maven build not working on some systems

[fbergmann]

Irina was noting that the maven build on her machine failed with:

vn install
[INFO] Scanning for projects...
[INFO] 
[INFO] ---------------------< com.github.libsbgn:libsbgn >---------------------
[INFO] Building libSBGN 0.3-SNAPSHOT
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The POM for com.sun.xml.bind:jaxb-impl:jar:2.2.11 is invalid, transitive dependencies (if any) will not be available, enable debug logging for more details
[WARNING] The POM for com.sun.xml.bind:jaxb-core:jar:2.2.11 is invalid, transitive dependencies (if any) will not be available, enable debug logging for more details
[INFO] 
[INFO] --- jaxb2-maven-plugin:1.6:xjc (xjc) @ libsbgn ---
[INFO] Generating source...
[INFO] parsing a schema...
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  1.710 s
[INFO] Finished at: 2019-05-09T15:14:44+02:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:jaxb2-maven-plugin:1.6:xjc (xjc) on project libsbgn: Execution xjc of goal org.codehaus.mojo:jaxb2-maven-plugin:1.6:xjc failed: A required class was missing while executing org.codehaus.mojo:jaxb2-maven-plugin:1.6:xjc: javax/activation/DataSource
[ERROR] -----------------------------------------------------
[ERROR] realm =    plugin>org.codehaus.mojo:jaxb2-maven-plugin:1.6
[ERROR] strategy = org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy
[ERROR] urls[0] = file:/Users/iroznovat/.m2/repository/org/codehaus/mojo/jaxb2-maven-plugin/1.6/jaxb2-maven-plugin-1.6.jar
[ERROR] urls[1] = file:/Users/iroznovat/.m2/repository/org/slf4j/slf4j-jdk14/1.5.6/slf4j-jdk14-1.5.6.jar
[ERROR] urls[2] = file:/Users/iroznovat/.m2/repository/org/slf4j/jcl-over-slf4j/1.5.6/jcl-over-slf4j-1.5.6.jar
[ERROR] urls[3] = file:/Users/iroznovat/.m2/repository/org/apache/maven/reporting/maven-reporting-api/2.2.1/maven-reporting-api-2.2.1.jar
[ERROR] urls[4] = file:/Users/iroznovat/.m2/repository/org/apache/maven/doxia/doxia-sink-api/1.1/doxia-sink-api-1.1.jar
[ERROR] urls[5] = file:/Users/iroznovat/.m2/repository/org/apache/maven/doxia/doxia-logging-api/1.1/doxia-logging-api-1.1.jar
[ERROR] urls[6] = file:/Users/iroznovat/.m2/repository/commons-cli/commons-cli/1.2/commons-cli-1.2.jar
[ERROR] urls[7] = file:/Users/iroznovat/.m2/repository/org/codehaus/plexus/plexus-interactivity-api/1.0-alpha-4/plexus-interactivity-api-1.0-alpha-4.jar
[ERROR] urls[8] = file:/Users/iroznovat/.m2/repository/backport-util-concurrent/backport-util-concurrent/3.1/backport-util-concurrent-3.1.jar
[ERROR] urls[9] = file:/Users/iroznovat/.m2/repository/org/sonatype/plexus/plexus-sec-dispatcher/1.3/plexus-sec-dispatcher-1.3.jar
[ERROR] urls[10] = file:/Users/iroznovat/.m2/repository/org/sonatype/plexus/plexus-cipher/1.4/plexus-cipher-1.4.jar
[ERROR] urls[11] = file:/Users/iroznovat/.m2/repository/org/codehaus/plexus/plexus-interpolation/1.11/plexus-interpolation-1.11.jar
[ERROR] urls[12] = file:/Users/iroznovat/.m2/repository/com/sun/xml/bind/jaxb-xjc/2.2.7/jaxb-xjc-2.2.7.jar
[ERROR] urls[13] = file:/Users/iroznovat/.m2/repository/com/sun/xml/bind/jaxb-core/2.2.7/jaxb-core-2.2.7.jar
[ERROR] urls[14] = file:/Users/iroznovat/.m2/repository/javax/xml/bind/jaxb-api/2.2.7/jaxb-api-2.2.7.jar
[ERROR] urls[15] = file:/Users/iroznovat/.m2/repository/com/sun/istack/istack-commons-runtime/2.16/istack-commons-runtime-2.16.jar
[ERROR] urls[16] = file:/Users/iroznovat/.m2/repository/com/sun/xml/bind/jaxb-jxc/2.2.7/jaxb-jxc-2.2.7.jar
[ERROR] urls[17] = file:/Users/iroznovat/.m2/repository/com/sun/xml/bind/jaxb-impl/2.2.7/jaxb-impl-2.2.7.jar
[ERROR] urls[18] = file:/Users/iroznovat/.m2/repository/com/sun/xml/fastinfoset/FastInfoset/1.2.12/FastInfoset-1.2.12.jar
[ERROR] urls[19] = file:/Users/iroznovat/.m2/repository/org/codehaus/plexus/plexus-compiler-api/1.9.1/plexus-compiler-api-1.9.1.jar
[ERROR] urls[20] = file:/Users/iroznovat/.m2/repository/org/codehaus/plexus/plexus-utils/3.0.16/plexus-utils-3.0.16.jar
[ERROR] urls[21] = file:/Users/iroznovat/.m2/repository/org/sonatype/plexus/plexus-build-api/0.0.7/plexus-build-api-0.0.7.jar
[ERROR] Number of foreign imports: 1
[ERROR] import: Entry[import  from realm ClassRealm[maven.api, parent: null]]
[ERROR] 
[ERROR] -----------------------------------------------------
[ERROR] : javax.activation.DataSource
[ERROR] -> [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/PluginContainerException

[cannin]

I'm not sure what to suggest. The best is more online searching on StackOverflow, etc. But one clue may be that Java 11 removed javax and requires additional entries to the pom.xml. https://stackoverflow.com/questions/43574426/how-to-resolve-java-lang-noclassdeffounderror-javax-xml-bind-jaxbexception-in-j

…

On Thu, May 9, 2019 at 4:48 PM Frank Bergmann ***@***.***> wrote: Irina was noting that the maven build on her machine failed with: vn install [INFO] Scanning for projects... [INFO] [INFO] ---------------------< com.github.libsbgn:libsbgn >--------------------- [INFO] Building libSBGN 0.3-SNAPSHOT [INFO] --------------------------------[ jar ]--------------------------------- [WARNING] The POM for com.sun.xml.bind:jaxb-impl:jar:2.2.11 is invalid, transitive dependencies (if any) will not be available, enable debug logging for more details [WARNING] The POM for com.sun.xml.bind:jaxb-core:jar:2.2.11 is invalid, transitive dependencies (if any) will not be available, enable debug logging for more details [INFO] [INFO] --- jaxb2-maven-plugin:1.6:xjc (xjc) @ libsbgn --- [INFO] Generating source... [INFO] parsing a schema... [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 1.710 s [INFO] Finished at: 2019-05-09T15:14:44+02:00 [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.codehaus.mojo:jaxb2-maven-plugin:1.6:xjc (xjc) on project libsbgn: Execution xjc of goal org.codehaus.mojo:jaxb2-maven-plugin:1.6:xjc failed: A required class was missing while executing org.codehaus.mojo:jaxb2-maven-plugin:1.6:xjc: javax/activation/DataSource [ERROR] ----------------------------------------------------- [ERROR] realm = plugin>org.codehaus.mojo:jaxb2-maven-plugin:1.6 [ERROR] strategy = org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy [ERROR] urls[0] = file:/Users/iroznovat/.m2/repository/org/codehaus/mojo/jaxb2-maven-plugin/1.6/jaxb2-maven-plugin-1.6.jar [ERROR] urls[1] = file:/Users/iroznovat/.m2/repository/org/slf4j/slf4j-jdk14/1.5.6/slf4j-jdk14-1.5.6.jar [ERROR] urls[2] = file:/Users/iroznovat/.m2/repository/org/slf4j/jcl-over-slf4j/1.5.6/jcl-over-slf4j-1.5.6.jar [ERROR] urls[3] = file:/Users/iroznovat/.m2/repository/org/apache/maven/reporting/maven-reporting-api/2.2.1/maven-reporting-api-2.2.1.jar [ERROR] urls[4] = file:/Users/iroznovat/.m2/repository/org/apache/maven/doxia/doxia-sink-api/1.1/doxia-sink-api-1.1.jar [ERROR] urls[5] = file:/Users/iroznovat/.m2/repository/org/apache/maven/doxia/doxia-logging-api/1.1/doxia-logging-api-1.1.jar [ERROR] urls[6] = file:/Users/iroznovat/.m2/repository/commons-cli/commons-cli/1.2/commons-cli-1.2.jar [ERROR] urls[7] = file:/Users/iroznovat/.m2/repository/org/codehaus/plexus/plexus-interactivity-api/1.0-alpha-4/plexus-interactivity-api-1.0-alpha-4.jar [ERROR] urls[8] = file:/Users/iroznovat/.m2/repository/backport-util-concurrent/backport-util-concurrent/3.1/backport-util-concurrent-3.1.jar [ERROR] urls[9] = file:/Users/iroznovat/.m2/repository/org/sonatype/plexus/plexus-sec-dispatcher/1.3/plexus-sec-dispatcher-1.3.jar [ERROR] urls[10] = file:/Users/iroznovat/.m2/repository/org/sonatype/plexus/plexus-cipher/1.4/plexus-cipher-1.4.jar [ERROR] urls[11] = file:/Users/iroznovat/.m2/repository/org/codehaus/plexus/plexus-interpolation/1.11/plexus-interpolation-1.11.jar [ERROR] urls[12] = file:/Users/iroznovat/.m2/repository/com/sun/xml/bind/jaxb-xjc/2.2.7/jaxb-xjc-2.2.7.jar [ERROR] urls[13] = file:/Users/iroznovat/.m2/repository/com/sun/xml/bind/jaxb-core/2.2.7/jaxb-core-2.2.7.jar [ERROR] urls[14] = file:/Users/iroznovat/.m2/repository/javax/xml/bind/jaxb-api/2.2.7/jaxb-api-2.2.7.jar [ERROR] urls[15] = file:/Users/iroznovat/.m2/repository/com/sun/istack/istack-commons-runtime/2.16/istack-commons-runtime-2.16.jar [ERROR] urls[16] = file:/Users/iroznovat/.m2/repository/com/sun/xml/bind/jaxb-jxc/2.2.7/jaxb-jxc-2.2.7.jar [ERROR] urls[17] = file:/Users/iroznovat/.m2/repository/com/sun/xml/bind/jaxb-impl/2.2.7/jaxb-impl-2.2.7.jar [ERROR] urls[18] = file:/Users/iroznovat/.m2/repository/com/sun/xml/fastinfoset/FastInfoset/1.2.12/FastInfoset-1.2.12.jar [ERROR] urls[19] = file:/Users/iroznovat/.m2/repository/org/codehaus/plexus/plexus-compiler-api/1.9.1/plexus-compiler-api-1.9.1.jar [ERROR] urls[20] = file:/Users/iroznovat/.m2/repository/org/codehaus/plexus/plexus-utils/3.0.16/plexus-utils-3.0.16.jar [ERROR] urls[21] = file:/Users/iroznovat/.m2/repository/org/sonatype/plexus/plexus-build-api/0.0.7/plexus-build-api-0.0.7.jar [ERROR] Number of foreign imports: 1 [ERROR] import: Entry[import from realm ClassRealm[maven.api, parent: null]] [ERROR] [ERROR] ----------------------------------------------------- [ERROR] : javax.activation.DataSource [ERROR] -> [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/PluginContainerException — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#46>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAGA6DAFCG3RX5AVMYMMWJLPUSEZZANCNFSM4HL54O6Q> .

[tczauderna]

Should be fixed with commit 8a9ca6c.

The jaxb2-maven-plugin needed to be updated to be able to update some jars.