[Debian-med-packaging] Help needed for gatk

[Andreas Tille]

Hi,

I'm lost again with a Java package: gatk[1].  The confusing part from
the build log is:


...
        /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar:/usr/lib/jvm/default-java/lib/tools.jar -Dmaven.home=/usr/share/maven -Dmaven.                            multiModuleProjectDirectory=/build/gatk-3.5\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/gatk-3.5\+    dfsg/debian -Dmaven.repo.local=/build/gatk-3.5\+dfsg/debian/maven-repo package -DskipTests -Dnotimestamp=true -Dlocale=en_US
[INFO] Scanning for projects...
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.broadinstitute.gatk:gsalib:pom:3.5
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-clean-plugin is missing. @ org.broadinstitute.gatk:gatk-aggregator:3.5, /build/gatk-3.5+dfsg/pom.xml, line 421, column 12
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.broadinstitute.gatk:gatk-utils:jar:3.5
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-clean-plugin is missing. @ org.broadinstitute.gatk:gatk-aggregator:3.5, /build/gatk-3.5+dfsg/pom.xml, line 421, column 12
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.broadinstitute.gatk:gatk-engine:jar:3.5
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-clean-plugin is missing. @ org.broadinstitute.gatk:gatk-aggregator:3.5, /build/gatk-3.5+dfsg/pom.xml, line 421, column 12
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.broadinstitute.gatk:gatk-tools-public:jar:3.5
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-clean-plugin is missing. @ org.broadinstitute.gatk:gatk-aggregator:3.5, /build/gatk-3.5+dfsg/pom.xml, line 421, column 12
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.broadinstitute.gatk:gatk-queue:jar:3.5
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-resources-plugin is missing. @ line 42, column 12
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-clean-plugin is missing. @ org.broadinstitute.gatk:gatk-aggregator:3.5, /build/gatk-3.5+dfsg/pom.xml, line 421, column 12
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.broadinstitute.gatk:gatk-queue-extensions-generator:jar:3.5
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-clean-plugin is missing. @ org.broadinstitute.gatk:gatk-aggregator:3.5, /build/gatk-3.5+dfsg/pom.xml, line 421, column 12
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.broadinstitute.gatk:gatk-queue-extensions-public:jar:3.5
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-clean-plugin is missing. @ org.broadinstitute.gatk:gatk-aggregator:3.5, /build/gatk-3.5+dfsg/pom.xml, line 421, column 12
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.broadinstitute.gatk:gatk-aggregator:pom:3.5
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-clean-plugin is missing. @ line 421, column 12
[WARNING]
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING]
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING]
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO]
[INFO] GATK Root
[INFO] GATK Aggregator
[INFO] GATK GSALib
[INFO] GATK Utils
[INFO] GATK Engine
[INFO] GATK Tools Public
[INFO] External Example
[INFO] GATK Queue
[INFO] GATK Queue Extensions Generator
[INFO] GATK Queue Extensions Public
[INFO] GATK Aggregator Public
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building GATK Root 3.5
[INFO] ------------------------------------------------------------------------
[WARNING] The POM for org.apache.maven.plugins:maven-install-plugin:jar:2.5 is missing, no dependency information available
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] GATK Root .......................................... FAILURE [  0.008 s]


I think the code for those missing JARs is in dir public - but I have no
idea how to tell this to the build system.  Any hint or commit to Git
would be really appreciated.

Kind regards

      Andreas.

[1] git://anonscm.debian.org/debian-med/gatk.git

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