Aaargh!
This was years ago, now. Sorry, this happened so long ago I can't recall my workaround. At all.
If anything hits my synapses I'll post it. I'm pretty sure I found a way to compile... I'm pretty sure it involved some workaround.

Brian King

> Date: Tue, 3 Apr 2012 09:14:04 +0000
> From: <email address hidden>
> To: <email address hidden>
> Subject: [Bug 486906] Re: ubuntu 9.10 imagej "Plugins>Compile and Run..." does	not work
> 
> Same problem here on 11.10 with the source version of imaegJ.
> Linking to tools.jar in /usr/lib/jvm/java-6-openjdk/jre/lib/ext/ fixes it.
> 
> -- 
> You received this bug notification because you are subscribed to the bug
> report.
> https://bugs.launchpad.net/bugs/486906
> 
> Title:
>   ubuntu 9.10 imagej "Plugins>Compile and Run..." does not work
> 
> Status in “imagej” package in Ubuntu:
>   Confirmed
> 
> Bug description:
>   Binary package hint: imagej
> 
>   I upgraded from Ubuntu 9.04 (fresh install) to Ubuntu 9.10 just last
>   night (great job, guys!). I opted to install the ImageJ package 1.43b-
>   1ubuntu1 (http://ca.archive.ubuntu.com karmic/universe Packages). I
>   can start ImageJ just fine from the Applications>Graphics menu (the
>   graphical icon in this menu does "imagej %f" according to its
>   Properties). It runs beautifully. BUT...
> 
>   But when I select "Plugins>Compile and Run..." I get the error:
>   "Unable to find the javac compiler, which comes with the Windows and
>   Linux versions of ImageJ that include Java in the ImageJ/jre
>   folder.<newline> java.home: /usr/lib/jvm/java-6-openjdk/jre" In this
>   case, I'm trying to compile and run a Plugin (My_Integrator.java) in
>   $HOME/.imagej/plugins.
> 
>   So at this point, with apologies, it becomes confusing. I had been
>   trying to get ImageJ running (same bug!) on 9.04, so my system's java
>   use/preferences may have changed. So let me point out the following
>   behaviours, for different choices of jre (using "sudo update-
>   alternatives --config java" to toggle between different javas
>   (javae??).
> 
>   IF I CHOOSE "/usr/bin/gij-4.3" or "/usr/bin/gij-4.4", THEN I replicate
>   Bug #471127. In this case, implementing the "hack" suggested by
>   linuxed on that report/thread (editing "/usr/bin/imagej") has no
>   effect and ImageJ will not launch from the Applications menu. Command-
>   line launch gives the "Exception in thread "main" java.awt.AWTError:
>   Cannot load AWT toolkit: gnu.java.awt.peer.gtk.GtkToolkit..." message
>   which - at first glance - seems to be the same as in Bug #471127.
> 
>   IF I CHOOSE "/usr/lib/jvm/java-6-openjdk/jre/bin/java" or
>   "/usr/lib/jvm/java-6-sun/jre/bin/java" THEN ImageJ launches/runs
>   great! However, when I attempt to "Plugins>Compile and Run..." I get
>   the above error. (Sorry! NEED to get this running, and am a bit of a
>   java newb, so though I understand repository-packagers aversion to
>   non-free-as-in-freedom java environments, I downloaded the Sun jdk
>   yesterday... and possibly Sun jre much earlier...)
> 
>   I apologize if fixing Bug #471127 fixes this as well. But my guess is
>   that perhaps the Ubuntu repository packaging has environment variables
>   which aren't pointing in the correct place (I see that the package's
>   imagej.jar has a "hack" in it from previous instances of this problem
>   - found on the web...).
> 
>   (Hopefully it will be possible to eventually just run ImageJ in all
>   its functionality directly from the Applications menu...)
> 
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