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

[Andreas Tille]

Hi Emmanuel,

On Mon, Nov 16, 2015 at 05:49:58PM +0100, Emmanuel Bourg wrote:
> Le 16/11/2015 17:22, Andreas Tille a écrit :
> 
> > 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.
> 
> biojava probably doesn't install the Maven artifacts , that's why
> mh_make can't find bioinfo-ngs.

This smells like a bug in biojava.  If this is the case - how to fix it?

> If it does install the artifacts but
> under a different name, then you need a replacement rule. If the Maven
> coordinates of the jar equivalent to bioinfo-ngs is foo:bar, then you
> need this rule:
> 
>     s/org.bioinfo/foo/ s/bioinfo-ngs/bar/ * s/.*/debian/ * *

After reading your explanation below I tried

    s/org.bioinfo/org.biojava/ s/bioinfo-ngs/nbio/ * s/.*/debian/ *

However, this also does not seem to be the proper solution.  Olivier,
do you have a better suggestion here?
 
> > 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] > 
> 
> Install libmaven-dependency-plugin-java and try again.

Hmmm, wouldn't it be helpful to add this to Recommends of
maven-debian-helper?  Anyway, the mh_make output looks better but
problem not fully solved:


In pom.xml: This plugin cannot be found in the Debian Maven repository. Ignore this plugin?  org.apache.maven.plugins:maven-antrun-plugin:maven-plugin:1.7
[y/N] > 
> dpkg --search /usr/share/maven-repo/org/apache/maven/plugins/maven-antrun-plugin/*/* 
dpkg failed to execute successfully
> apt-file search /usr/share/maven-repo/org/apache/maven/plugins/maven-antrun-plugin 
Found /usr/share/maven-repo/org/apache/maven/plugins/maven-antrun-plugin/1.7/maven-antrun-plugin-1.7.pom in libmaven-antrun-plugin-java
> dpkg --search /usr/share/java/maven-antrun-plugin.jar 
dpkg failed to execute successfully
> apt-file search /usr/share/java/maven-antrun-plugin.jar 
Found libmaven-antrun-plugin-java
[error] Package libmaven-antrun-plugin-java does not contain Maven dependency org.apache.maven.plugins:maven-antrun-plugin:maven-plugin:1.7 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:


I simply decided to install the package libmaven-antrun-plugin-java and
pressed enter to try again:


Try again to resolve the dependency?
[Y/n] > 
Rescanning /usr/share/maven-repo...
Resolving org.apache.maven.plugins:maven-antrun-plugin:maven-plugin:1.7 of scope runtime...
Dependency org.apache.maven.plugins:maven-antrun-plugin:maven-plugin:1.7 found in package libmaven-antrun-plugin-java
[ok]

ERROR:
pom.xml: dependency is not packaged in the Maven repository for Debian: org.bioinfo:bioinfo-ngs:0.1.0
pom.xml: dependency is not packaged in the Maven repository for Debian: org.bioinfo:bioinfo-commons:0.10.1
pom.xml: dependency is not packaged in the Maven repository for Debian: org.bioinfo:bioinfo-commons:0.10.1
pom.xml: plugin is not packaged in the Maven repository for Debian: org.apache.maven.plugins:maven-antrun-plugin:1.7
--------
Checking dependencies for documentation packages...
Some problems were found in this project, exiting...


Well, it seems that your hints while sounding very sensible did not
fully enlighten me but anyway - I've got some rough packaging out
now at

    git://anonscm.debian.org/debian-med/qualimap.git

and my plan was to try to polish further without mh_make.  Unfortunately
even the clean target fails with


...
NOTE: Maven is executing in offline mode. Any artifacts not already in your local
repository will be inaccessible.

[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Building qualimap
[INFO]    task-segment: [clean]
[INFO] ------------------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[ERROR] BUILD ERROR
[INFO] ------------------------------------------------------------------------
[INFO] Error building POM (may not be this project's POM).


Project ID: org.apache.maven.plugins:maven-antrun-plugin

Reason: POM 'org.apache.maven.plugins:maven-antrun-plugin' not found in repository: System is offline.

  org.apache.maven.plugins:maven-antrun-plugin:pom:1.7


 for project org.apache.maven.plugins:maven-antrun-plugin

...


I guess I'm doing something seriousely wrong. :-(

> Let's start with some Maven basics then :)
> ...
> I hope it's clearer now :)

Yes, it makes sense and I'll put it under my pillow to help
reducing the frequence of showing up here with always the same
question.

Thanks for any help

       Andreas.

-- 
http://fam-tille.de