[Debian-med-packaging] Bug#989961: picard-tools: Wrong classpath in PicardCommandLine

[Vincent Danjean]

On 17/06/2021 12:23, Andreas Tille wrote:
> On Wed, Jun 16, 2021 at 10:00:25PM +0200, Vincent Danjean wrote:
>>   The package correctly depends on libcommons-math3-java,
>> but /usr/share/java/commons-math3.jar is not added in the classpath
>> in /usr/bin/PicardCommandLine, leading to errors (in some situations)
>> such as:
>> [Tue Jun 15 15:59:20 CEST 2021] picard.analysis.CollectWgsMetrics done. Elapsed time: 135.31 minutes.
>> Runtime.totalMemory()=6954156032
>> To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
>> ...
> 
> I wonder whether this is a grave issue and should be fixed in testing?

Not all workload are affected, but on the one where the class is needed,
the fix is required.
  PicardCommandLine uses the -cp option, so the CLASSPATH envvar is
ignored. The script must be modified to fix the bug.

  It seems to me that the fix is small and simple, so a freeze exception
for testing might be asked.

  Latter, for unstable, a fix that also add CLASSPATH (if defined) to
the -cp option might be considered.

  Regards,
    Vincent


> 
> Kind regards
> 
>         Andreas.
>