Dear all, I want to thanks Brandon Hurr for his advice in getting the JGR app up and running (see below) as a lead-in to using Deducer.
I'd also like to thank Ian Fellows for his useful pointers to installing and running Deducer on a Mac from within the R GUI.  The note on installation (http://www.deducer.org/pmwiki/pmwiki.php?n=Main.MacOSXInstallation) made all the difference and it worked perfectly.
Thanks to you both.
Alan Kelly



On 1 Aug 2011, at 14:20, Brandon Hurr wrote:

Does it happen like that if you click on the JGR.app that you downloaded from sourceforge?

I get the following...

It autoloads this on startup...
> Loading required package: JGR
Loading required package: rJava
Loading required package: JavaGD
Loading required package: iplots
starting httpd help server ... done

Then I load Deducer...
> require(Deducer)
Loading required package: Deducer
Loading required package: ggplot2
Loading required package: reshape
Loading required package: plyr

Attaching package: 'reshape'

The following object(s) are masked from 'package:plyr':

    rename, round_any

Loading required package: grid
Loading required package: proto
Loading required package: car
Loading required package: MASS
Loading required package: nnet
Loading required package: survival
Loading required package: splines
Loading required package: multcomp
Loading required package: mvtnorm
Loading required package: effects
Loading required package: lattice
Loading required package: nlme
Loading required package: colorspace

Attaching package: 'effects'

The following object(s) are masked from 'package:car':

    Prestige

The following object(s) are masked from 'package:datasets':

    Titanic

Loading required package: foreign

Attaching package: 'Deducer'

The following object(s) are masked from 'package:stats':

    summary.lm

No idea what to do with it at this point, but at least it loads.

Brandon

On Mon, Aug 1, 2011 at 14:04, Alan Kelly <AKELLY@tcd.ie<mailto:AKELLY@tcd.ie>> wrote:
Brandon - I tried both the SL version (lots of errors and failed to load) and the alternative JGR.dmg.
When trying library(JGR) I still get the same message:
starting httpd help server ... done
Loading required package: rJava
Loading required package: JavaGD
Loading required package: iplots
Note: On Mac OS X we strongly recommend using iplots from within JGR.
Proceed at your own risk as iplots cannot resolve potential ev.loop deadlocks.
'Yes' is assumed for all dialogs as they cannot be shown without a deadlock,
also ievent.wait() is disabled.
Error in .jnew("org/rosuda/iplots/Framework") :
  java.lang.InternalError: Can't start the AWT because Java was started on the first thread.  Make sure StartOnFirstThread is not specified in your application's Info.plist or on the command line
Error: package 'iplots' could not be loaded

JAVA starting on the first thread seems to be the issue - but no idea how to correct this.
I'll wait and see if I get any other responses before updating my query.
Many thanks for your efforts.
Alan
PS: holding off (this time!) on rushing to update to latest MAC OS - just in case of incompatibility problems.

On 1 Aug 2011, at 13:54, Brandon Hurr wrote:

I'm on Lion and downloaded the SL one. It seems to work. Haven't had a chance to try it out really though. Let me know how you get on...

B

On Mon, Aug 1, 2011 at 13:52, Alan Kelly <AKELLY@tcd.ie<mailto:AKELLY@tcd.ie>> wrote:
Thanks Brandon - it was as a result of reading the same thread that lead me to the problem also.
Looking at the Rforge link you supplied I see JGR-1.6-SL.dmg and JRG.dmg - both with dates 12 months back.
Which did you download - or does it matter?
Alan

On 1 Aug 2011, at 13:46, Brandon Hurr wrote:

Funny enough I was trying the same thing today after reading the discussion in Baptiste's Physicists thread. I get a very similar error when I started it in R...

> require(deducer)
Loading required package: deducer
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'deducer'
> require(Deducer)
Loading required package: Deducer
Loading required package: rJava
Loading required package: JGR
Loading required package: JavaGD
Loading required package: iplots
Note: On Mac OS X we strongly recommend using iplots from within JGR.
Proceed at your own risk as iplots cannot resolve potential ev.loop deadlocks.
'Yes' is assumed for all dialogs as they cannot be shown without a deadlock,
also ievent.wait() is disabled.
Error : .onLoad failed in loadNamespace() for 'iplots', details:
  call: .jnew("org/rosuda/iplots/Framework")
  error: java.lang.InternalError: Can't start the AWT because Java was started on the first thread.  Make sure StartOnFirstThread is not specified in your application's Info.plist or on the command line
Failed with error:  ‘package 'iplots' could not be loaded’

> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] JavaGD_0.5-4    rJava_0.9-1     edgeR_2.2.5     quantmod_0.3-15 TTR_0.20-2      xts_0.8-0
 [7] zoo_1.7-2       Defaults_1.1-1  tis_1.17        ggplot2_0.8.9   proto_0.3-9.2   reshape_0.8.4
[13] plyr_1.6

loaded via a namespace (and not attached):
[1] digest_0.5.0    lattice_0.19-30 limma_3.8.2     tools_2.13.1


But I downloaded the application from JGR directly and ran it. In JGR it loaded all the packages just fine. http://www.rforge.net/JGR/files/

I can't say I know how to use it yet though... Just need to RTFM I guess.

Brandon





On Mon, Aug 1, 2011 at 13:20, Alan Kelly <AKELLY@tcd.ie<mailto:AKELLY@tcd.ie>> wrote:
dear all, my intention was to check-out Deducer for teaching purposes.  Deducer would not load indicating problems with loading "iplots".  The error message is the same as that repoduced below when I try to load JGR.  I've checked the Info.plist file in the R folder and there is no "StartOnFirstThread" command line.
Any advice on how I might proceed?
Many thanks,
Alan Kelly
Trinity College Dublin


> library(JGR)
Loading required package: rJava
Loading required package: JavaGD
Loading required package: iplots
Note: On Mac OS X we strongly recommend using iplots from within JGR.
Proceed at your own risk as iplots cannot resolve potential ev.loop deadlocks.
'Yes' is assumed for all dialogs as they cannot be shown without a deadlock,
also ievent.wait() is disabled.
Error in .jnew("org/rosuda/iplots/Framework") :
 java.lang.InternalError: Can't start the AWT because Java was started on the first thread.  Make sure StartOnFirstThread is not specified in your application's Info.plist or on the command line
Error: package 'iplots' could not be loaded

Session Info
> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US/en_US/en_US/C/en_US/en_US

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] JavaGD_0.5-4 rJava_0.9-1

loaded via a namespace (and not attached):
[1] coda_0.14-2     grid_2.13.1     lattice_0.19-30

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