Re: [R] JGR, Java and Kubuntu 7.04 ...

2007-06-15 Thread Stefan Grosse
You could download the latest R (2.5.0) directly from CRAN, this just as
a side remark, You find instructions here:
http://cran.au.r-project.org/bin/linux/ubuntu/README

With java you should make sure that you have the Java 5 JDK installed. 
I dont know how it is with Ubuntu but on fedora I have to set the java
alternative (sun java installation does not change the default java
there). Which java is installed you can check with java -version there
you see it it is properly installed and a R CMD javareconf also
indicates if your java is configured correctly. Additionally on Fedora I
had to set JAVA_HOME to the JDK directory manually.

Stefan

 Original Message  
Subject: [R] JGR, Java and Kubuntu 7.04 ...
From: John Logsdon [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Date: 14.06.2007 19:16
 R-ists

 Yet again Java rears its ugly head.  

 I have Kubuntu 7.04 running the Kubuntu-repository version of R 2.4.1-1.  
 Yes it isn't the  very latest version but this is not the issue here.  

 I want a Windows-like environment and everyone is talking about JGR.

 I downloaded it and installed it along with rJava.  Both compile and install 
 satisfactorily.

 But when I come to run it:

   
 library('JGR')
   
 Loading required package: rJava
 Error in dyn.load(x, as.logical(local), as.logical(now)) :
 unable to load shared library
 '/usr/local/lib/R/site-library/rJava/libs/rJava.so':
 /usr/local/lib/R/site-library/rJava/libs/rJava.so: undefined symbol:
 JNI_GetCreatedJavaVMs Error: .onLoad failed in 'loadNamespace' for 'rJava'
 Error: package 'rJava' could not be loaded
 


 When I first tried to run it without Java being installed, I got a message 
 saying that JDK wasn't installed but mentioned 1.4.2.  The version of Java 
 actually installed as the latest from the Ubuntu repository is Sun 1.5.0.11.  
 I don't see the point in installing old versions of Java just for one 
 application because the language, or at least the writing, should be 
 backwards compatible.  

 In all aspects I have seen Kubuntu is a very impressive in checking 
 compatibility.  Unfortunately this is frequently not the case with Java.  I 
 steer clear of Java as much as possible.  

 Can anyone suggest what I should do?  Use Windows perhaps?  Run Windows in a 
 kvm virtual machine just to run R?  Put my head in a bucket of cold water?  
 Is there an alternative IDE?  Is there a later JGR somewhere that is not yet 
 on CRAN?

 TIA



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Re: [R] JGR, Java and Kubuntu 7.04 ...

2007-06-15 Thread Dirk Eddelbuettel

On 15 June 2007 at 12:32, Stefan Grosse wrote:
| You could download the latest R (2.5.0) directly from CRAN, this just as
| a side remark, You find instructions here:
| http://cran.au.r-project.org/bin/linux/ubuntu/README

Yes indeed, thanks for our fearless backporters.
 
| With java you should make sure that you have the Java 5 JDK installed. 
| I dont know how it is with Ubuntu but on fedora I have to set the java
| alternative (sun java installation does not change the default java
| there). Which java is installed you can check with java -version there
| you see it it is properly installed and a R CMD javareconf also
| indicates if your java is configured correctly. Additionally on Fedora I
| had to set JAVA_HOME to the JDK directory manually.

It all worked -- I don't run Java much myself, but I think starting with
the previous Ubuntu release and the actual Sun packages directly acessible
via apt-get, it worked.

However, with the current packages in my Kubuntu setup at work, I do get a
segfault once JGR is up and loaded.   I suspect, as Stefan said here, that
this is due to the Java 6 packages in Ubuntu.  As I said, sun-java5-jdk seems
to have work along with 'sudo R CMD javareconf', Simon's powerful Java
parameter setter for R.

In any event, we should carry this over to r-sig-debian.

Dirk

| 
| Stefan
| 
|  Original Message  
| Subject: [R] JGR, Java and Kubuntu 7.04 ...
| From: John Logsdon [EMAIL PROTECTED]
| To: r-help@stat.math.ethz.ch
| Date: 14.06.2007 19:16
|  R-ists
| 
|  Yet again Java rears its ugly head.  
| 
|  I have Kubuntu 7.04 running the Kubuntu-repository version of R 2.4.1-1.
  
|  Yes it isn't the  very latest version but this is not the issue here.  
| 
|  I want a Windows-like environment and everyone is talking about JGR.
| 
|  I downloaded it and installed it along with rJava.  Both compile and 
install 
|  satisfactorily.
| 
|  But when I come to run it:
| 
|
|  library('JGR')
|
|  Loading required package: rJava
|  Error in dyn.load(x, as.logical(local), as.logical(now)) :
|  unable to load shared library
|  '/usr/local/lib/R/site-library/rJava/libs/rJava.so':
|  /usr/local/lib/R/site-library/rJava/libs/rJava.so: undefined symbol:
|  JNI_GetCreatedJavaVMs Error: .onLoad failed in 'loadNamespace' for 'rJava'
|  Error: package 'rJava' could not be loaded
|  
| 
| 
|  When I first tried to run it without Java being installed, I got a message 
|  saying that JDK wasn't installed but mentioned 1.4.2.  The version of Java 
|  actually installed as the latest from the Ubuntu repository is Sun 
1.5.0.11.  
|  I don't see the point in installing old versions of Java just for one 
|  application because the language, or at least the writing, should be 
|  backwards compatible.  
| 
|  In all aspects I have seen Kubuntu is a very impressive in checking 
|  compatibility.  Unfortunately this is frequently not the case with Java.  I 
|  steer clear of Java as much as possible.  
| 
|  Can anyone suggest what I should do?  Use Windows perhaps?  Run Windows in 
a 
|  kvm virtual machine just to run R?  Put my head in a bucket of cold water?  
|  Is there an alternative IDE?  Is there a later JGR somewhere that is not 
yet 
|  on CRAN?
| 
|  TIA
| 
| 
| 
| __
| R-help@stat.math.ethz.ch mailing list
| https://stat.ethz.ch/mailman/listinfo/r-help
| PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
| and provide commented, minimal, self-contained, reproducible code.

-- 
Hell, there are no rules here - we're trying to accomplish something. 
  -- Thomas A. Edison

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[R] JGR, Java and Kubuntu 7.04 ...

2007-06-14 Thread John Logsdon
R-ists

Yet again Java rears its ugly head.  

I have Kubuntu 7.04 running the Kubuntu-repository version of R 2.4.1-1.  
Yes it isn't the  very latest version but this is not the issue here.  

I want a Windows-like environment and everyone is talking about JGR.

I downloaded it and installed it along with rJava.  Both compile and install 
satisfactorily.

But when I come to run it:

  library('JGR')

 Loading required package: rJava
 Error in dyn.load(x, as.logical(local), as.logical(now)) :
 unable to load shared library
 '/usr/local/lib/R/site-library/rJava/libs/rJava.so':
 /usr/local/lib/R/site-library/rJava/libs/rJava.so: undefined symbol:
 JNI_GetCreatedJavaVMs Error: .onLoad failed in 'loadNamespace' for 'rJava'
 Error: package 'rJava' could not be loaded


When I first tried to run it without Java being installed, I got a message 
saying that JDK wasn't installed but mentioned 1.4.2.  The version of Java 
actually installed as the latest from the Ubuntu repository is Sun 1.5.0.11.  
I don't see the point in installing old versions of Java just for one 
application because the language, or at least the writing, should be 
backwards compatible.  

In all aspects I have seen Kubuntu is a very impressive in checking 
compatibility.  Unfortunately this is frequently not the case with Java.  I 
steer clear of Java as much as possible.  

Can anyone suggest what I should do?  Use Windows perhaps?  Run Windows in a 
kvm virtual machine just to run R?  Put my head in a bucket of cold water?  
Is there an alternative IDE?  Is there a later JGR somewhere that is not yet 
on CRAN?

TIA

-- 
Best wishes

John

John Logsdon   Try to make things as simple
Quantex Research Ltd, Manchester UK as possible but not simpler
[EMAIL PROTECTED]  [EMAIL PROTECTED]
+44(0)161 445 4951/G:+44(0)7717758675   www.quantex-research.com

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[R] JGR and big list of packages.

2007-06-12 Thread Ronaldo Reis Junior
Hi,

I have all CRAN packages installed on my Linux. Now I have problems with JGR.

When I make a plot and close a device, the device dont work anymore, I nedd to 
use before javaGD() and after plot(). When I try do close JGR and save a 
session, It return a erro and dont close. Look:

 Exception in thread Thread-2 java.lang.IllegalArgumentException: Value too 
long: aaMI,abind,accuracy,acepack,actuar,ada,adabag,adapt,AdaptFit,ade4,
.
.
.
.
tools,utils
at 
java.util.prefs.AbstractPreferences.put(AbstractPreferences.java:228)
at org.rosuda.JGR.toolkit.JGRPrefs.writePrefs(JGRPrefs.java:281)
at 
org.rosuda.JGR.toolkit.JGRPrefs.writeCurrentPackagesWhenExit(JGRPrefs.java:314)
at org.rosuda.JGR.JGR.exit(JGR.java:241)
at org.rosuda.JGR.JGRConsole.rReadConsole(JGRConsole.java:480)
at org.rosuda.JRI.Rengine.jriReadConsole(Rengine.java:371)
at org.rosuda.JRI.Rengine.rniRunMainLoop(Native Method)
at org.rosuda.JRI.Rengine.run(Rengine.java:533)

I think that is a problem with the JGR's package manager. It is possible to 
disable package manager from JGR?

Thanks
Inte
Ronaldo
-- 
I guess the Little League is even littler than we thought.
-- D. Cavett
--
 Prof. Ronaldo Reis Júnior
|  .''`. UNIMONTES/Depto. Biologia Geral/Lab. de Ecologia
| : :'  : Campus Universitário Prof. Darcy Ribeiro, Vila Mauricéia
| `. `'` CP: 126, CEP: 39401-089, Montes Claros - MG - Brasil
|   `- Fone: (38) 3229-8187 | [EMAIL PROTECTED] | [EMAIL PROTECTED]
| http://www.ppgcb.unimontes.br/ | ICQ#: 5692561 | LinuxUser#: 205366

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[R] JGR

2007-05-29 Thread Ronaldo Reis Junior
Hi,

I dont find any site to make suggestions about JGR.

It is possible to make a keyboard link do automatic attribution sign - like 
Emacs use Shift -

Thanks
Ronaldo
-- 
The most exciting phrase to hear in science, the one that heralds new
discoveries, is not Eureka! (I found it!) but That's funny ...
-- Isaac Asimov
--
 Prof. Ronaldo Reis Júnior
|  .''`. UNIMONTES/Depto. Biologia Geral/Lab. de Ecologia
| : :'  : Campus Universitário Prof. Darcy Ribeiro, Vila Mauricéia
| `. `'` CP: 126, CEP: 39401-089, Montes Claros - MG - Brasil
|   `- Fone: (38) 3229-8187 | [EMAIL PROTECTED] | [EMAIL PROTECTED]
| http://www.ppgcb.unimontes.br/ | ICQ#: 5692561 | LinuxUser#: 205366

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[R] JGR starter problems

2007-04-30 Thread J Dougherty
I'm running R 2.4.1 on SuSE Linux 10.2.  My system is an AMD based PC with 2 
Gigs of ram and abundant HD space. 

I have always run R from the console without problems, but in the interests of 
broadening R's user-base, and reducing the complexity of my computing 
environment, I am hoping to convince my PTB that R is a viable alternative to 
Excel under Windows - heh.  Since they like pretty pictures I'm experimenting 
with graphic interfaces for R in linux.  The Windows interface is fine, but I 
would prefer to stick to linux if at all possible.  I've been trying the JGR 
environment and so far it loads and looks nice but it doesn't seem to be able 
to find the key libraries such as base.  There are two errors that appear 
in the initial messages - one being that JGR can't load .../stats.so, and 
that R_GlobalEnv is an undefined symbol.  And the other is that 
options(defaultPackages) is not as shown below.  I presume this is probably 
a compilation error on my part and would like to know what I've done wrong.  
The initial messages when JGR loads are below.

Thanks, JWDougherty

Error in dyn.load(x, as.logical(local), as.logical(now)) : 
unable to load shared library 
'/usr/local/lib/R/library/stats/libs/stats.so':
  /usr/local/lib/R/library/stats/libs/stats.so: undefined symbol: R_GlobalEnv
Loading required package: JavaGD
Loading required package: iplots
Creating per-session help links...
Loading required package: grDevices
During startup - Warning message:
package stats in options(defaultPackages) was not found

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[R] JGR launcher for linux

2007-02-22 Thread Ronaldo Reis Junior
Hi,

anybody have a JGR launcher for linux? Maybe a script that launch JGR directly 
without open R then library(JGR) and JGR().

Thanks
Ronaldo
-- 
Deflector shields just came on, Captain.
--
 Prof. Ronaldo Reis Júnior
|  .''`. UNIMONTES/Depto. Biologia Geral/Lab. Ecologia Evolutiva
| : :'  : Campus Universitário Prof. Darcy Ribeiro, Vila Mauricéia
| `. `'` CP: 126, CEP: 39401-089, Montes Claros - MG - Brasil
|   `- Fone: (38) 3229-8190 | [EMAIL PROTECTED] | [EMAIL PROTECTED]
| ICQ#: 5692561 | LinuxUser#: 205366

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Re: [R] JGR launcher for linux

2007-02-22 Thread Liaw, Andy
Isn't it right in front of you?  I get:

 JGR()
Starting JGR ...
(You can use /usr/local/lib64/R/library/JGR/cont/run to start JGR directly)
 ^^^

Andy

From: Ronaldo Reis Junior
 
 Hi,
 
 anybody have a JGR launcher for linux? Maybe a script that 
 launch JGR directly without open R then library(JGR) and JGR().
 
 Thanks
 Ronaldo
 --
 Deflector shields just came on, Captain.
 --
  Prof. Ronaldo Reis Júnior
 |  .''`. UNIMONTES/Depto. Biologia Geral/Lab. Ecologia Evolutiva
 | : :'  : Campus Universitário Prof. Darcy Ribeiro, Vila Mauricéia `. 
 | `'` CP: 126, CEP: 39401-089, Montes Claros - MG - Brasil
 |   `- Fone: (38) 3229-8190 | [EMAIL PROTECTED] | 
 | [EMAIL PROTECTED]
 | ICQ#: 5692561 | LinuxUser#: 205366
 
 __
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[R] JGR data editor question

2007-02-10 Thread Muenchen, Robert A (Bob)
Hi All,

I'm learning JGR 1.4-15 with R 2.4.1 in Windows XP (all patches
applied). JGR looks great but I'm having trouble getting the data editor
to save my results. I don't see anything in R-help about it. Here are
the steps I followed:

1. I chose ToolsObject Browser  double-clicked on a data frame,
mydata. 
2. A spreadsheet editor popped up and allowed me to make changes. 
3. I clicked Update at the bottom right of the data editor screen. 
4. It asked, Export to R? and has Export as: mydata filled in. 
5. I clicked Yes and then closed the window by clicking the usual [X]
in the top right corner. 
6. Double-clicking the data file again opened it back up but the changes
were gone. 

Am I missing a step?

Thanks,
Bob

=
Bob Muenchen (pronounced Min'-chen), Manager 
Statistical Consulting Center
U of TN Office of Information Technology
200 Stokely Management Center, Knoxville, TN 37996-0520
Voice: (865) 974-5230 
FAX: (865) 974-4810
Email: [EMAIL PROTECTED]
Web: http://oit.utk.edu/scc, 
News: http://listserv.utk.edu/archives/statnews.html

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Re: [R] JGR data editor question

2007-02-10 Thread Jim Porzak
Hi Bob,

I can not reproduce your problem, with possible exception in your step 2:
In data editor, you need to click off of the last cell you edited for
the changes to take

On 2/10/07, Muenchen, Robert A (Bob) [EMAIL PROTECTED] wrote:
 Hi All,

 I'm learning JGR 1.4-15 with R 2.4.1 in Windows XP (all patches
 applied). JGR looks great but I'm having trouble getting the data editor
 to save my results. I don't see anything in R-help about it. Here are
 the steps I followed:

 1. I chose ToolsObject Browser  double-clicked on a data frame,
 mydata.
 2. A spreadsheet editor popped up and allowed me to make changes.
 3. I clicked Update at the bottom right of the data editor screen.
 4. It asked, Export to R? and has Export as: mydata filled in.
 5. I clicked Yes and then closed the window by clicking the usual [X]
 in the top right corner.
 6. Double-clicking the data file again opened it back up but the changes
 were gone.

 Am I missing a step?

 Thanks,
 Bob

 =
 Bob Muenchen (pronounced Min'-chen), Manager
 Statistical Consulting Center
 U of TN Office of Information Technology
 200 Stokely Management Center, Knoxville, TN 37996-0520
 Voice: (865) 974-5230
 FAX: (865) 974-4810
 Email: [EMAIL PROTECTED]
 Web: http://oit.utk.edu/scc,
 News: http://listserv.utk.edu/archives/statnews.html

 __
 R-help@stat.math.ethz.ch mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.



-- 
HTH,
Jim Porzak
Loyalty Matrix Inc.
San Francisco, CA
http://www.linkedin.com/in/jimporzak

__
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Re: [R] JGR data editor question

2007-02-10 Thread Muenchen, Robert A (Bob)
That's it! I tried an absurd number of variations, but never that! I had
only changed one value and never left the cell. I assumed hitting Enter
would do it. Thanks! -Bob

=
Bob Muenchen (pronounced Min'-chen), Manager 
Statistical Consulting Center
U of TN Office of Information Technology
200 Stokely Management Center, Knoxville, TN 37996-0520
Voice: (865) 974-5230 
FAX: (865) 974-4810
Email: [EMAIL PROTECTED]
Web: http://oit.utk.edu/scc, 
News: http://listserv.utk.edu/archives/statnews.html
=


-Original Message-
From: Jim Porzak [mailto:[EMAIL PROTECTED] 
Sent: Saturday, February 10, 2007 11:46 AM
To: Muenchen, Robert A (Bob)
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] JGR data editor question

Hi Bob,

I can not reproduce your problem, with possible exception in your step
2:
In data editor, you need to click off of the last cell you edited for
the changes to take

On 2/10/07, Muenchen, Robert A (Bob) [EMAIL PROTECTED] wrote:
 Hi All,

 I'm learning JGR 1.4-15 with R 2.4.1 in Windows XP (all patches
 applied). JGR looks great but I'm having trouble getting the data
editor
 to save my results. I don't see anything in R-help about it. Here are
 the steps I followed:

 1. I chose ToolsObject Browser  double-clicked on a data frame,
 mydata.
 2. A spreadsheet editor popped up and allowed me to make changes.
 3. I clicked Update at the bottom right of the data editor screen.
 4. It asked, Export to R? and has Export as: mydata filled in.
 5. I clicked Yes and then closed the window by clicking the usual
[X]
 in the top right corner.
 6. Double-clicking the data file again opened it back up but the
changes
 were gone.

 Am I missing a step?

 Thanks,
 Bob

 =
 Bob Muenchen (pronounced Min'-chen), Manager
 Statistical Consulting Center
 U of TN Office of Information Technology
 200 Stokely Management Center, Knoxville, TN 37996-0520
 Voice: (865) 974-5230
 FAX: (865) 974-4810
 Email: [EMAIL PROTECTED]
 Web: http://oit.utk.edu/scc,
 News: http://listserv.utk.edu/archives/statnews.html

 __
 R-help@stat.math.ethz.ch mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.



-- 
HTH,
Jim Porzak
Loyalty Matrix Inc.
San Francisco, CA
http://www.linkedin.com/in/jimporzak

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[R] JGR installation (Was: 2 linux/R environment questions)

2006-10-11 Thread Dirk Eddelbuettel

On 11 October 2006 at 16:05, Stefan Grosse wrote:
| Prof Brian Ripley schrieb:
| 
|  Which arch and how did you install R?  For me, it works with R
|  compiled from the sources (but not installed from RPM) on FC5 i686,
|  but not x86_64.
|  The issue is a run-time one:
| 
| I have i686, no x86_64 ...
| 
| OK, so I have to compile R from source ...

I had very good success on Debian and Ubuntu using the new

$ R CMD javareconf

that was added in R 2.4.0.  

After that, the usual install.packages() call as shown on the RoSuDa.org site
seems to install JGR reliably provided a Sun Java JDK is in the proper places
-- and using the pre-packaged and apt-get'able sun-java5-jdk package from the
non-free / multiverse repository for Debian / Ubuntu works just fine.  

Dirk

-- 
Hell, there are no rules here - we're trying to accomplish something. 
  -- Thomas A. Edison

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Re: [R] JGR on SUSE 10.1 AMD 64

2006-09-10 Thread Rainer Volz
Tomas Willebrand tomas.willebrand at szooek.slu.se writes:

 
 Dear list;
 
 I have R Version 2.3.1 (2006-06-01) installed on a AMD 64 machine with SUSE 
 10.1. 
 
 I have Sun Java version 1.5.0-sun installed. 
 
 I have used install.packages(JGR, dep=TRUE) to install rJava, iplots and 
 JGR. I would like to do a presentation of linux and R for the department!
 
 Compiling rJava do not give any error messages!
 
 But when trying to load library(JGR) or just library(rJava) I get the 
 following error message:
  Error in dyn.load(x, as.logical(local), as.logical(now)) :
  unable to load shared library  '/usr/lib64/R/library/rJava/libs/rJava.so':
  libjvm.so: kan inte öppna delad objektfil: Filen eller katalogen finns inte
  Error in library(rJava) : .First.lib failed for 'rJava'
 
I have the same configuration: adding various library paths for the 
missing libs before calling R made the installation succeed:

export
LD_LIBRARY_PATH=/usr/lib64/R/lib:
/usr/lib64/jvm/java-1.5.0-sun-1.5.0_07/jre/lib/amd64/server:
/usr/lib64/jvm/java-1.5.0-sun-1.5.0_07/jre/lib/amd64:
$LD_LIBRARY_PATH
   

HTH
Rainer

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Re: [R] JGR on SUSE 10.1 AMD 64

2006-09-10 Thread Prof Brian Ripley
On Sun, 10 Sep 2006, Rainer Volz wrote:

 Tomas Willebrand tomas.willebrand at szooek.slu.se writes:
 
  I have R Version 2.3.1 (2006-06-01) installed on a AMD 64 machine with 
  SUSE 10.1.

Installed how is the usual question: from sources or an RPM?

  I have Sun Java version 1.5.0-sun installed. 
  
  I have used install.packages(JGR, dep=TRUE) to install rJava, 
  iplots and JGR. I would like to do a presentation of linux and R for 
  the department!
  
  Compiling rJava do not give any error messages!
  
  But when trying to load library(JGR) or just library(rJava) I get 
  the following error message:
   Error in dyn.load(x, as.logical(local), as.logical(now)) :
   unable to load shared library  '/usr/lib64/R/library/rJava/libs/rJava.so':
   libjvm.so: kan inte öppna delad objektfil: Filen eller katalogen finns 
   inte
   Error in library(rJava) : .First.lib failed for 'rJava'
  
 I have the same configuration: adding various library paths for the 
 missing libs before calling R made the installation succeed:
 
 export
 LD_LIBRARY_PATH=/usr/lib64/R/lib:
 /usr/lib64/jvm/java-1.5.0-sun-1.5.0_07/jre/lib/amd64/server:
 /usr/lib64/jvm/java-1.5.0-sun-1.5.0_07/jre/lib/amd64:
 $LD_LIBRARY_PATH

This is something that is set up when R is configured, and stored in 
R_HOME/etc/ldpaths.  Has perchance your Java subsystem been updated since 
R was installed?  In which case update R_HOME/etc/ldpaths as appropriate, 
or set R_JAVA_LD_LIBRARY_PATH (not LD_LIBRARY_PATH) to override the 
setting there.

-- 
Brian D. Ripley,  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595__
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Re: [R] JGR on SUSE 10.1 AMD 64

2006-09-10 Thread Rainer Volz
Prof Brian Ripley ripley at stats.ox.ac.uk writes:

 This is something that is set up when R is configured, and stored in 
 R_HOME/etc/ldpaths.  Has perchance your Java subsystem been updated since 
 R was installed?  

True.

 In which case update R_HOME/etc/ldpaths as appropriate, 
 or set R_JAVA_LD_LIBRARY_PATH (not LD_LIBRARY_PATH) to override the 
 setting there.

That's much better. Thank you.

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Re: [R] JGR on SUSE 10.1 AMD 64

2006-09-10 Thread Tomas Willebrand
Prof Ripley and Rainer;

Thanks for the help. 

I changed the file /usr/lib64/R/etc/ldpaths so that the first line looked 
like

:${R_JAVA_LD_LIBRARY_PATH= 
/usr/lib64/jvm/java-1.5.0-sun-1.5.0_07/jre/lib/amd64/server:
/usr/lib64/jvm/java-1.5.0-sun-1.5.0_07/jre/lib/amd64:} 

and then everything worked OK!

But when I tested a fresh install of the R-base*rpm and changed the ldpaths 
file before attempting to install JGR it did not install properly!! Not the 
same error as previously when iplots was suppose to load! (ldpaths identical 
in both cases)

-- Install R-base - failed installation of rJava - edit ldpaths - reinstall 
rJava,iplots, JGR - SUCCESS

-- Install R-base - edit ldpaths - loading rJava fails after compiling  
- 

Not sure what is going on and do not need to know! 
But maybe someone would find this note useful.

Thanks again

Tomas



söndag 10 september 2006 14:02 skrev Rainer Volz:
 Prof Brian Ripley ripley at stats.ox.ac.uk writes:
  This is something that is set up when R is configured, and stored in
  R_HOME/etc/ldpaths.  Has perchance your Java subsystem been updated since
  R was installed?

 True.

  In which case update R_HOME/etc/ldpaths as appropriate,
  or set R_JAVA_LD_LIBRARY_PATH (not LD_LIBRARY_PATH) to override the
  setting there.

 That's much better. Thank you.

 __
 R-help@stat.math.ethz.ch mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html and provide commented, minimal,
 self-contained, reproducible code.

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+46 70 288 02 03

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[R] JGR on SUSE 10.1 AMD 64

2006-09-08 Thread Tomas Willebrand
Dear list;

I have R Version 2.3.1 (2006-06-01) installed on a AMD 64 machine with SUSE 
10.1. 

I have Sun Java version 1.5.0-sun installed. 

I have used install.packages(JGR, dep=TRUE) to install rJava, iplots and 
JGR. I would like to do a presentation of linux and R for the department!

Compiling rJava do not give any error messages!

But when trying to load library(JGR) or just library(rJava) I get the 
following error message:
 Error in dyn.load(x, as.logical(local), as.logical(now)) :
 unable to load shared library  '/usr/lib64/R/library/rJava/libs/rJava.so':
 libjvm.so: kan inte öppna delad objektfil: Filen eller katalogen finns inte
 Error in library(rJava) : .First.lib failed for 'rJava'

I desperately tried to symlink libjvm.so from 
   /usr/lib64/jvm/java-1.5.0-sun-1.5.0_07/jre/lib/amd64/server
to
   /usr/lib64/R/library/rJava/libs
but without success.

Any suggestions appreciated!

Regards,

Tomas

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[R] JGR help()

2006-07-18 Thread Michael Kubovy
Dear R-helpers,

In JGR, how to I get the help() to update when I install a new package?

  sessionInfo()
Version 2.3.1 (2006-06-01)
powerpc-apple-darwin8.6.0

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

other attached packages:
lattice   MASSJGR JavaGD  rJava
   0.13-9 7.2-27.11.4-20.3-30.4-3

_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
 McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/

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[R] JGR :: Can't Run Graphics Demo

2006-06-08 Thread Alex Restrepo
Hello:

I am using JGR 1.4, the Java GUI for R and I am trying to run the demo for 
graphics using the command:

demo(graphics)

I keep on getting the following errror:

Error in get(getOption(device))() : unable to start device JavaGD


FYI, the version of Java I am using is:

 1.5.0_07-b03


Do I need to use a different version of Java?  Does anyone have any 
recommendations/suggestions?


Many Thanks In Advance:

Alex

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Re: [R] JGR :: Can't Run Graphics Demo

2006-06-08 Thread ronggui

Have you installed the following packages?They are javaGD,rJava,iplots,iWidgets?

It seems that you have installed the javaGD package.

2006/6/8, Alex Restrepo [EMAIL PROTECTED]:

Hello:

I am using JGR 1.4, the Java GUI for R and I am trying to run the demo for
graphics using the command:

demo(graphics)

I keep on getting the following errror:

Error in get(getOption(device))() : unable to start device JavaGD


FYI, the version of Java I am using is:

 1.5.0_07-b03


Do I need to use a different version of Java?  Does anyone have any
recommendations/suggestions?


Many Thanks In Advance:

Alex

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--
黄荣贵
Deparment of Sociology
Fudan University

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Re: [R] JGR :: Can't Run Graphics Demo

2006-06-08 Thread Alex Restrepo

Hi:

I have verified that javaGD, rJava, iplots, and iwidgets are installed.I 
am still not able to run any of the graphics demos.


I still get the following error:

  if (dev.cur() = 1) get(getOption(device))()
  Error in get(getOption(device))() : unable to start device JavaGD

Any help would be appreciated,

Thanks:

Alex




From: ronggui [EMAIL PROTECTED]
To: Alex Restrepo [EMAIL PROTECTED]
CC: r-help@stat.math.ethz.ch
Subject: Re: [R] JGR :: Can't Run Graphics Demo
Date: Thu, 8 Jun 2006 21:47:07 +0800

Have you installed the following packages?They are 
javaGD,rJava,iplots,iWidgets?


It seems that you have installed the javaGD package.

2006/6/8, Alex Restrepo [EMAIL PROTECTED]:

Hello:

I am using JGR 1.4, the Java GUI for R and I am trying to run the demo for
graphics using the command:

demo(graphics)

I keep on getting the following errror:

Error in get(getOption(device))() : unable to start device JavaGD


FYI, the version of Java I am using is:

 1.5.0_07-b03


Do I need to use a different version of Java?  Does anyone have any
recommendations/suggestions?


Many Thanks In Advance:

Alex

__
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--
»ÆÈÙ¹ó
Deparment of Sociology
Fudan University


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Re: [R] JGR :: Can't Run Graphics Demo

2006-06-08 Thread Alex Restrepo

I tried to create a pie chart in JGR, via the command:

 pie(rep(1, 24), col = rainbow(24), radius = 0.9)


and I still get the following error:

   Error in JavaGD() : unable to start device JavaGD






From: Alex Restrepo [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
CC: r-help@stat.math.ethz.ch
Subject: Re: [R] JGR :: Can't Run Graphics Demo
Date: Thu, 08 Jun 2006 15:48:07 -0500

Hi:

I have verified that javaGD, rJava, iplots, and iwidgets are installed.
I am still not able to run any of the graphics demos.


I still get the following error:

  if (dev.cur() = 1) get(getOption(device))()
  Error in get(getOption(device))() : unable to start device JavaGD

Any help would be appreciated,

Thanks:

Alex




From: ronggui [EMAIL PROTECTED]
To: Alex Restrepo [EMAIL PROTECTED]
CC: r-help@stat.math.ethz.ch
Subject: Re: [R] JGR :: Can't Run Graphics Demo
Date: Thu, 8 Jun 2006 21:47:07 +0800

Have you installed the following packages?They are 
javaGD,rJava,iplots,iWidgets?


It seems that you have installed the javaGD package.

2006/6/8, Alex Restrepo [EMAIL PROTECTED]:

Hello:

I am using JGR 1.4, the Java GUI for R and I am trying to run the demo 
for

graphics using the command:

demo(graphics)

I keep on getting the following errror:

Error in get(getOption(device))() : unable to start device JavaGD


FYI, the version of Java I am using is:

 1.5.0_07-b03


Do I need to use a different version of Java?  Does anyone have any
recommendations/suggestions?


Many Thanks In Advance:

Alex

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--
»ÆÈÙ¹ó
Deparment of Sociology
Fudan University






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[R] JGR (Java GUI) on Solaris

2006-05-11 Thread Alex Restrepo
Hi:

I am trying to build the JGR (Java GUI) on a solaris 8 machine.

I started R and I ran the following command:

install.packages(c(JGR,JavaGD,rJava,iWidgets,iplots),,c(http://cran.r-project.org,http://www.rosuda.org/R/nightly;))


I get the following errors when I  try to install:
make: Fatal error in reader: Makevars, line 3: Unexpected end of line seen
ERROR: compilation failed for package 'JavaGD'
** Removing '/mmrg/usr/local/lib/R/library/JavaGD'


rJava.c:10: error: parse error before vm1_args
rJava.c:10: warning: data definition has no type or storage class
rJava.c: In function `initJVM':
rJava.c:92: error: request for member `classpath' in something not a 
structure or union
*** Error code 1
make: Fatal error: Command failed for target `rJava.o'
ERROR: compilation failed for package 'rJava'


Has anyone been able to install JGR on a solaris system? If so, do you have 
any recommendations.

Many Thanks:

Alex

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[R] JGR problem

2006-04-24 Thread Fernando Saldanha
I just installed JGR version 1.3 and I am having a problem. When I try
to load the library RQuantLib I get an error message. The same program
runs perfectly well when I just run rgui.exe. I have pasted the screen
below. The version of R I am using is 2.2.1.

Thanks for any help.

FS


 rm(list=ls())

 # Import libraries
 library(tseries)
Loading required package: quadprog
Loading required package: zoo

'tseries' version: 0.9-30

'tseries' is a package for time series analysis and computational finance.

See 'library(help=tseries)' for details.

 library(zoo)
 library(RQuantLib)
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library 'C:/Program
Files/R/R-2.2.1/library/RQuantLib/libs/RQuantLib.dll':
  LoadLibrary failure:  Invalid access to memory location.
Error in library(RQuantLib) : .First.lib failed for 'RQuantLib'

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[R] JGR doesn't launch after updating to R 2.2.1

2006-03-06 Thread Michael Kubovy
Dear r-helpers,

After updating to R version 2.2.1, 2005-12-20, powerpc-apple- 
darwin7.9.0 (from binary), JGR wouldn't launch. I then deleted  
everything I could find related to JGR, and reinstalled it from the  
latest binary. Both R and JGR are installed in /Applications/ 
\~LocalApps/mathStat/.

Advice on how to identify the source of the problem?

My machine:
   Machine Name: PowerBook G4 15
   Machine Model: PowerBook5,6
   CPU Type: PowerPC G4  (1.2)
   Number Of CPUs: 1
   CPU Speed: 1.67 GHz
   L2 Cache (per CPU): 512 KB
   Memory: 2 GB
   System Version: Mac OS X 10.4.5 (8H14)
   Kernel Version: Darwin 8.5.0
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
 McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/

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Re: [R] JGR doesn't launch after updating to R 2.2.1

2006-03-06 Thread roger bos
Where did you get a verion that was supposed to support 2.2.1?  On the JGR
website it lists the different binaries for the different version of R and
the latest one I saw was 2.2.0.

http://stats.math.uni-augsburg.de/JGR/


On 3/6/06, Michael Kubovy [EMAIL PROTECTED] wrote:

 Dear r-helpers,

 After updating to R version 2.2.1, 2005-12-20, powerpc-apple-
 darwin7.9.0 (from binary), JGR wouldn't launch. I then deleted
 everything I could find related to JGR, and reinstalled it from the
 latest binary. Both R and JGR are installed in /Applications/
 \~LocalApps/mathStat/.

 Advice on how to identify the source of the problem?

 My machine:
   Machine Name: PowerBook G4 15
   Machine Model: PowerBook5,6
   CPU Type: PowerPC G4  (1.2)
   Number Of CPUs: 1
   CPU Speed: 1.67 GHz
   L2 Cache (per CPU): 512 KB
   Memory: 2 GB
   System Version: Mac OS X 10.4.5 (8H14)
   Kernel Version: Darwin 8.5.0
 _
 Professor Michael Kubovy
 University of Virginia
 Department of Psychology
 USPS: P.O.Box 400400Charlottesville, VA 22904-4400
 Parcels:Room 102Gilmer Hall
 McCormick RoadCharlottesville, VA 22903
 Office:B011+1-434-982-4729
 Lab:B019+1-434-982-4751
 Fax:+1-434-982-4766
 WWW:http://www.people.virginia.edu/~mk9y/

 __
 R-help@stat.math.ethz.ch mailing list
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 http://www.R-project.org/posting-guide.html


[[alternative HTML version deleted]]

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Re: [R] JGR doesn't launch after updating to R 2.2.1

2006-03-06 Thread Michael Kubovy
Hi Roger,

Thanks for the reply. Indeed the JGR site says that it runs with  
2.2.0. I assumed that a minor update to R wouldn't break the link to  
JGR, and inferred that I had done something wrong.

On Mar 6, 2006, at 8:51 AM, roger bos wrote:

 Where did you get a verion that was supposed to support 2.2.1?  On  
 the JGR website it lists the different binaries for the different  
 version of R and the latest one I saw was 2.2.0.

 http://stats.math.uni-augsburg.de/JGR/


 On 3/6/06, Michael Kubovy [EMAIL PROTECTED] wrote:
 Dear r-helpers,

 After updating to R version 2.2.1, 2005-12-20, powerpc-apple-
 darwin7.9.0 (from binary), JGR wouldn't launch. I then deleted
 everything I could find related to JGR, and reinstalled it from the
 latest binary. Both R and JGR are installed in /Applications/
 \~LocalApps/mathStat/.

 Advice on how to identify the source of the problem?

_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
 McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/



[[alternative HTML version deleted]]

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[R] JGR problem with installPackages()?

2006-02-23 Thread Michael Kubovy
Dear r-helpers,

When I pull down the Packages:Package Installer menu, I get:
==
  installPackages()
stack imbalance in .External, 22 then 66
stack imbalance in -, 20 then 64
stack imbalance in -, 117 then 118
stack imbalance in {, 115 then 116
stack imbalance in if, 113 then 114
stack imbalance in {, 111 then 112
stack imbalance in -, 105 then 106
stack imbalance in {, 103 then 104
stack imbalance in for, 96 then 97
stack imbalance in {, 94 then 95
stack imbalance in if, 92 then 93
stack imbalance in {, 90 then 91
stack imbalance in if, 88 then 89
stack imbalance in {, 86 then 85
stack imbalance in standardGeneric, 78 then 77
stack imbalance in -, 76 then 75
stack imbalance in {, 74 then 73
stack imbalance in {, 68 then 67
stack imbalance in {, 18 then 61
stack imbalance in -, 12 then 55
stack imbalance in internal ls, 66 then 87stack imbalance  
in .Internal, 65 then 67
stack imbalance in -, 63 then 65
stack imbalance in {, 61 then 63
stack imbalance in c, 53 then 55
stack imbalance in -, 51 then 53
stack imbalance in {, 49 then 51
stack imbalance in for, 42 then 44
stack imbalance in {, 40 then 42
stack imbalance in {, 33 then 35
stack imbalance in if, 31 then 33
stack imbalance in {, 29 then 31
stack imbalance in .External, 67 then 24
stack imbalance in -, 65 then 22
stack imbalance in if, 63 then 20
stack imbalance in {, 61 then 18
stack imbalance in invisible, 55 then 12
Warning message:
'CRAN.packages' is deprecated.
Use 'available.packages' instead.
See help(Deprecated)

running
--
R version 2.2.1, 2005-12-20, powerpc-apple-darwin7.9.0

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

other attached packages:
 nlme   simpleboot boot gridBaseHmisc  
latticeExtra  car
   3.1-68.1  1.1-1 1.2-24  0.4-2  
3.0-10  0.1-4 1.0-18
 MASS   Matrix  JGR   JavaGDrJava  
multcomp  mvtnorm
 7.2-240.995-4 0.1-10  0.2-1   
0.3-6  0.4-8  0.7-2
abind  lattice
  1.1-00.12-11

Package:   JGR
Version:   0.1-10
Date:  2005-05-27
Title: JGR - Java Gui for R
Built: R 2.2.0; ; 2005-10-12 16:22:13; unix
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
 McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/

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[R] JGR help.search

2005-10-18 Thread Brian Haney
If there is a better forum for JGR questions, please redirect me.

Whenever I try to open the help browser in JGR (by clicking on Help - R
Help, or by entering help() or help.start() at the console), it pops
open a window complaining that a path was not found and that help will
not be available, followed (after ack of the first) by another window
that complains along the lines URL Error:
/tmp/Rtmpk7DtNG/.R/doc/html/packages.html (No such file or directory)

After acknowledgement of the second window a help browser opens but
seems to have no content.  Searching on the word list opens a new tab
attached to an empty page.

I expected the help browser to open without complains and offer a series
of topics and links by which to peruse the help files.

I am ever so grateful for any insight that may be offered.

-- 
Brian Haney, Software Engineer  UNIX Systems Administrator
University of Washington, Dept of Biostatistics

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[R] JGR font rendering on Windows

2005-06-28 Thread Mike Prager
JGR users on Windows may be interested that Sun has released a preview 
of its latest Java development kit and runtime engine at

http://www.java.net/download/jdk6/binaries/

This removes the main problem I have had with JGR and other Java 
programs on Windows: poor font rendering.  On Windows XP with an LCD 
display, the improvement is striking, as this uses Windows native font 
smoothing (CoolType).  I believe it uses the default Windows font 
smoothing on other versions of Windows or other displays.

MHP

-- 
Michael Prager, Ph.D.
NOAA Center for Coastal Fisheries and Habitat Research
Beaufort, North Carolina  28516
http://shrimp.ccfhrb.noaa.gov/~mprager/
*** Opinions are personal, not official. No government endorsement
is made of any commercial or noncommercial product. ***

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[R] JGR and R 2.0.X

2005-05-04 Thread Christoph Scherber
Dear all,
I am running Windows XP with several parallel installations of R (2.0.1; 
2.1 and so on). How can I install JGR for the 2.0.1 version? I keep on 
getting error messages when trying to install it.

Best wishes
Christoph
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Re: [R] JGR and R 2.0.X

2005-05-04 Thread Sundar Dorai-Raj

Christoph Scherber wrote on 5/4/2005 4:44 AM:
Dear all,
I am running Windows XP with several parallel installations of R (2.0.1; 
2.1 and so on). How can I install JGR for the 2.0.1 version? I keep on 
getting error messages when trying to install it.

Best wishes
Christoph
Hi Christoph,
Which version of R comes first in your PATH?
--sundar
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Re: [R] JGR and R 2.0.X

2005-05-04 Thread Uwe Ligges
Christoph Scherber wrote:
Dear all,
I am running Windows XP with several parallel installations of R (2.0.1; 
2.1 and so on). How can I install JGR for the 2.0.1 version? I keep on 
getting error messages when trying to install it.

I am sure Simon Urbanek et al. are happy to help you, but even the 
winners of the John Chambers Statistical Software Award are unable to 
help if you don't say what the error messages are and which versions of 
JGR you tried...

Uwe Ligges

Best wishes
Christoph
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Re: [R] JGR and R 2.0.X

2005-05-04 Thread Simon Urbanek
On May 4, 2005, at 9:18 AM, Uwe Ligges wrote:
Christoph Scherber wrote:
Dear all,
I am running Windows XP with several parallel installations of R  
(2.0.1; 2.1 and so on). How can I install JGR for the 2.0.1  
version? I keep on getting error messages when trying to install it.
I am sure Simon Urbanek et al. are happy to help you, but even the  
winners of the John Chambers Statistical Software Award are unable  
to help if you don't say what the error messages are and which  
versions of JGR you tried...
Markus is the winner, I'm just changing oil and doing dirty  
things ;). I'd be glad to help and, yes, http://www.rosuda.org/ 
lists.shtml is the right place to discuss JGR-related things in more  
detail.

In general JGR (and also JRI, rJava and JavaGD) uses the registry  
setting to determine the location and version of R. This setting is  
updated by the R installer if you leave the (D)COM setting checked  
(which is the default). This implies, however, that the sequence in  
which you install the various R versions matters - you should install  
the latest version last. If you want to edit the setting manually,  
use regedit and look into HKEY_LOCAL_MACHINE/SOFTWARE/R-core/R - it  
contains both the version and the path (at your own risk).

The most recent JGR for Windows can be installed simply with
install.packages(JGR,,http://www.rosuda.org/R;)
and then starting JGR.exe which can be found in $R_HOME/library/JGR.  
The package installation fetches the correct version for your R (2.0  
and 2.1 are supported only). The convenience installer is still  
provided at http://www.rosuda.org/JGR/1.2/JGR-12.exe
Mac binary and Linux sources of the new release should become  
available this week.

Cheers,
Simon
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[R] JGR Tablet PC

2004-11-18 Thread White, Charles E WRAIR-Wash DC
(1) A minor point; the JGR console recognizes when the input panel (think tool 
bar) is docked at the top of the screen and acts appropriately. However, the 
editor opens under the input panel. I can close the input panel, move the 
editor, and open the input panel to continue work. On the other hand, it would 
be real nice if the editor just opened in a more appropriate place.

(2) I am very impressed with JGR as it is and I have completely switched from 
XEmacs to JGR.

Chuck

Charles E. White, Senior Biostatistician, MS
Walter Reed Army Institute of Research
503 Robert Grant Ave., Room 1w102
Silver Spring, MD 20910-1557
301 319-9781
Personal/Professional Site: http://users.starpower.net/cwhite571/professional/

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