[Debian-med-packaging] Problems understanding maven rules to package qualimap

[Andreas Tille]

Hi,

I intend to package qualimap[1].  When trying mh_make I'm running into
questions like:


In pom.xml: This dependency cannot be found in the Debian Maven repository. Ignore this dependency?  org.bioinfo:bioinfo-ngs:jar:0.1.0
[y/N] > n
> dpkg --search /usr/share/maven-repo/org/bioinfo/bioinfo-ngs/*/* 
dpkg failed to execute successfully
> apt-file search /usr/share/maven-repo/org/bioinfo/bioinfo-ngs 
> dpkg --search /usr/share/java/bioinfo-ngs.jar 
dpkg failed to execute successfully
> apt-file search /usr/share/java/bioinfo-ngs.jar 
[error] Cannot resolve Maven dependency org.bioinfo:bioinfo-ngs:jar:0.1.0. If you know a package that contains a compatible dependency,
try to enter a substitution rule of the form s/groupId/newGroupId/ s/artifactId/newArtifactId/ jar s/version/newVersion/ here:


While I know that these classes are part of BioJava I fail to understand
how to craft these magical regexps maven wants me to provide.  Further
examples are:

In pom.xml: This plugin cannot be found in the Debian Maven repository. Ignore this plugin?  org.apache.maven.plugins:maven-dependency-plugin:maven-plugin:2.7
[y/N] > 
> dpkg --search /usr/share/maven-repo/org/apache/maven/plugins/maven-dependency-plugin/*/* 
dpkg failed to execute successfully
> apt-file search /usr/share/maven-repo/org/apache/maven/plugins/maven-dependency-plugin 
Found /usr/share/maven-repo/org/apache/maven/plugins/maven-dependency-plugin/2.7/maven-dependency-plugin-2.7.pom in libmaven-dependency-plugin-java
> dpkg --search /usr/share/java/maven-dependency-plugin.jar 
dpkg failed to execute successfully
> apt-file search /usr/share/java/maven-dependency-plugin.jar 
[error] Cannot resolve Maven dependency org.apache.maven.plugins:maven-dependency-plugin:maven-plugin:2.7. If you know a package that contains a compatible dependency,
try to enter a substitution rule of the form s/groupId/newGroupId/ s/artifactId/newArtifactId/ jar s/version/newVersion/ here:


or even


In pom.xml: This dependency cannot be found in the Debian Maven repository. Ignore this dependency?  net.sf.picard:picard:jar:1.70
[y/N] > n
> dpkg --search /usr/share/maven-repo/net/sf/picard/picard/*/*
dpkg failed to execute successfully
> apt-file search /usr/share/maven-repo/net/sf/picard/picard
> dpkg --search /usr/share/java/picard.jar
dpkg failed to execute successfully
> apt-file search /usr/share/java/picard.jar
Found picard-tools
[error] Package picard-tools does not contain Maven dependency net.sf.picard:picard:jar:1.70 but there seem to be a match
If the package contains already Maven artifacts but the names don't match, try to enter a substitution rule
of the form s/groupId/newGroupId/ s/artifactId/newArtifactId/ jar s/version/newVersion/ here:


where Maven was able to find the correct package - but what the hell are
groupID and artifactId.  This looks like pure magic to me.

Any help would be welcome

      Andreas.


[1] http://qualimap.bioinfo.cipf.es/

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