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

[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.<init>(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