[Debian-med-packaging] Bug#759543: fastqc: commons-math3 not found

[Danya Alexeyevsky]

Package: fastqc
Version: 0.11.2+dfsg-2
Severity: important

Dear Maintainer,

Thank you for supporting fastqc!

Please add commons-math3 to class-path in the manifest.

--- fastqc-0.11.2+dfsg/debian/manifest 2014-08-26 14:54:22.048426545 +0400
+++ fastqc-0.11.2+dfsg-1/debian/manifest  2014-08-26 14:38:09.196491481 +0400
@@ -1,3 +1,3 @@
 /usr/share/fastqc/fastqc.jar:
   Main-Class: uk.ac.babraham.FastQC.FastQCApplication
   - Class-Path: /usr/share/java/jbzip2.jar /usr/share/java/sam.jar
   + Class-Path: /usr/share/java/jbzip2.jar /usr/share/java/sam.jar /usr/share/java/commons-math3.jar

Before the suggested change fastqc exposed the following symptoms on any data file: it
started analysis, produced exception trace (see below) and then gets stuck. (In UI mode
nothing changes after printing the exception trace).

Started analysis of Intoshia_ATGTCA_L008_R1.fastq
Approx 5% complete for Intoshia_ATGTCA_L008_R1.fastq
Approx 10% complete for Intoshia_ATGTCA_L008_R1.fastq
Approx 15% complete for Intoshia_ATGTCA_L008_R1.fastq
Approx 20% complete for Intoshia_ATGTCA_L008_R1.fastq
Approx 25% complete for Intoshia_ATGTCA_L008_R1.fastq
Approx 30% complete for Intoshia_ATGTCA_L008_R1.fastq
Approx 35% complete for Intoshia_ATGTCA_L008_R1.fastq
Approx 40% complete for Intoshia_ATGTCA_L008_R1.fastq
Approx 45% complete for Intoshia_ATGTCA_L008_R1.fastq
Approx 50% complete for Intoshia_ATGTCA_L008_R1.fastq
Approx 55% complete for Intoshia_ATGTCA_L008_R1.fastq
Approx 60% complete for Intoshia_ATGTCA_L008_R1.fastq
Approx 65% complete for Intoshia_ATGTCA_L008_R1.fastq
Approx 70% complete for Intoshia_ATGTCA_L008_R1.fastq
Approx 75% complete for Intoshia_ATGTCA_L008_R1.fastq
Approx 80% complete for Intoshia_ATGTCA_L008_R1.fastq
Approx 85% complete for Intoshia_ATGTCA_L008_R1.fastq
Approx 90% complete for Intoshia_ATGTCA_L008_R1.fastq
Approx 95% complete for Intoshia_ATGTCA_L008_R1.fastq
Approx 100% complete for Intoshia_ATGTCA_L008_R1.fastq
Exception in thread "Thread-1" java.lang.NoClassDefFoundError: org/apache/commons/math3/distribution/BinomialDistribution
        at uk.ac.babraham.FastQC.Modules.KmerContent.calculateEnrichment(KmerContent.java:229)
        at uk.ac.babraham.FastQC.Modules.KmerContent.raisesError(KmerContent.java:390)
        at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:334)
        at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
        at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:163)
        at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:110)
        at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ClassNotFoundException: org.apache.commons.math3.distribution.BinomialDistribution
        at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
        ... 7 more

Cheers,
Daniil

-- System Information:
Debian Release: jessie/sid
  APT prefers testing
  APT policy: (990, 'testing'), (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)

Kernel: Linux 3.12-1-amd64 (SMP w/2 CPU cores)
Locale: LANG=en_US.utf8, LC_CTYPE=en_US.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages fastqc depends on:
ii  libcommons-math3-java  3.3-1
ii  libjbzip2-java         0.9.1-3
ii  libsam-java            1.113-1

fastqc recommends no packages.

fastqc suggests no packages.

-- no debconf information