Bug#989961: picard-tools: Wrong classpath in PicardCommandLine

2021-06-17 Thread Andreas Tille 
Hi Vincent,

On Thu, Jun 17, 2021 at 01:04:30PM +0200, Vincent Danjean wrote:
> 
> 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.

Thank you for the analysis.  Given that you are Uploader for this
package would you consider at least commiting the needed changes.  If
you have no capacity for an upload I'd happily volunteer to do so.

Kind regards

  Andreas. 

-- 
http://fam-tille.de

Bug#989961: picard-tools: Wrong classpath in PicardCommandLine

2021-06-17 Thread 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.
>

Bug#989961: picard-tools: Wrong classpath in PicardCommandLine

2021-06-17 Thread Andreas Tille 
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?

Kind regards

Andreas.

-- 
http://fam-tille.de

Bug#989961: picard-tools: Wrong classpath in PicardCommandLine

2021-06-16 Thread Vincent Danjean 
Package: picard-tools
Version: 2.24.1+dfsg-1
Severity: normal
Tags: patch

  Hi,

  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
Exception in thread "main" java.lang.NoClassDefFoundError: 
org/apache/commons/math3/random/RandomGenerator
at 
picard.analysis.CollectWgsMetrics$WgsMetrics.calculateDerivedFields(CollectWgsMetrics.java:433)
at 
picard.analysis.CollectWgsMetrics$WgsMetrics.(CollectWgsMetrics.java:248)
at 
picard.analysis.CollectWgsMetrics.generateWgsMetrics(CollectWgsMetrics.java:551)
at 
picard.analysis.CollectWgsMetrics.generateWgsMetrics(CollectWgsMetrics.java:591)
at 
picard.analysis.AbstractWgsMetricsCollector.getMetrics(AbstractWgsMetricsCollector.java:175)
at 
picard.analysis.AbstractWgsMetricsCollector.addToMetricsFile(AbstractWgsMetricsCollector.java:132)
at 
picard.analysis.WgsMetricsProcessorImpl.addToMetricsFile(WgsMetricsProcessorImpl.java:127)
at picard.analysis.CollectWgsMetrics.doWork(CollectWgsMetrics.java:494)
at 
picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295)
at 
picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
Caused by: java.lang.ClassNotFoundException: 
org.apache.commons.math3.random.RandomGenerator
at 
java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581)
at 
java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:522)
... 11 more

  Adding the jar to the classpath in the script fixes the problem.

  Regards
Vincent

-- System Information:
Debian Release: 11.0
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'unstable'), (500, 'testing'), 
(500, 'stable'), (500, 'oldstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386, armel, mipsel

Kernel: Linux 5.10.0-7-amd64 (SMP w/4 CPU threads)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=fr_FR.utf8, LC_CTYPE=fr_FR.utf8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages picard-tools depends on:
ii  default-jre [java6-runtime] 2:1.11-72
ii  libpicard-java  2.24.1+dfsg-1
ii  openjdk-11-jre [java6-runtime]  11.0.12+4-1
ii  openjdk-17-jre [java6-runtime]  17~24-1

picard-tools recommends no packages.

picard-tools suggests no packages.

-- no debconf information