Apologies, but having trouble installing JGR and Deducer

[jwh...@mac.com]

Sorry for the trouble, but I am having no luck installing JGR and Deducer on one of my two Macs.

Works fine on my 3 year old laptop, installed six weeks ago: (Mac OS X 10.8.4, R 3.0.1, JGR-1.6-SL, java 1.7.0_25); however it repeatedly fails on my newer iMac (same OS, R, JGR, java versions).

After install.packages(c("JGR","Deducer","DeducerExtras")) is successful in a fresh installation of R 3.0.1, I will get variations of the following in R:

> library(Deducer)

Loading required package: rJava

Loading required package: ggplot2

Loading required package: scales

Loading required package: JGR

Loading required package: JavaGD

Loading required package: iplots

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

Error: package ‘iplots’ could not be loaded

or 

> library(JGR)

Loading required package: iplots

Error : .onLoad failed in loadNamespace() for 'iplots', details:

  call: .jnew("org/rosuda/iplots/Framework")

  error: java.lang.NoClassDefFoundError: Could not initialize class org.rosuda.ibase.Common

Error: package ‘iplots’ could not be loaded

If I launch JGR.app, it doesn't load completely (like it does on my laptop), and I get in JGR Console

>

Loading required package: JGR

Loading required package: rJava

Loading required package: JavaGD

Loading required package: iplots

starting httpd help server ... done

>

But it never finishes loading the remaining packages, it's completely non-functional (can't enter anything on the command line in Console, or quit), and I have to force quit JGR. I have tried the sequence and script on the front page multiple times, as well as the sequence I found in the previous thread about a previous version of JGR below.

Does anyone have an idea of what the problem(s) might be? I have uninstalled R, Java, and JGR.app multiple times, and also the .plist files that I could identify.

Thanks in advance for any help,

John

[Ian Fellows]

This was discussed on list a bit ago (https://groups.google.com/d/msg/deducer/PttbnjStZMc/T5zrej_7yEcJ).

It turns out that Apple broke Swing with their Java update back in June. They fixed it, but for users who updated during a certain period, all Swing apps will freeze. You can download a patch at http://support.apple.com/kb/DL1572. Alternatively you can download and use Sun's Java.

You can check if you have the broken version by doing java -version . The broken one has has the string M4508 in the build.

best,

Ian

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[jwh...@mac.com]

Outstanding! Worked perfectly, and I'm off and running.

Many thanks to Ian for taking the time to help, and the original thread participants for figuring it all out.

cheers,

John

[mspin...@gmail.com]

Hi John,

Were you able to run deducer with java 1.7.0_25?  I still have a RjavaClassLoader in the JGR/Deducer window.

Best, 

Manuel

[rudolf....@gmail.com]

Hi Manuel

I was playing around a bit with this. 

The actual versions you are using play an important role here.

I am assuming all the latest versions from cran, Apple and Oracle are installed, which are deducer 0.7-6, jgr 1-7.15, R 3.01, Oracle's java jdk1.7.0_25.jdk and Apple's java  1.6 (java version "1.6.0_51", Build …M4509) on MacOS 10.8.4.

With Oracle's java set as default I get the same RjacvaClassLoader as you do, when starting JGR . Other than that, JGR and Deducer appear to be fully functional though.

You can change this by directing JGR back to Apple's java version. There are two ways of doing this, change the default java for all programs on the Mac or just redirect the java pathway for the specific program (JGR in this case) that you want to start with Apple's java (while other programs will still be using the default java).

If have described in detail in a recent post here how redirecting JGR to Apple's java can be achieved. Pls take a look at https://groups.google.com/forum/#!topic/deducer/H7rqPFE9qY8.

Installing the most recent development version of JGR (as recently posted by Ian here) would be an alternative solution that takes care of the problem, as far as I can tell.

Hope that helps.

Best regards

Rudolf

[Manuel Spínola]

Thank you very much Rudolf.

I am teaching statistics and data visualization with Deducer but the troubleshooting of JGR could be very time consuming and confusing for the students that don´t know anything about programming. I hope soon it will be an easy way to install JGR and DEducer in Mac.  In Windows I am avoiding the JGR launcher.  I couldn´t do this in Mac.

Also, I couldn´t download the development version of JGR.

Best,

Manuel

2013/9/2 <rudolf....@gmail.com>

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Manuel Spínola, Ph.D.
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
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[Ian Fellows]

Manuel,

Did you try the steps at https://groups.google.com/forum/#!topic/deducer/dwfi45tCWew in order to try out the development versions? These should solve any Oracle Java 7 issues.

Ian