igv shell wrapper missing class dependency

Bug #1602389 reported by Bruce Walker
6
This bug affects 1 person
Affects Status Importance Assigned to Milestone
igv (Ubuntu)
Fix Released
Undecided
Unassigned

Bug Description

This is a packaging issue; the igv shell script classpath is missing /usr/share/java/commons-io.jar

The result is that when trying to create a .genome file from a fasta, igv crashes with the following error:

INFO [2016-07-12 14:20:48,781] [CommandListener.java:106] [Thread-6] Listening on port 60151
ERROR [2016-07-12 14:21:22,493] [DefaultExceptionHandler.java:49] [AWT-EventQueue-0] Unhandled exception
java.lang.NoClassDefFoundError: org/apache/commons/io/FilenameUtils
 at org.broad.igv.util.FileUtils.getRelativePath(FileUtils.java:118)
 at org.broad.igv.util.FileUtils.getRelativePath(FileUtils.java:196)
 at org.broad.igv.feature.genome.GenomeImporter.createGenomeArchive(GenomeImporter.java:146)
 at org.broad.igv.feature.genome.GenomeManager.defineGenome(GenomeManager.java:1240)
 at org.broad.igv.ui.IGV.doDefineGenome(IGV.java:508)
 at org.broad.igv.ui.IGVMenuBar$13.actionPerformed(IGVMenuBar.java:585)

I have verified that adding the missing class lib to the shell script fixes the problem.

ProblemType: Bug
DistroRelease: Ubuntu 16.04
Package: igv 2.3.68+dfsg-1
ProcVersionSignature: Ubuntu 4.4.0-28.47-generic 4.4.13
Uname: Linux 4.4.0-28-generic x86_64
NonfreeKernelModules: nvidia_uvm nvidia_modeset nvidia
ApportVersion: 2.20.1-0ubuntu2.1
Architecture: amd64
CurrentDesktop: XFCE
Date: Tue Jul 12 15:02:16 2016
InstallationDate: Installed on 2015-09-29 (287 days ago)
InstallationMedia: Xubuntu 15.04 "Vivid Vervet" - Release amd64 (20150422.1)
PackageArchitecture: all
SourcePackage: igv
UpgradeStatus: Upgraded to xenial on 2016-05-26 (46 days ago)

Revision history for this message
Bruce Walker (bru2e) wrote :
Bruce Walker (bru2e)
summary: - igv missing class dependency
+ igv shell wrapper missing class dependency
Revision history for this message
Launchpad Janitor (janitor) wrote :

This bug was fixed in the package igv - 2.4.14+dfsg-2

---------------
igv (2.4.14+dfsg-2) unstable; urgency=medium

  [ Olivier Sallou ]
  fix for FTBS openjdk 11, Closes: #895765
    - thanks to Markus Koschany <email address hidden>

 -- Olivier Sallou <email address hidden> Tue, 23 Oct 2018 14:55:18 +0200

Changed in igv (Ubuntu):
status: New → Fix Released
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