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
