[Debian-med-packaging] Bug#741052: [igv] Unhandled exception java.lang.NoClassDefFoundError: com/google/java/contract/util/Objects

[Diane Trout]

Thank you for working on this dependency.

I tried to build and run the libcofoja package, and it didn't work for me.

I did a git checkout of the debian-med repoistory, and set up the pristine-tar 
and upstream branches for gbp. I used pristine-tar checkout libcofoja-
java_1.1-r150.orig.tar.xz to extract the source tar-ball.

I built it with cowbuilder-dist sid. 

I was getting exceptions like the following.:

ERROR [2014-03-10 14:37:36,472]  [DefaultExceptionHandler.java:42] [AWT-
EventQueue-1]  Unhandled exception
java.lang.UnsupportedClassVersionError: com/google/java/contract/util/Objects
  at org.broad.igv.data.Interval.contains(Interval.java:59)
  at 
org.broad.igv.track.LoadedDataInterval.contains(LoadedDataInterval.java:46)
  at org.broad.igv.track.DataTrack.render(DataTrack.java:83)
  at org.broad.igv.ui.panel.DataPanelPainter.draw(DataPanelPainter.java:260)
  at 
org.broad.igv.ui.panel.DataPanelPainter.paintFrame(DataPanelPainter.java:234)
  at org.broad.igv.ui.panel.DataPanelPainter.paint(DataPanelPainter.java:176)
  at org.broad.igv.ui.panel.DataPanel.paintComponent(DataPanel.java:138)

One other thing odd I noticed about the package was the version number 
appeared to be included in the base name.

/usr/share/java/cofoja-1.1-20140310-1.1.jar
/usr/share/java/cofoja-1.1-20140310-bare-1.1.jar
/usr/share/java/cofoja-1.1-20140310-bare.jar -> cofoja-1.1-20140310-
bare-1.1.jar
/usr/share/java/cofoja-1.1-20140310.jar -> cofoja-1.1-20140310-1.1.jar

While a symlink more consistent with the other java packages would look more 
like: cofoja.jar -> cofoja-1.1-20140310-1.1-jar.

I tried with both the 1.1 and bare jar files by loading a bigwig file and then 
trying to scroll around the file.

Diane

On Sunday, March 09, 2014 23:06:54 Andreas Tille wrote:
> Hi Diane,
> 
> would you mind testing
> 
>    git://anonscm.debian.org/debian-med/libcofoja-java.git
> 
> whether it works as expected?
> 
> Kind regards
> 
>          Andreas.
> 
> On Fri, Mar 07, 2014 at 02:13:29PM -0800, Diane Trout wrote:
> > Package: igv
> > Version: 2.3.14+dfsg-1
> > Severity: normal
> > 
> > --- Please enter the report below this line. ---
> > 
> > Hi,
> > 
> > In a few different cases I gotten a very similar a java stack trace.
> > 
> > * I tried to download a new genome using the drop down box.
> > * Hitting the X maximize window decoration
> > * Several things that trigger tool tip popups.