[Debian-med-packaging] Help to detect java classes in drop-seq (covid-19 relevant) needed

[Andreas Tille]

Hi,

On Wed, May 20, 2020 at 10:07:48PM +0200, Andreas Tille wrote:
> 
> Thanks.  This was pretty helpful.  Now I need to package the
> remaining JAR which is not yet packaged from
> 
>    http://la4j.org/

I made some progress and also uploaded libla4j-java[1] to new.  With
this I tried to build drop-seq[2] and stumbled upon two issues:

At first a lintian issue:

W: drop-seq-tools: classpath-contains-relative-path usr/share/java/dropseq-2.3.0.jar: lib/FastInfoset-1.2.12.jar, lib/FastInfoset.jar, lib/FastInf
N: 
N:    The classpath listed in the jar file refers to a potential missing jar
N:    file. This could be the remnants of a build-time classpath that are not
N:    relevant for a JAR bundled in a Debian package.
N:    
N:    Alternatively, the classpath may be correct, but the package is lacking
N:    a jar file or a symlink to it.
N:    
N:    Note, Lintian assumes that all (relative) classpaths pointing to
N:    /usr/share/java/ (but not subdirs thereof) are satisfied by dependencies
N:    as long as there is at least one strong libX-java dependency.
N:    
N:    Severity: warning
N:    
N:    Check: languages/java

I have no idea what this means.  A `grep -Ri fastinfoset` inside the source
tree remains empty.

The other one is a runtime error of the wrapper script:

$ drop-seq 
Error: Could not find or load main class org.broadinstitute.dropseqrna.cmdline.DropSeqMain
Caused by: java.lang.NoClassDefFoundError: picard/cmdline/PicardCommandLine

Any idea what might be wrong here?

Thanks a lot for any help

      Andreas.


[1] https://salsa.debian.org/med-team/libla4j-java
[2] https://salsa.debian.org/med-team/drop-seq

-- 
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