................... SKIPPED
[INFO] Cytoscape Swing Utility API (swing-util-api) ....... SKIPPED
[INFO] Cytoscape Presentation API (presentation-api) ...... SKIPPED
[INFO] Cytoscape Application API (application-api) ........ SKIPPED
[INFO] Cytoscape Property API (property-api) .............. SKIPPED
[INFO] Cytoscape VizMap API (vizmap-api) .................. SKIPPED
[INFO] Cytoscape Session API (session-api) ................ SKIPPED
[INFO] Cytoscape Filter API (filter-api) .................. SKIPPED
[INFO] Cytoscape IO API (io-api) .......................... SKIPPED
[INFO] Cytoscape Core Task API (core-task-api) ............ SKIPPED
[INFO] Cytoscape Equations API (equations-api) ............ SKIPPED
[INFO] Cytoscape Layout API (layout-api) .................. SKIPPED
[INFO] Cytoscape Groups API (group-api) ................... SKIPPED
[INFO] Cytoscape Groups API (jobs-api) .................... SKIPPED
[INFO] Cytoscape Webservice API (webservice-api) .......... SKIPPED
[INFO] Cytoscape Data Source API (datasource-api) ......... SKIPPED
[INFO] Cytoscape Command Executor API (command-executor-api) SKIPPED
[INFO] Cytoscape OpenCL API (cycl-api) .................... SKIPPED
[INFO] Cytoscape App API (app-api) ........................ SKIPPED
[INFO] Cytoscape Work Swing API (work-swing-api) .......... SKIPPED
[INFO] Cytoscape Swing Application API (swing-application-api) SKIPPED
[INFO] Cytoscape VizMap GUI API (vizmap-gui-api) .......... SKIPPED
[INFO] Cytoscape Webservice Swing API (webservice-swing-api) SKIPPED
[INFO] Cytoscape Swing App API (swing-app-api) ............ SKIPPED
[INFO] Cytoscape API (api-bundle) ......................... SKIPPED
[INFO] Cytoscape Implementation Parent Project POM ........ SKIPPED
[INFO] Cytoscape Equations Impl (equations-impl) .......... SKIPPED
[INFO] Cytoscape Model Impl Parent (model-impl-parent) .... SKIPPED
[INFO] Cytoscape Model Impl (model-impl) .................. SKIPPED
[INFO] Cytoscape Command Executor Impl (command-executor-impl) SKIPPED
[INFO] Cytoscape Custom Graphics Internal (custom-graphics-internal) SKIPPED
[INFO] Cytoscape View Model Impl Parent (viewmodel-impl-parent) SKIPPED
[INFO] Cytoscape View Model Impl (viewmodel-impl) ......... SKIPPED
[INFO] Cytoscape Ding Impl Parent (ding-impl) ............. SKIPPED
[INFO] Cytoscape Ding View/Presentation Impl (ding-presentation-impl) SKIPPED
[INFO] Cytoscape Groups Impl (group-impl) ................. SKIPPED
[INFO] Cytoscape Event Impl Parent (event-impl-parent) .... SKIPPED
[INFO] Cytoscape Event Impl (event-impl) .................. SKIPPED
[INFO] Cytoscape Filters Impl (filter-impl) ............... SKIPPED
[INFO] Cytoscape Filters 2 Impl (filter2-impl) ............ SKIPPED
[INFO] Cytoscape IO Impl Parent (io-impl-parent) .......... SKIPPED
[INFO] Cytoscape IO Impl (io-impl) ........................ SKIPPED
[INFO] Cytoscape Layout Impl (layout-impl) ................ SKIPPED
[INFO] Cytoscape Ding View/Presentation Impl Performance (ding-impl-performance-debug) SKIPPED
[INFO] Cytoscape Editor Impl (editor-impl) ................ SKIPPED
[INFO] Cytoscape Equation Functions Impl (equations-functions-impl) SKIPPED
[INFO] Cytoscape GraphML Impl (graphml-impl) .............. SKIPPED
[INFO] Cytoscape IO Impl Performance (io-impl-performance)  SKIPPED
[INFO] Cytoscape Jobs Impl (jobs-impl) .................... SKIPPED
[INFO] Cytoscape Layout Algorithms Impl (layout-cytoscape-impl) SKIPPED
[INFO] Cytoscape JGraph Layout Impl (layout-jgraph-impl) .. SKIPPED
[INFO] Cytoscape Prefuse Layout Impl (layout-prefuse-impl)  SKIPPED
[INFO] Cytoscape Linkout Impl (linkout-impl) .............. SKIPPED
[INFO] Cytoscape Log Swing Impl (log-swing-impl) .......... SKIPPED
[INFO] Cytoscape Manual Layout Impl (manual-layout-impl) .. SKIPPED
[INFO] Cytoscape Model Impl Performance Debug (model-impl-performance-debug) SKIPPED
[INFO] Cytoscape Model Impl Table Performance Debug (model-impl-table-performance-debug) SKIPPED
[INFO] Cytoscape App Impl (app-impl) ...................... SKIPPED
[INFO] Cytoscape Presentation Impl (presentation-impl) .... SKIPPED
[INFO] Cytoscape Property Impl (property-impl) ............ SKIPPED
[INFO] Cytoscape Search Impl 2 (search2-impl) ............. SKIPPED
[INFO] Cytoscape Session Impl (session-impl) .............. SKIPPED
[INFO] Cytoscape Swing Utility Impl (swing-util-impl) ..... SKIPPED
[INFO] Cytoscape Swing Application Impl (swing-application-impl) SKIPPED
[INFO] Cytoscape Table Browser Impl (table-browser-impl) .. SKIPPED
[INFO] Cytoscape Table Import Impl (table-import-impl) .... SKIPPED
[INFO] Cytoscape Table Renderer (table-presentation-impl) . SKIPPED
[INFO] Cytoscape VizMap GUI Core Impl (vizmap-gui-core-impl) SKIPPED
[INFO] Cytoscape VizMap GUI Impl (vizmap-gui-impl) ........ SKIPPED
[INFO] Cytoscape VizMap Impl Parent (vizmap-impl-parent) .. SKIPPED
[INFO] Cytoscape VizMap Impl (vizmap-impl) ................ SKIPPED
[INFO] Cytoscape Webservice Impl (webservice-impl) ........ SKIPPED
[INFO] org.cytoscape.work-headless-impl ................... SKIPPED
[INFO] org.cytoscape.work-impl ............................ SKIPPED
[INFO] Cytoscape Work Swing Impl Parent (work-swing-impl-parent) SKIPPED
[INFO] Cytoscape Work Swing Impl (work-swing-impl) ........ SKIPPED
[INFO] Cytoscape Application Impl (application-impl) ...... SKIPPED
[INFO] Cytoscape Datasource Impl (datasource-impl) ........ SKIPPED
[INFO] Cytoscape Support Parent Project POM ............... SUCCESS [  0.006 s]
[INFO] Cytoscape Launch Framework ......................... SUCCESS [  0.004 s]
[INFO] CommandLine Provider ............................... FAILURE [  0.213 s]
[INFO] Cytoscape GUI Command Line Parser Impl (gui-cmdline-parser-impl) SKIPPED
[INFO] Cytoscape Edge Bundler Impl (edge-bundler-impl) .... SKIPPED
[INFO] Cytoscape Core Task Impl (core-task-impl) .......... SKIPPED
[INFO] Cytoscape CyCL Impl (cycl-impl) .................... SKIPPED
[INFO] Cytoscape Utils org.cytoscape.util-impl ............ SKIPPED
[INFO] Cytoscape Headless Application Impl (headless-application-impl) SKIPPED
[INFO] org.cytoscape.cy-commons-cli ....................... FAILURE [  0.232 s]
[INFO] Cytoscape Headless Command Line Parser Impl (headless-cmdline-parser-impl) SKIPPED
[INFO] Cytoscape 3 App Archetypes Parent .................. SUCCESS [  0.090 s]
[INFO] Cytoscape 3 Archetype - Creates an App providing public API SUCCESS [  0.218 s]
[INFO] Cytoscape 3 Archetype - Creates an App with a Task . SUCCESS [  0.035 s]
[INFO] Cytoscape 3 Archetype - Creates a CyAction (menu item) for desktop application SUCCESS [  0.029 s]
[INFO] Cytoscape 3 Archetype - Creates a Meta-App to install multiple related apps SUCCESS [  0.030 s]
[INFO] Cytoscape 3 Archetype - Creates a Starter App ...... SUCCESS [  0.046 s]
[INFO] org.cytoscape.integration-test-support ............. FAILURE [  0.035 s]
[INFO] Launcher ........................................... SKIPPED
[INFO] StartLevel Assembly ................................ SUCCESS [  0.319 s]
[INFO] Tasks for Testing .................................. SKIPPED
[INFO] Cytoscape Desktop Application Distribution ......... SUCCESS [  0.005 s]
[INFO] Cytoscape Third-Party Dependencies (third-party) ... FAILURE [ 11.030 s]
[INFO] SplashScreen Launcher .............................. SKIPPED
[INFO] Cytoscape Launcher ................................. FAILURE [  0.775 s]
[INFO] Splash Updater ..................................... SKIPPED
[INFO] Cytoscape Command Line Provider Implementation ..... SKIPPED
[INFO] Cytoscape Diagnostics .............................. SKIPPED
[INFO] Cytoscape Branding ................................. SUCCESS [  0.884 s]
[INFO] Cytoscape Application Implementation Metadata ...... SUCCESS [  0.120 s]
[INFO] Cytoscape GUI-Distribution Integration Test (integration-test) SKIPPED
[INFO] Cytoscape Feature Repository ....................... SUCCESS [  0.127 s]
[INFO] Cytoscape Karaf Distribution ....................... FAILURE [57:45 min]
[INFO] Distribution ....................................... SKIPPED
[INFO] Cytoscape Project POM .............................. SUCCESS [  0.028 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  58:05 min
[INFO] Finished at: 2023-07-13T23:48:25+08:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project property-api: Could not resolve dependencies for project org.cytoscape:property-api:bundle:3.11.0-SNAPSHOT: Could not transfer artifact org.cytoscape:event-api:jar:3.11.0-SNAPSHOT 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), cytoscape_thirdparty (http://nrnb-nexus.ucsd.edu/repository/cytoscape_thirdparty/, default, releases)] -> [Help 1]
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.0:compile (default-compile) on project cmdline: Fatal error compiling: 错误: 不支持发行版本 17 -> [Help 2]
[ERROR] Failed to execute goal on project cy-commons-cli: Could not resolve dependencies for project org.cytoscape:cy-commons-cli:bundle:3.11.0-SNAPSHOT: Failed to collect dependencies at org.apache.commons:com.springsource.org.apache.commons.lang:jar:2.4.0: Failed to read artifact descriptor for org.apache.commons:com.springsource.org.apache.commons.lang:jar:2.4.0: Could not transfer artifact org.apache.commons:com.springsource.org.apache.commons.lang:pom:2.4.0 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), cytoscape_thirdparty (http://nrnb-nexus.ucsd.edu/repository/cytoscape_thirdparty/, default, releases)] -> [Help 1]
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.0:compile (default-compile) on project integration-test-support: Fatal error compiling: 错误: 不支持发行版本 17 -> [Help 2]
[ERROR] Failed to execute goal on project third-party: Could not resolve dependencies for project org.cytoscape.distribution:third-party:bundle:3.11.0-SNAPSHOT: Failed to collect dependencies at cytoscape-temp:l2fprod-common-sheet:jar:7.3: Failed to read artifact descriptor for cytoscape-temp:l2fprod-common-sheet:jar:7.3: Could not transfer artifact cytoscape-temp:l2fprod-common-sheet:pom:7.3 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), cytoscape_thirdparty (http://nrnb-nexus.ucsd.edu/repository/cytoscape_thirdparty/, default, releases)] -> [Help 1]
[ERROR] Failed to execute goal on project karaf-launcher: Could not resolve dependencies for project org.cytoscape.distribution:karaf-launcher:bundle:3.11.0-SNAPSHOT: Failed to collect dependencies at com.apple.developer:AppleJavaExtensions:jar:1.6: Failed to read artifact descriptor for com.apple.developer:AppleJavaExtensions:jar:1.6: Could not transfer artifact com.apple.developer:AppleJavaExtensions:pom:1.6 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), cytoscape_thirdparty (http://nrnb-nexus.ucsd.edu/repository/cytoscape_thirdparty/, default, releases)] -> [Help 1]
[ERROR] Failed to execute goal org.apache.karaf.tooling:karaf-maven-plugin:4.3.7:features-add-to-repository (add-features-to-repo) on project cytoscape: Error populating repository: Error resolving feature cytoscape-gui/3.11.0.SNAPSHOT: Error resolving artifact mvn:org.cytoscape.distribution/diagnostics-impl/3.11.0-SNAPSHOT: Can't resolve artifact org.cytoscape.distribution:diagnostics-impl:jar:3.11.0-SNAPSHOT: Could not transfer artifact org.cytoscape.distribution:diagnostics-impl:jar:3.11.0-SNAPSHOT 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), cytoscape_thirdparty (http://nrnb-nexus.ucsd.edu/repository/cytoscape_thirdparty/, default, releases)]
[ERROR]   org.cytoscape.distribution:diagnostics-impl:jar:3.11.0-SNAPSHOT
[ERROR] 
[ERROR] from the specified remote repositories:
[ERROR]   maven-default-http-blocker (http://0.0.0.0/, releases=true, snapshots=true),
[ERROR]   central (https://repo.maven.apache.org/maven2, releases=true, snapshots=false)
[ERROR] -> [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/DependencyResolutionException
[ERROR] [Help 2] 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 :property-api

may report later

Deleted user commented

you don't have computer?

what about java 17?

  • 👎1
starsareintherose commented

you don't have computer?

what about java 17?

@Kiri2002 explain what you mean

hubutui commented 
xxx  has been compiled by a more recent version of the Java Runtime (class file version 61.0), this version of the Java Runtime only recognizes class file versions up to 55.0

means the app is compiled with a new JDK but you run it with an old JDK. You could check the coressponding class file version and JDK version here. It seems that the app is compiled with JDK 17, but you run it with JDK 11.

According to

Packages/BioArchLinux/cytoscape/PKGBUILD

Line 13 in 4fc21ef

source=("https://github.com/cytoscape/cytoscape/releases/download/${pkgver}/cytoscape-unix-${pkgver}.tar.gz"

this pkg is compiled by upstream, we just repack it, and they use JDK 17.
So, we need to update the deps:

Packages/BioArchLinux/cytoscape/PKGBUILD

Line 12 in 4fc21ef

depends=('java-runtime=11' 'bash')

@starsareintherose

Deleted user commented 
$ archlinux-java status
Available Java environments:
  java-11-openjdk
  java-17-openjdk (default)
  java-20-openjdk
  java-8-openjdk
$ cytoscape
karaf: JAVA_HOME not set; results may vary
Error: LinkageError occurred while loading main class org.cytoscape.launcher.internal.Launcher
        java.lang.UnsupportedClassVersionError: org/cytoscape/launcher/internal/Launcher has been compiled by a more recent version of the Java Runtime (class file version 61.0), this version of the Java Runtime only recognizes class file versions up to 55.0

  I already tried all,  java-20 18 11 17-openjdk, all same err
hubutui commented

@ReKiritsugu You could run /opt/cytoscape/cytoscape.sh, /usr/bin/cytoscape will modify your PATH. Also check your PATH. What's the ouput of echo $PATH?

Deleted user commented

@ReKiritsugu You could run /opt/cytoscape/cytoscape.sh, /usr/bin/cytoscape will modify your PATH. Also check your PATH. What's the ouput of echo $PATH?

run /opt/cytoscape/cytoscape.sh works! 20 and17 works, while 8 and 11 down.

retried, 20 also down (stuck at the start GUI)
image

so deps change to >=17 ==17
you r so smart!!!!!

Deleted user commented

and also should modify the entry to using java-17 to run /opt/cytoscape/cytoscape.sh