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Groups > linux.debian.maint.java > #8615 > unrolled thread

Need a (hopefully) last kick for finalising qualimap

Started byAndreas Tille <andreas@an3as.eu>
First post2015-12-02 13:20 +0100
Last post2015-12-03 11:20 +0100
Articles 10 — 2 participants

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  Need a (hopefully) last kick for finalising qualimap Andreas Tille <andreas@an3as.eu> - 2015-12-02 13:20 +0100
    Re: Need a (hopefully) last kick for finalising qualimap Emmanuel Bourg <ebourg@apache.org> - 2015-12-02 13:30 +0100
      Re: Need a (hopefully) last kick for finalising qualimap Andreas Tille <andreas@an3as.eu> - 2015-12-02 15:40 +0100
        Re: Need a (hopefully) last kick for finalising qualimap Andreas Tille <andreas@an3as.eu> - 2015-12-02 17:20 +0100
          Re: Need a (hopefully) last kick for finalising qualimap Emmanuel Bourg <ebourg@apache.org> - 2015-12-02 17:50 +0100
            Re: Need a (hopefully) last kick for finalising qualimap Andreas Tille <andreas@an3as.eu> - 2015-12-02 18:20 +0100
              Re: Need a (hopefully) last kick for finalising qualimap Emmanuel Bourg <ebourg@apache.org> - 2015-12-02 18:50 +0100
                Re: Need a (hopefully) last kick for finalising qualimap Andreas Tille <andreas@an3as.eu> - 2015-12-02 22:30 +0100
                  Re: Need a (hopefully) last kick for finalising qualimap Emmanuel Bourg <ebourg@apache.org> - 2015-12-02 22:50 +0100
                    Re: Need a (hopefully) last kick for finalising qualimap Andreas Tille <andreas@an3as.eu> - 2015-12-03 11:20 +0100

#8615 — Need a (hopefully) last kick for finalising qualimap

FromAndreas Tille <andreas@an3as.eu>
Date2015-12-02 13:20 +0100
SubjectNeed a (hopefully) last kick for finalising qualimap
Message-ID<qBey5-72N-5@gated-at.bofh.it>
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

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#8617

FromEmmanuel Bourg <ebourg@apache.org>
Date2015-12-02 13:30 +0100
Message-ID<qBeHN-76w-27@gated-at.bofh.it>
In reply to#8615
Le 2/12/2015 13:18, Andreas Tille a écrit :
> "only dependency with system scope can specify systemPath."

Just add <scope>system</scope> where you added <systemPath>.

*kick*

Emmanuel Bourg

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#8622

FromAndreas Tille <andreas@an3as.eu>
Date2015-12-02 15:40 +0100
Message-ID<qBgJz-8no-9@gated-at.bofh.it>
In reply to#8617
Hi Emmanuel,

On Wed, Dec 02, 2015 at 01:25:24PM +0100, Emmanuel Bourg wrote:
> Le 2/12/2015 13:18, Andreas Tille a écrit :
> > "only dependency with system scope can specify systemPath."
> 
> Just add <scope>system</scope> where you added <systemPath>.
> 
> *kick*

Done (and pushed) and better but seems not to be final. :-(


[INFO] ------------------------------------------------------------------------
[ERROR] BUILD ERROR
[INFO] ------------------------------------------------------------------------
[INFO] Failed to resolve artifact.
        
Missing:
----------
1) org.bioinfo:bioinfo-ngs:jar:debian
        
  Try downloading the file manually from the project website.

  Then, install it using the command:.
      mvn install:install-file -DgroupId=org.bioinfo -DartifactId=bioinfo-ngs -Dversion=debian -Dpackaging=jar -Dfile=/path/to/file

  Alternatively, if you host your own repository you can deploy the file there:.
      mvn deploy:deploy-file -DgroupId=org.bioinfo -DartifactId=bioinfo-ngs -Dversion=debian -Dpackaging=jar -Dfile=/path/to/file -Durl=[url] -DrepositoryId=[id]

  Path to dependency:.
  	1) org.bioinfo.ngs:qualimap:jar:2.1.3-dev
  	2) org.bioinfo:bioinfo-ngs:jar:debian

2) org.bioinfo:bioinfo-commons:jar:debian

  Try downloading the file manually from the project website.

  Then, install it using the command:.
      mvn install:install-file -DgroupId=org.bioinfo -DartifactId=bioinfo-commons -Dversion=debian -Dpackaging=jar -Dfile=/path/to/file

  Alternatively, if you host your own repository you can deploy the file there:.
      mvn deploy:deploy-file -DgroupId=org.bioinfo -DartifactId=bioinfo-commons -Dversion=debian -Dpackaging=jar -Dfile=/path/to/file -Durl=[url] -DrepositoryId=[id]

  Path to dependency:.
  	1) org.bioinfo.ngs:qualimap:jar:2.1.3-dev
  	2) org.bioinfo:bioinfo-commons:jar:debian
        
3) org.ejml:ejml:jar:debian
        
  Try downloading the file manually from the project website.

  Then, install it using the command:.
      mvn install:install-file -DgroupId=org.ejml -DartifactId=ejml -Dversion=debian -Dpackaging=jar -Dfile=/path/to/file

  Alternatively, if you host your own repository you can deploy the file there:.
      mvn deploy:deploy-file -DgroupId=org.ejml -DartifactId=ejml -Dversion=debian -Dpackaging=jar -Dfile=/path/to/file -Durl=[url] -DrepositoryId=[id]

  Path to dependency:.
  	1) org.bioinfo.ngs:qualimap:jar:2.1.3-dev
  	2) org.ejml:ejml:jar:debian


1)+2) are the "own" java files inside the source tree and 3) should come
from /usr/share/java/EJML.jar (libejml-java package).

Seems I did not git it right yet. :-(

Sorry for my constant bothering here

      Andreas.

-- 
http://fam-tille.de

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#8623

FromAndreas Tille <andreas@an3as.eu>
Date2015-12-02 17:20 +0100
Message-ID<qBiim-161-5@gated-at.bofh.it>
In reply to#8622
Hi again,

I became better now by patching pom.xml further and ejml is found now.

But why the local files coming with the source are not found is
mysterious to me ... :-(

Kind regards

       Andreas.

On Wed, Dec 02, 2015 at 03:37:21PM +0100, Andreas Tille wrote:
> Hi Emmanuel,
> 
> On Wed, Dec 02, 2015 at 01:25:24PM +0100, Emmanuel Bourg wrote:
> > Le 2/12/2015 13:18, Andreas Tille a écrit :
> > > "only dependency with system scope can specify systemPath."
> > 
> > Just add <scope>system</scope> where you added <systemPath>.
> > 
> > *kick*
> 
> Done (and pushed) and better but seems not to be final. :-(
> 
> 
> [INFO] ------------------------------------------------------------------------
> [ERROR] BUILD ERROR
> [INFO] ------------------------------------------------------------------------
> [INFO] Failed to resolve artifact.
>         
> Missing:
> ----------
> 1) org.bioinfo:bioinfo-ngs:jar:debian
>         
>   Try downloading the file manually from the project website.
> 
>   Then, install it using the command:.
>       mvn install:install-file -DgroupId=org.bioinfo -DartifactId=bioinfo-ngs -Dversion=debian -Dpackaging=jar -Dfile=/path/to/file
> 
>   Alternatively, if you host your own repository you can deploy the file there:.
>       mvn deploy:deploy-file -DgroupId=org.bioinfo -DartifactId=bioinfo-ngs -Dversion=debian -Dpackaging=jar -Dfile=/path/to/file -Durl=[url] -DrepositoryId=[id]
> 
>   Path to dependency:.
>   	1) org.bioinfo.ngs:qualimap:jar:2.1.3-dev
>   	2) org.bioinfo:bioinfo-ngs:jar:debian
> 
> 2) org.bioinfo:bioinfo-commons:jar:debian
> 
>   Try downloading the file manually from the project website.
> 
>   Then, install it using the command:.
>       mvn install:install-file -DgroupId=org.bioinfo -DartifactId=bioinfo-commons -Dversion=debian -Dpackaging=jar -Dfile=/path/to/file
> 
>   Alternatively, if you host your own repository you can deploy the file there:.
>       mvn deploy:deploy-file -DgroupId=org.bioinfo -DartifactId=bioinfo-commons -Dversion=debian -Dpackaging=jar -Dfile=/path/to/file -Durl=[url] -DrepositoryId=[id]
> 
>   Path to dependency:.
>   	1) org.bioinfo.ngs:qualimap:jar:2.1.3-dev
>   	2) org.bioinfo:bioinfo-commons:jar:debian
>         
> 3) org.ejml:ejml:jar:debian
>         
>   Try downloading the file manually from the project website.
> 
>   Then, install it using the command:.
>       mvn install:install-file -DgroupId=org.ejml -DartifactId=ejml -Dversion=debian -Dpackaging=jar -Dfile=/path/to/file
> 
>   Alternatively, if you host your own repository you can deploy the file there:.
>       mvn deploy:deploy-file -DgroupId=org.ejml -DartifactId=ejml -Dversion=debian -Dpackaging=jar -Dfile=/path/to/file -Durl=[url] -DrepositoryId=[id]
> 
>   Path to dependency:.
>   	1) org.bioinfo.ngs:qualimap:jar:2.1.3-dev
>   	2) org.ejml:ejml:jar:debian
> 
> 
> 1)+2) are the "own" java files inside the source tree and 3) should come
> from /usr/share/java/EJML.jar (libejml-java package).
> 
> Seems I did not git it right yet. :-(
> 
> Sorry for my constant bothering here
> 
>       Andreas.
> 
> -- 
> http://fam-tille.de

-- 
http://fam-tille.de

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#8624

FromEmmanuel Bourg <ebourg@apache.org>
Date2015-12-02 17:50 +0100
Message-ID<qBiLn-1hG-1@gated-at.bofh.it>
In reply to#8623
Le 2/12/2015 17:14, Andreas Tille a écrit :

> But why the local files coming with the source are not found is
> mysterious to me ... :-(

Maven complains about bioinfo-ngs and bioinfo-commons. Are these
dependencies packaged yet? They don't seem to be part of the qualimap
source package.

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#8625

FromAndreas Tille <andreas@an3as.eu>
Date2015-12-02 18:20 +0100
Message-ID<qBjer-1JE-31@gated-at.bofh.it>
In reply to#8624
On Wed, Dec 02, 2015 at 05:42:24PM +0100, Emmanuel Bourg wrote:
> Le 2/12/2015 17:14, Andreas Tille a écrit :
> 
> > But why the local files coming with the source are not found is
> > mysterious to me ... :-(
> 
> Maven complains about bioinfo-ngs and bioinfo-commons. Are these
> dependencies packaged yet? They don't seem to be part of the qualimap
> source package.

At least I see

    src/main/java/org/bioinfo/ngs

in the qualimap source tree and at least this should be found, shouldn't
it?  How can I approach this or is my assumption wrong?

I think I need to ask upstream since I see what seems to be missing
here:

    http://www.massapi.com/package/org/bioinfo/index.html

Kind regards

     Andreas.

-- 
http://fam-tille.de

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#8626

FromEmmanuel Bourg <ebourg@apache.org>
Date2015-12-02 18:50 +0100
Message-ID<qBjHv-1WC-71@gated-at.bofh.it>
In reply to#8625
Le 2/12/2015 18:14, Andreas Tille a écrit :

> in the qualimap source tree and at least this should be found, shouldn't
> it?  How can I approach this or is my assumption wrong?

You are confusing the Maven coordinates of the libraries (here
org.bioinfo:bioinfo-ngs) with the Java package name. qualimap and
bioinfo-ng share the same base package (org.bioinfo.ngs) but eventually
live in different packages (org.bioinfo.ngs.qc.qualimap for qualimap,
org.bioinfo.ngs.data and org.bioinfo.ngs.map for bioinfo-ngs).

Your next step is to find the sources of these jars:

http://repos.bioinfo.cipf.es/maven2/org/bioinfo/bioinfo-ngs/0.1.0/bioinfo-ngs-0.1.0.jar
http://repos.bioinfo.cipf.es/maven2/org/bioinfo/bioinfo-commons/0.10.1/bioinfo-commons-0.10.1.jar

Emmanuel Bourg

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#8627

FromAndreas Tille <andreas@an3as.eu>
Date2015-12-02 22:30 +0100
Message-ID<qBn8m-4el-17@gated-at.bofh.it>
In reply to#8626
On Wed, Dec 02, 2015 at 06:44:15PM +0100, Emmanuel Bourg wrote:
> You are confusing the Maven coordinates of the libraries (here
> org.bioinfo:bioinfo-ngs) with the Java package name. qualimap and
> bioinfo-ng share the same base package (org.bioinfo.ngs) but eventually
> live in different packages (org.bioinfo.ngs.qc.qualimap for qualimap,
> org.bioinfo.ngs.data and org.bioinfo.ngs.map for bioinfo-ngs).
> 
> Your next step is to find the sources of these jars:
> 
> http://repos.bioinfo.cipf.es/maven2/org/bioinfo/bioinfo-ngs/0.1.0/bioinfo-ngs-0.1.0.jar
> http://repos.bioinfo.cipf.es/maven2/org/bioinfo/bioinfo-commons/0.10.1/bioinfo-commons-0.10.1.jar

When I was asking last week[1] I was seeking in this direction but I've
git no answer and so I was plainly hoping that the answer is inside the
code itself.  The problem is I was doing websearches in various
directions but did not found anything.  I have now directed my question
to the forum maintained by the authors[2] of qualimap any hope that they
might enlighten me since I have not found any trace of the code.

I really wonder why the maven repository does not contain any metadata
which reversely points to the URL of the project it is providing maven
input for. :-(

Any hint for a successful search strategy would be welcome.

Kind regards

      Andreas.

[1] https://lists.debian.org/debian-java/2015/11/msg00072.html
[2] https://groups.google.com/forum/#!topic/qualimap/KVJ8m5ZsAhU

-- 
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#8628

FromEmmanuel Bourg <ebourg@apache.org>
Date2015-12-02 22:50 +0100
Message-ID<qBnrI-4ln-9@gated-at.bofh.it>
In reply to#8627
Le 2/12/2015 22:20, Andreas Tille a écrit :

> I really wonder why the maven repository does not contain any metadata
> which reversely points to the URL of the project it is providing maven
> input for. :-(
> 
> Any hint for a successful search strategy would be welcome.

I got a quick look and couldn't find the source of these libraries.
Their respective poms do not point to a publicly accessible source
repository, and the Maven repository at repos.bioinfo.cipf.es doesn't
contain the source artifacts. The Bitbucket repository contains only the
qualimap code and not the bioinfo libraries.

Maybe the upstream authors didn't open source this part of the project yet?

Emmanuel Bourg

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#8630

FromAndreas Tille <andreas@an3as.eu>
Date2015-12-03 11:20 +0100
Message-ID<qBz9v-3CM-13@gated-at.bofh.it>
In reply to#8628
On Wed, Dec 02, 2015 at 10:42:47PM +0100, Emmanuel Bourg wrote:
> > Any hint for a successful search strategy would be welcome.
> 
> I got a quick look and couldn't find the source of these libraries.
> Their respective poms do not point to a publicly accessible source
> repository, and the Maven repository at repos.bioinfo.cipf.es doesn't
> contain the source artifacts. The Bitbucket repository contains only the
> qualimap code and not the bioinfo libraries.

Thanks for checking.
 
> Maybe the upstream authors didn't open source this part of the project yet?

I forwarded this to the forum of the qualimap authors.

Thanks again for your patience

      Andreas.

-- 
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