See
<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/131/changes>
Changes:
[pwang] Fixed bug#518
[pwang] Fixed bug#509
[mes] refactored CyApplication to work with CyNetworks and CyNetworkViews
instead of suids
[pwang] Fixed bug#511
------------------------------------------
[...truncated 4295 lines...]
Running org.cytoscape.equations.internal.builtins.RadiansTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec
Running org.cytoscape.equations.internal.builtins.NthTest
Error while compiling "=NTH(${list2}, 5)": 6: unknown variable reference name:
"list2"!
Error while compiling "=NTH(${list2}, 0)": 6: unknown variable reference name:
"list2"!
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec
Running org.cytoscape.equations.internal.builtins.IListTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec
Running org.cytoscape.equations.internal.builtins.TodayTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec
Running org.cytoscape.equations.internal.builtins.ProductTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec
Running org.cytoscape.equations.internal.builtins.LargestTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec
Running org.cytoscape.equations.internal.builtins.SListTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec
Running org.cytoscape.equations.internal.builtins.LastTest
Error while compiling "=LAST(${list2})": 7: unknown variable reference name:
"list2"!
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec
Running org.cytoscape.equations.internal.builtins.RoundTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec
Running org.cytoscape.equations.internal.builtins.SignTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec
Running org.cytoscape.equations.internal.builtins.MinTest
Error while compiling "=MIN()": 4: invalid number or type of arguments in call
to MIN()!
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec
Running org.cytoscape.equations.internal.builtins.NowTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec
Running org.cytoscape.equations.internal.builtins.ASinTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec
Results :
Tests run: 94, Failures: 0, Errors: 0, Skipped: 0
[JENKINS] Recording test results
[INFO]
[INFO] --- maven-bundle-plugin:2.3.4:bundle (default-bundle) @ equations-impl
---
ignoring exception during new ExecutedMojo null
[INFO]
[INFO] --- maven-source-plugin:2.1.2:jar (attach-sources) @ equations-impl ---
[INFO] Building jar:
<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/equations-impl/target/equations-impl-3.0.0-alpha8-SNAPSHOT-sources.jar>
[INFO] [INFO] Installing
<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/equations-impl/target/equations-impl-3.0.0-alpha8-SNAPSHOT.jar>
to
/opt/tomcat-home/.m2/repository/org/cytoscape/equations-impl/3.0.0-alpha8-SNAPSHOT/equations-impl-3.0.0-alpha8-SNAPSHOT.jar
[INFO] Installing
<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/equations-impl/pom.xml>
to
/opt/tomcat-home/.m2/repository/org/cytoscape/equations-impl/3.0.0-alpha8-SNAPSHOT/equations-impl-3.0.0-alpha8-SNAPSHOT.pom
[INFO] Installing
<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/equations-impl/target/equations-impl-3.0.0-alpha8-SNAPSHOT-sources.jar>
to
/opt/tomcat-home/.m2/repository/org/cytoscape/equations-impl/3.0.0-alpha8-SNAPSHOT/equations-impl-3.0.0-alpha8-SNAPSHOT-sources.jar
[INFO] --- maven-install-plugin:2.3.1:install (default-install) @
equations-impl ---
[INFO]
[INFO] --- maven-bundle-plugin:2.3.4:install (default-install) @ equations-impl
---
[INFO] Installing
org/cytoscape/equations-impl/3.0.0-alpha8-SNAPSHOT/equations-impl-3.0.0-alpha8-SNAPSHOT.jar
[INFO] Writing OBR metadata
[INFO] Downloading:
http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/equations-impl/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml
[INFO] --- maven-deploy-plugin:2.7:deploy (default-deploy) @ equations-impl ---
Downloaded:
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(2 KB at 2.2 KB/sec)
Uploading:
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Uploaded:
http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/equations-impl/3.0.0-alpha8-SNAPSHOT/equations-impl-3.0.0-alpha8-20111205.230405-267.jar
(119 KB at 687.8 KB/sec)
Uploading:
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Uploaded:
http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/equations-impl/3.0.0-alpha8-SNAPSHOT/equations-impl-3.0.0-alpha8-20111205.230405-267.pom
(3 KB at 30.6 KB/sec)
Downloading:
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Downloaded:
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(554 B at 21.6 KB/sec)
Uploading:
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(2 KB at 13.4 KB/sec)
Uploading:
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Uploaded:
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(554 B at 6.1 KB/sec)
Uploading:
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Uploaded:
http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/equations-impl/3.0.0-alpha8-SNAPSHOT/equations-impl-3.0.0-alpha8-20111205.230405-267-sources.jar
(131 KB at 749.9 KB/sec)
Uploading:
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(2 KB at 8.3 KB/sec)
[INFO] [INFO] Remote OBR update disabled (enable with -DremoteOBR)
[INFO] --- maven-bundle-plugin:2.3.4:deploy (default-deploy) @ equations-impl
---
[JENKINS] Archiving
<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/equations-impl/pom.xml>
to /opt/tomcat-home/jenkins/jobs/Cytoscape 3
Implementation/modules/org.cytoscape$equations-impl/builds/2011-12-05_18-03-09/archive/org.cytoscape/equations-impl/3.0.0-alpha8-SNAPSHOT/equations-impl-3.0.0-alpha8-SNAPSHOT.pom
[JENKINS] Archiving
<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/equations-impl/target/equations-impl-3.0.0-alpha8-SNAPSHOT.jar>
to /opt/tomcat-home/jenkins/jobs/Cytoscape 3
Implementation/modules/org.cytoscape$equations-impl/builds/2011-12-05_18-03-09/archive/org.cytoscape/equations-impl/3.0.0-alpha8-20111205.230405-267/equations-impl-3.0.0-alpha8-20111205.230405-267.jar
[JENKINS] Archiving
<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/equations-impl/target/equations-impl-3.0.0-alpha8-SNAPSHOT-sources.jar>
to /opt/tomcat-home/jenkins/jobs/Cytoscape 3
Implementation/modules/org.cytoscape$equations-impl/builds/2011-12-05_18-03-09/archive/org.cytoscape/equations-impl/3.0.0-alpha8-20111205.230405-267/equations-impl-3.0.0-alpha8-20111205.230405-267-sources.jar
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building model-impl-parent 3.0.0-alpha8-SNAPSHOT
[INFO] ------------------------------------------------------------------------
ignoring exception during new ExecutedMojo null
[INFO]
[INFO] --- maven-source-plugin:2.1.2:jar (attach-sources) @ model-impl-parent
---
[INFO]
[INFO] --- maven-install-plugin:2.3.1:install (default-install) @
model-impl-parent ---
[INFO] Installing
<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/pom.xml>
to
/opt/tomcat-home/.m2/repository/org/cytoscape/model-impl-parent/3.0.0-alpha8-SNAPSHOT/model-impl-parent-3.0.0-alpha8-SNAPSHOT.pom
[INFO]
[INFO] --- maven-deploy-plugin:2.5:deploy (default-deploy) @ model-impl-parent
---
Downloading:
http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml
Downloaded:
http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml
(625 B at 10.2 KB/sec)
Uploading:
http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/3.0.0-alpha8-SNAPSHOT/model-impl-parent-3.0.0-alpha8-20111205.230406-267.pom
Uploaded:
http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/3.0.0-alpha8-SNAPSHOT/model-impl-parent-3.0.0-alpha8-20111205.230406-267.pom
(4 KB at 34.5 KB/sec)
Downloading:
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Downloaded:
http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/maven-metadata.xml
(411 B at 3.3 KB/sec)
Uploading:
http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml
Uploaded:
http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/3.0.0-alpha8-SNAPSHOT/maven-metadata.xml
(625 B at 4.5 KB/sec)
Uploading:
http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/maven-metadata.xml
Uploaded:
http://code.cytoscape.org/nexus/content/repositories/snapshots/org/cytoscape/model-impl-parent/maven-metadata.xml
(411 B at 3.4 KB/sec)
[JENKINS] Archiving
<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/pom.xml>
to /opt/tomcat-home/jenkins/jobs/Cytoscape 3
Implementation/modules/org.cytoscape$model-impl-parent/builds/2011-12-05_18-03-09/archive/org.cytoscape/model-impl-parent/3.0.0-alpha8-SNAPSHOT/model-impl-parent-3.0.0-alpha8-SNAPSHOT.pom
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building org.cytoscape.model-impl 3.0.0-alpha8-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] [debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 3 resources
[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @
model-impl ---
[INFO]
[INFO] --- maven-compiler-plugin:2.3.2:compile (default-compile) @ model-impl
---
[INFO] Compiling 27 source files to
<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/impl/target/classes>
[INFO] [debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory
<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/impl/src/test/resources>
[INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @
model-impl ---
[INFO]
[INFO] --- maven-compiler-plugin:2.3.2:testCompile (default-testCompile) @
model-impl ---
[INFO] Compiling 19 source files to
<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/impl/target/test-classes>
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR :
[INFO] -------------------------------------------------------------
[ERROR]
<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableTest.java>:[34,-1]
cannot access org.cytoscape.equations.BooleanList
bad class file:
org/cytoscape/equations/BooleanList.class(org/cytoscape/equations:BooleanList.class)
unable to access file: corrupted zip file
[INFO] 1 error
[INFO] -------------------------------------------------------------
[JENKINS] Archiving
<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/impl/pom.xml>
to /opt/tomcat-home/jenkins/jobs/Cytoscape 3
Implementation/modules/org.cytoscape$model-impl/builds/2011-12-05_18-03-09/archive/org.cytoscape/model-impl/3.0.0-alpha8-SNAPSHOT/model-impl-3.0.0-alpha8-SNAPSHOT.pom
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Cytoscape Implementation Parent Project POM ....... SUCCESS [7.098s]
[INFO] org.cytoscape.biopax-impl [org.cytoscape.biopax] .. SUCCESS [13.601s]
[INFO] Command Executor .................................. SUCCESS [6.637s]
[INFO] org.cytoscape.equations-impl ...................... SUCCESS [15.728s]
[INFO] model-impl-parent ................................. SUCCESS [0.803s]
[INFO] org.cytoscape.model-impl .......................... FAILURE [4.698s]
[INFO] viewmodel-impl-parent ............................. SKIPPED
[INFO] org.cytoscape.viewmodel-impl ...................... SKIPPED
[INFO] Ding Implementation Parent Pom .................... SKIPPED
[INFO] org.cytoscape.util-intr ........................... SKIPPED
[INFO] org.cytoscape.spacial ............................. SKIPPED
[INFO] org.cytoscape.graph-render ........................ SKIPPED
[INFO] org.cytoscape.ding-presentation-impl .............. SKIPPED
[INFO] org.cytoscape.core-task-impl ...................... SKIPPED
[INFO] org.cytoscape.cpath2-impl [org.cytoscape.cpath2] .. SKIPPED
[INFO] org.cytoscape.ding-customgraphics-manager-impl .... SKIPPED
[INFO] io-impl-parent .................................... SKIPPED
[INFO] org.cytoscape.io-impl [org.cytoscape.io.internal] . SKIPPED
[INFO] event-impl-parent ................................. SKIPPED
[INFO] org.cytoscape.event-impl .......................... SKIPPED
[INFO] org.cytoscape.layout-impl ......................... SKIPPED
[INFO] org.cytoscape.ding-impl-performance-debug ......... SKIPPED
[INFO] org.cytoscape.editor-impl ......................... SKIPPED
[INFO] org.cytoscape.equations-functions-impl ............ SKIPPED
[INFO] org.cytoscape.event-impl-it ....................... SKIPPED
[INFO] org.cytoscape.filter-impl [org.cytoscape.filter.internal] SKIPPED
[INFO] GraphML Reader and Writer for Cytoscape 3 ......... SKIPPED
[INFO] org.cytoscape.io-impl-performance ................. SKIPPED
[INFO] org.cytoscape.layout-cytoscape-impl [csplugins.layout] SKIPPED
[INFO] org.cytoscape.layout-jgraph-impl [csplugins.layout] SKIPPED
[INFO] org.cytoscape.layout-prefuse-impl
[org.cytoscape.prefuse.layouts.internal] SKIPPED
[INFO] org.cytoscape.linkout-impl [org.cytoscape.linkout.internal] SKIPPED
[INFO] org.cytoscape.log-swing-impl [org.cytoscape.log.internal] SKIPPED
[INFO] Manual Layout ..................................... SKIPPED
[INFO] NetworkAnalyzer ................................... SKIPPED
[INFO] Advanced Network Merge ............................ SKIPPED
[INFO] org.cytoscape.plugin-impl ......................... SKIPPED
[INFO] org.cytoscape.presentation-impl
[org.cytoscape.view.presentation.internal] SKIPPED
[INFO] org.cytoscape.property.internal ................... SKIPPED
[INFO] org.cytoscape.psi-mi-impl [org.cytoscape.psi_mi.internal] SKIPPED
[INFO] org.cytoscape.sbml-impl [org.cytoscape.sbml.internal] SKIPPED
[INFO] org.cytoscape.search-impl [org.cytoscape.search.internal] SKIPPED
[INFO] org.cytoscape.session-impl ........................ SKIPPED
[INFO] Cytoscape Swing Application Impl .................. SKIPPED
[INFO] Cytoscape Table Browser Implementation ............ SKIPPED
[INFO] org.cytoscape.table-import-impl [org.cytoscape.tableimport.internal]
SKIPPED
[INFO] org.cytoscape.vizmap-gui-impl ..................... SKIPPED
[INFO] vizmap-impl-parent ................................ SKIPPED
[INFO] org.cytoscape.view.vizmap-impl .................... SKIPPED
[INFO] org.cytoscape.io.webservice-biomart-client-impl
[org.cytoscape.io.webservice.biomart] SKIPPED
[INFO] org.cytoscape.webservice-impl [org.cytoscape.webservice.internal]
SKIPPED
[INFO] org.cytoscape.webservice-ncbi-client-impl
[org.cytoscape.webservice.ncbi] SKIPPED
[INFO] work-swing-impl-parent ............................ SKIPPED
[INFO] org.cytoscape.work-swing-impl ..................... SKIPPED
[INFO] org.cytoscape.application-impl .................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 54.787s
[INFO] Finished at: Mon Dec 05 18:04:12 GMT-05:00 2011
[INFO] Final Memory: 30M/79M
[INFO] ------------------------------------------------------------------------
mavenExecutionResult exceptions not empty
message : Failed to execute goal
org.apache.maven.plugins:maven-compiler-plugin:2.3.2:testCompile
(default-testCompile) on project model-impl: Compilation failure
<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableTest.java>:[34,-1]
cannot access org.cytoscape.equations.BooleanList
bad class file:
org/cytoscape/equations/BooleanList.class(org/cytoscape/equations:BooleanList.class)
unable to access file: corrupted zip file
cause : Compilation failure
<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableTest.java>:[34,-1]
cannot access org.cytoscape.equations.BooleanList
bad class file:
org/cytoscape/equations/BooleanList.class(org/cytoscape/equations:BooleanList.class)
unable to access file: corrupted zip file
Stack trace :
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal
org.apache.maven.plugins:maven-compiler-plugin:2.3.2:testCompile
(default-testCompile) on project model-impl: Compilation failure
<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableTest.java>:[34,-1]
cannot access org.cytoscape.equations.BooleanList
bad class file:
org/cytoscape/equations/BooleanList.class(org/cytoscape/equations:BooleanList.class)
unable to access file: corrupted zip file
at
org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:213)
at
org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
at
org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
at
org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:84)
at
org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59)
at
org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183)
at
org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:319)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:156)
at
org.jvnet.hudson.maven3.launcher.Maven3Launcher.main(Maven3Launcher.java:79)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at
org.codehaus.plexus.classworlds.launcher.Launcher.launchStandard(Launcher.java:329)
at
org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:239)
at org.jvnet.hudson.maven3.agent.Maven3Main.launch(Maven3Main.java:158)
at hudson.maven.Maven3Builder.call(Maven3Builder.java:112)
at hudson.maven.Maven3Builder.call(Maven3Builder.java:70)
at hudson.remoting.UserRequest.perform(UserRequest.java:118)
at hudson.remoting.UserRequest.perform(UserRequest.java:48)
at hudson.remoting.Request$2.run(Request.java:287)
at
java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:636)
Caused by: org.apache.maven.plugin.CompilationFailureException: Compilation
failure
<http://code.cytoscape.org/jenkins/job/Cytoscape%203%20Implementation/ws/trunk/model-impl/impl/src/test/java/org/cytoscape/model/CyTableTest.java>:[34,-1]
cannot access org.cytoscape.equations.BooleanList
bad class file:
org/cytoscape/equations/BooleanList.class(org/cytoscape/equations:BooleanList.class)
unable to access file: corrupted zip file
at
org.apache.maven.plugin.AbstractCompilerMojo.execute(AbstractCompilerMojo.java:656)
at
org.apache.maven.plugin.TestCompilerMojo.execute(TestCompilerMojo.java:161)
at
org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101)
at
org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209)
... 27 more
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