Path: csiph.com!eternal-september.org!feeder.eternal-september.org!aioe.org!bofh.it!news.nic.it!robomod From: Andreas Tille Newsgroups: linux.debian.maint.java Subject: Need a (hopefully) last kick for finalising qualimap Date: Wed, 02 Dec 2015 13:20:01 +0100 Message-ID: X-Original-To: debian-java@lists.debian.org, Debian Med Packaging Team X-Mailbox-Line: From debian-java-request@lists.debian.org Wed Dec 2 12:18:50 2015 Old-Return-Path: X-Amavis-Spam-Status: No, score=-5.245 tagged_above=-10000 required=5.3 tests=[BAYES_00=-2, FOURLA=0.1, LDO_WHITELIST=-5, MEDS2=2, RP_MATCHES_RCVD=-0.345] autolearn=no autolearn_force=no X-Policyd-Weight: using cached result; rate:hard: -6.1 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.23 (2014-03-12) X-Mailing-List: archive/latest/18935 List-ID: List-URL: List-Archive: https://lists.debian.org/msgid-search/20151202121830.GD28902@an3as.eu Approved: robomod@news.nic.it Lines: 58 Organization: linux.* mail to news gateway Sender: robomod@news.nic.it X-Original-Date: Wed, 2 Dec 2015 13:18:30 +0100 X-Original-Message-ID: <20151202121830.GD28902@an3as.eu> Xref: csiph.com linux.debian.maint.java:8615 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