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

[Andreas Tille]

Hi Diane,

On Mon, Mar 10, 2014 at 02:44:44PM -0700, Diane Trout wrote:
> 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 think this is a bit complicated.  The easy way would have been:

    gbp-clone ssh://git.debian.org/git/debian-med/libcofoja-java.git
    cd libcofoja-java
    git-buildpackage

> 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)

These errors do occure when running igv right?  The building of
libcofaja-java went fine so far I assume.

> 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 need to admit that I totally blindly applied javahelper without
fiddling around with symlinks at all.
 
> I tried with both the 1.1 and bare jar files by loading a bigwig file and then 
> trying to scroll around the file.

I admit I have no real clue but have set Olivier put in CC explicitly -
perhaps he might be able to help.

Kind regards

      Andreas.

-- 
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