[Debian-med-packaging] Bug#923731: Bug#923731: Any volunteer to fix the "usual" issues when upgrading to new version of igv?

[Olivier Sallou]

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 All input files are considered out-of-date for incremental task ':compileJava'.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

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