Path: csiph.com!news.mixmin.net!weretis.net!feeder1.news.weretis.net!news.mb-net.net!open-news-network.org!aioe.org!bofh.it!news.nic.it!robomod From: Andreas Tille Newsgroups: linux.debian.maint.java Subject: Problems understanding maven rules to package qualimap Date: Mon, 16 Nov 2015 17:30:02 +0100 Message-ID: X-Original-To: Debian Java List , Debian Med Packaging Team X-Mailbox-Line: From debian-java-request@lists.debian.org Mon Nov 16 16:22:16 2015 Old-Return-Path: X-Amavis-Spam-Status: No, score=-7.345 tagged_above=-10000 required=5.3 tests=[BAYES_00=-2, LDO_WHITELIST=-5, RP_MATCHES_RCVD=-0.345] autolearn=ham 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/18879 List-ID: List-URL: List-Archive: https://lists.debian.org/msgid-search/20151116162200.GQ24766@an3as.eu Approved: robomod@news.nic.it Lines: 64 Organization: linux.* mail to news gateway Sender: robomod@news.nic.it X-Original-Date: Mon, 16 Nov 2015 17:22:00 +0100 X-Original-Message-ID: <20151116162200.GQ24766@an3as.eu> Xref: csiph.com linux.debian.maint.java:8560 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