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
