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Groups > linux.debian.maint.java > #8734
| From | Andreas Tille <andreas@an3as.eu> |
|---|---|
| Newsgroups | linux.debian.maint.java |
| Subject | Help needed for gatk |
| Date | 2016-01-21 09:50 +0100 |
| Message-ID | <qTj6h-2ML-1@gated-at.bofh.it> (permalink) |
| Organization | linux.* mail to news gateway |
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
--
http://fam-tille.de
Back to linux.debian.maint.java | Previous | Next — Next in thread | Find similar
Help needed for gatk Andreas Tille <andreas@an3as.eu> - 2016-01-21 09:50 +0100
Re: Help needed for gatk Thorsten Glaser <t.glaser@tarent.de> - 2016-01-21 10:00 +0100
Re: Help needed for gatk Andreas Tille <andreas@an3as.eu> - 2016-01-21 10:10 +0100
Re: Help needed for gatk gregor herrmann <gregoa@debian.org> - 2016-01-21 10:10 +0100
Re: Help needed for gatk Thorsten Glaser <t.glaser@tarent.de> - 2016-01-21 10:20 +0100
Re: Help needed for gatk Emmanuel Bourg <ebourg@apache.org> - 2016-01-21 10:30 +0100
Re: Help needed for gatk Andreas Tille <andreas@an3as.eu> - 2016-01-21 10:50 +0100
Re: Help needed for gatk Emmanuel Bourg <ebourg@apache.org> - 2016-01-21 11:10 +0100
Re: Help needed for gatk Andreas Tille <andreas@an3as.eu> - 2016-01-27 15:10 +0100
Re: Help needed for gatk Andrew Schurman <arcticwaters@gmail.com> - 2016-01-28 00:00 +0100
Re: Help needed for gatk Andreas Tille <andreas@an3as.eu> - 2016-01-28 16:30 +0100
Re: Help needed for gatk Andrew Schurman <arcticwaters@gmail.com> - 2016-01-29 19:50 +0100
Re: Help needed for gatk Andreas Tille <andreas@an3as.eu> - 2016-01-29 22:40 +0100
Packaging maven-scala-plugin (Was: Help needed for gatk) Andreas Tille <tille@debian.org> - 2016-01-28 19:40 +0100
Re: Packaging maven-scala-plugin (Was: Help needed for gatk) Andreas Tille <andreas@an3as.eu> - 2016-01-30 15:00 +0100
Re: Packaging maven-scala-plugin (Was: Help needed for gatk) Emmanuel Bourg <ebourg@apache.org> - 2016-01-30 15:50 +0100
Re: Packaging maven-scala-plugin (Was: Help needed for gatk) Andreas Tille <andreas@an3as.eu> - 2016-01-30 18:10 +0100
Re: Packaging maven-scala-plugin (Was: Help needed for gatk) Andrew Schurman <arcticwaters@gmail.com> - 2016-01-30 22:10 +0100
Re: Packaging maven-scala-plugin (Was: Help needed for gatk) Andreas Tille <andreas@an3as.eu> - 2016-02-01 10:00 +0100
Re: Packaging maven-scala-plugin (Was: Help needed for gatk) Andrew Schurman <arcticwaters@gmail.com> - 2016-02-01 12:10 +0100
Re: Packaging maven-scala-plugin (Was: Help needed for gatk) Andreas Tille <andreas@an3as.eu> - 2016-02-01 12:20 +0100
Re: Packaging maven-scala-plugin (Was: Help needed for gatk) Andrew Schurman <arcticwaters@gmail.com> - 2016-02-01 13:40 +0100
Re: Packaging maven-scala-plugin (Was: Help needed for gatk) Emmanuel Bourg <ebourg@apache.org> - 2016-02-01 14:40 +0100
Re: Packaging maven-scala-plugin (Was: Help needed for gatk) Andreas Tille <andreas@an3as.eu> - 2016-02-01 14:50 +0100
Re: Packaging maven-scala-plugin (Was: Help needed for gatk) Andreas Tille <andreas@an3as.eu> - 2016-02-01 22:00 +0100
Re: Packaging maven-scala-plugin (Was: Help needed for gatk) David Bernard <david.bernard.31@gmail.com> - 2016-02-01 23:10 +0100
Re: Packaging maven-scala-plugin (Was: Help needed for gatk) Andreas Tille <andreas@fam-tille.de> - 2016-02-01 23:10 +0100
Re: Packaging maven-scala-plugin (Was: Help needed for gatk) David Bernard <david.bernard.31@gmail.com> - 2016-02-01 23:20 +0100
Re: Packaging maven-scala-plugin (Was: Help needed for gatk) Andreas Tille <andreas@an3as.eu> - 2016-02-01 14:40 +0100
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