Path: csiph.com!news.mixmin.net!feeds.phibee-telecom.net!news.panservice.it!diesel.cu.mi.it!bofh.it!news.nic.it!robomod From: Andreas Tille Newsgroups: linux.debian.maint.java Subject: Re: Problems understanding maven rules to package qualimap Date: Thu, 19 Nov 2015 16:20:02 +0100 Message-ID: References: X-Original-To: Debian Java List X-Mailbox-Line: From debian-java-request@lists.debian.org Thu Nov 19 15:16:05 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=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit User-Agent: Mutt/1.5.23 (2014-03-12) X-Mailing-List: archive/latest/18893 List-ID: List-URL: List-Archive: https://lists.debian.org/msgid-search/20151119151548.GD13664@an3as.eu Approved: robomod@news.nic.it Lines: 126 Organization: linux.* mail to news gateway Sender: robomod@news.nic.it X-Original-Cc: Debian Med Packaging Team , Olivier Sallou X-Original-Date: Thu, 19 Nov 2015 16:15:48 +0100 X-Original-Message-ID: <20151119151548.GD13664@an3as.eu> X-Original-References: <20151116162200.GQ24766@an3as.eu> <564A0936.2050907@apache.org> Xref: csiph.com linux.debian.maint.java:8574 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