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/
--
http://fam-tille.de
