[Debian-med-packaging] Bug#923731: Help with gradle needed (Was: Bug#923731: Any volunteer to fix the "usual" issues when upgrading to new version of igv?)

[Andreas Tille]

Hi,

any comment from Debian Java team?

Kind regards

    Andreas.

On Mon, Sep 16, 2019 at 09:57:58AM +0200, Olivier Sallou wrote:
> 
> On 9/13/19 3:43 PM, Andreas Tille wrote:
> > Hi,
> >
> > I upgraded the igv packaging Git[1] to the latest upstream version.  I
> > never experienced a smooth upgrade to any igv version - but I always
> > experienced help from a Java expert here on the list.  May be it is time
> > again to fix:
> 
> I had a quick look, but no idea here.
> 
> Related Java 11 module loading. Should ask debian Java team I think on
> hjow to handle this.
> 
> Dependencies are in maven-repo, but gradle does not seem to find them as
> "modules" or related jar files are not seen as modules.
> 
> 
> Olivier
> 
> >
> >
> > All input files are considered out-of-date for incremental task ':compileJava'.
> > Compiling with JDK Java compiler API.
> > /build/igv-2.6.3+dfsg/src/main/java11/module-info.java:7: error: module not found: ant
> >     requires ant;
> >              ^
> > /build/igv-2.6.3+dfsg/src/main/java11/module-info.java:8: error: module not found: com.google.common
> >     requires com.google.common;
> >                        ^
> > /build/igv-2.6.3+dfsg/src/main/java11/module-info.java:9: error: module not found: commons.io
> >     requires commons.io;
> >                     ^
> > /build/igv-2.6.3+dfsg/src/main/java11/module-info.java:10: error: module not found: commons.math
> >     requires commons.math;
> >                     ^
> > /build/igv-2.6.3+dfsg/src/main/java11/module-info.java:12: error: module not found: gson
> >     requires gson;
> >              ^
> > /build/igv-2.6.3+dfsg/src/main/java11/module-info.java:13: error: module not found: htsjdk
> >     requires htsjdk;
> >              ^
> > /build/igv-2.6.3+dfsg/src/main/java11/module-info.java:22: error: module not found: log4j
> >     requires log4j;
> >              ^
> > /build/igv-2.6.3+dfsg/src/main/java11/module-info.java:23: error: module not found: org.apache.logging.log4j
> >     requires org.apache.logging.log4j;
> >                                ^
> > /build/igv-2.6.3+dfsg/src/main/java11/module-info.java:24: error: module not found: org.apache.logging.log4j.core
> >     requires org.apache.logging.log4j.core;
> >                                      ^
> > /build/igv-2.6.3+dfsg/src/main/java11/module-info.java:25: error: module not found: swing.layout
> >     requires swing.layout;
> >                   ^
> > 10 errors
> > :compileJava FAILED
> > :compileJava (Thread[Task worker for ':',5,main]) completed. Took 4.782 secs.
> >
> > FAILURE: Build failed with an exception.
> >
> >
> > The failures are looking like missing Build-Depends at first look but these
> > should be OK.  Any volunteer?
> >
> > Kind regards
> >
> >        Andreas.
> >
> >
> > [1] https://salsa.debian.org/med-team/igv
> >
> -- 
> Olivier Sallou
> Univ Rennes, Inria, CNRS, IRISA
> Irisa, Campus de Beaulieu
> F-35042 RENNES - FRANCE
> Tel: 02.99.84.71.95
> 
> gpg key id: 4096R/326D8438  (keyring.debian.org)
> Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438
> 
> 

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