[Debian-med-packaging] Need a (hopefully) last kick for finalising qualimap

[Andreas Tille]

Hi,

I keep on struggling with qualimap[1] but I can not come past this
error despite I think I followed all hints on Debian-Java list (may
be I missed something?):

...
Project ID: org.bioinfo.ngs:qualimap
POM Location: /build/qualimap-2.1.3+dfsg/pom.xml
Validation Messages:

    [0]  For dependency Dependency {groupId=net.sf.picard, artifactId=picard, version=debian, type=jar}: only dependency with system scope can specify systemPath.
    [1]  For dependency Dependency {groupId=net.sf.samtools, artifactId=samtools, version=debian, type=jar}: only dependency with system scope can specify systemPath.


Reason: Failed to validate POM for project org.bioinfo.ngs:qualimap at /build/qualimap-2.1.3+dfsg/pom.xml


[INFO] ------------------------------------------------------------------------
[INFO] Trace
org.apache.maven.reactor.MavenExecutionException: Failed to validate POM for project org.bioinfo.ngs:qualimap at /build/qualimap-2.1.3+dfsg/pom.xml
	at org.apache.maven.DefaultMaven.getProjects(DefaultMaven.java:404)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:272)
	at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:138)
	at org.apache.maven.cli.MavenCli.main(MavenCli.java:362)
	at org.apache.maven.cli.compat.CompatibleMain.main(CompatibleMain.java:60)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:606)
	at org.codehaus.classworlds.Launcher.launchEnhanced(Launcher.java:315)
	at org.codehaus.classworlds.Launcher.launch(Launcher.java:255)
	at org.codehaus.classworlds.Launcher.mainWithExitCode(Launcher.java:430)
	at org.codehaus.classworlds.Launcher.main(Launcher.java:375)
Caused by: org.apache.maven.project.InvalidProjectModelException: Failed to validate POM for project org.bioinfo.ngs:qualimap at /build/qualimap-2.1.3+dfsg/pom.xml
	at org.apache.maven.project.DefaultMavenProjectBuilder.processProjectLogic(DefaultMavenProjectBuilder.java:1077)
	at org.apache.maven.project.DefaultMavenProjectBuilder.buildInternal(DefaultMavenProjectBuilder.java:880)
	at org.apache.maven.project.DefaultMavenProjectBuilder.buildFromSourceFileInternal(DefaultMavenProjectBuilder.java:508)
	at org.apache.maven.project.DefaultMavenProjectBuilder.build(DefaultMavenProjectBuilder.java:200)
	at org.apache.maven.DefaultMaven.getProject(DefaultMaven.java:604)
	at org.apache.maven.DefaultMaven.collectProjects(DefaultMaven.java:487)
	at org.apache.maven.DefaultMaven.getProjects(DefaultMaven.java:391)
	... 12 more
[INFO] ------------------------------------------------------------------------
[INFO] Total time: < 1 second
[INFO] Finished at: Wed Dec 02 12:10:24 UTC 2015
[INFO] Final Memory: 4M/117M


Any help would be really welcome

      Andreas.


[1] git://git.debian.org/git/debian-med/qualimap.git

-- 
http://fam-tille.de