R SIG Debian - Mar 2010 - Issue w/JGR after 2.10 upgrade: Error: could not find function...

After upgrading to R 2.10 and upgrading and testing JGR 1.7, I and other 
Ubuntu users are getting repeated error messages in JGR that look like this:

 > Error: could not find function ".getModels"
Error: could not find function ".getDataObjects"
Error: could not find function ".getOtherObjects"
Error: could not find function ".getFunctionsInWS"

The object browser and package manager also do not work.

See: http://ubuntuforums.org/showthread.php?t=1402621

Any thoughts on this?  It's not that JAVA_HOME is set.  I also removed 
my local R library and re-installed the JGR package and still got the 
same errors.  I ran R with sudo permissions and also got the same error.
I ran sudo R CMD javareconf before re-installing JGR and also no change.
Installed without and without sudo and same errors.
I'm using sun-java6 (jre and jdk).

On Mon, Mar 15, 2010 at 3:05 PM, Doug Holton <doug.holton at gmail.com>
wrote:
> After upgrading to R 2.10 and upgrading and testing JGR 1.7, I and other
> Ubuntu users are getting repeated error messages in JGR that look like
this:
>
>> Error: could not find function ".getModels"
> Error: could not find function ".getDataObjects"
> Error: could not find function ".getOtherObjects"
> Error: could not find function ".getFunctionsInWS"
>
> The object browser and package manager also do not work.
>
Hmm.  I have Ubuntu with JGR 1.7, and i don't see any of those messages.

I see only:
> library(JGR)
Loading required package: rJava
Loading required package: JavaGD
Loading required package: iplots

Please use the corresponding JGR launcher to start JGR.
Run JGR() for details. You can also use JGR(update=TRUE) to update
JGR.
> JGR()
Please consider running JGR() as root to create a start script in
/home/pauljohn/R/i486-pc-linux-gnu-library/2.10/JGR/scripts/run
automatically.
Starting JGR ...
Warning message:
In file(con, "w") :
  cannot open file
'/home/pauljohn/R/i486-pc-linux-gnu-library/2.10/JGR/scripts/run':
Permission denied

I need to track down that "Permission denied" in my home directory,
but JGR still seems to run. I can load datasets, do ordinary stuff.

What commands do you run to make the bad things happen.?


I wonder if you have more than one java development environment
installed.  It could be you have openjdk, which is the default, as
well as the Sun packages.  I suppose if your /etc/alternatives links
are not proper, it could confuse a lot of things.

The only *flashing warning* thing I noted about your post that might
be a sign of trouble is this comment:

"I'm using sun-java6 (jre and jdk)."

If you install the Sun JDK, it includes the JRE within it, and
installing both the jdk and the jre could cause the problem you see.
If R CMD javareconf finds the JRE (which you installed separately from
the JDK), then it has runtime stuff but no access to the devel
libraries.


-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas

This won't help your specific problem, but FYI I had a few issues with
JGR on Ubuntu in the past, and then I discovered this:

http://rgedit.sourceforge.net/

which is very light and integrates well with gedit. This is what I've
been using since on Ubuntu, and I'm pretty happy with it. Of course it
doesn't have all the feature of JGR, but if you're only interested in
the script editor capabilities then Rgedit should be fine.
-- 
Etienne Lalibert?
===============================School of Forestry
University of Canterbury
Private Bag 4800
Christchurch 8140, New Zealand
Phone: +64 3 366 7001 ext. 8365
Fax: +64 3 364 2124
www.elaliberte.info