[kepler-users] Question about R workflow in Mac OS X

[Jorge A. Ahumada]

Dan,

Thanks. I am using R 2.3.1 RC.

I tried the workflow you sent..but it didn¹t work either. Attached is the
error message I got..I downloaded the new ImageJ and replaced the ij.jar in
/Applications/kepler-1.0.0beta1/lib/jar, restarted Kepler and tried to run
the workflow, but still no success..


Thanks,

Jorge

On 6/16/06 1:58 PM, "Dan Higgins" <higgins at nceas.ucsb.edu> wrote:

> Hello Jorge, 
> 
>     Sorry that you are having a problem with Kepler, (but thanks for
> reporting the problem). I thought that having X11 open and setting the
> DISPLAY problem avoided this problem for Mac PPC machines. It seems to
> work on machines in use here, but obviously not for you. [Incidently,
> interfacing with X11 is a known problem for the new Mac Intel machines,
> although we are not sure why.] I'll have to dig into this to see if I
> can find the problem. What version of R is installed on you Mac? [Kepler
> launches R the same way as you would by entering 'R' on the command line.]
> 
>     The problem is related to the fact that R on the Mac uses some X11
> code for the jpeg display device, and I picked that device for the
> Kepler RExpression actor because we could display jpegs easily in Kepler
> on Windows, Mac, and Linux. A better display device for the Mac would be
> a PDF device (since that is handled natively), and I have been looking
> at changing the default behavior in Kepler. [Note that RExpression
> actors work on the Mac if you disable the 'Graphics Output' parameter
> and just look at text output]
> 
>     Attached is an example Kepler workflow showing how to use a 'pdf'
> command within an R script to override the default setup and display the
> pdf file using an IJMacro actor. Note that this workflow will not
> execute with the Kepler beta1 release until you replace the ij.jar in
> the $KEPLER/lib/jar/ directory with an updated version of this ImageJ
> jar (see http://rsb.info.nih.gov/ij/download.html and get the 1.36 version).
> 
> Dan Higgins 
> 
> 
>    
> 
> Jorge A. Ahumada wrote:
>> > Hello, 
>> > 
>> > I am interested in using Kepler for creating workflows with R. I have a MAC
>> > 10.4.6 PPC Dual G5 and downloaded the beta 6.1 of Kepler. When attempting
>> to 
>> > run the linear regression workflow I get this error:
>> > 
>> > [R]> setwd('/Users/jorge')
>> > [R]> jpeg(filename = '1150472825782.jpg',width = 480, height = 480,
>> > pointsize = 12,quality = 75, bg = 'white')
>> > 
>> > Erro en X11(paste(\"jpeg::\", quality, \":\", filename, sep = \"\"), width,
>> > : 
>> >     no fue posible iniciar el dispositivo JPEG
>> > Adem·s: Warning message:
>> > no fue posible abrir la conecciÛn con el dispositivo X11 ''
>> > EjecuciÛn interrumpida
>> > 
>> > X11 is open and I typed setenv DISPLAY localhost:0.0
>> > 
>> > Seems that the X11 command has the wrong syntax for Mac or Linux:
>> > X11(paste(/"jpeg::/". Etc..)
>> > 
>> > How do I change it? Is this the problem..Any ideas?
>> > 
>> > Thanks, 
>> > 
>> > Jorge 
>> >   
> 


-- 
Jorge A. Ahumada, Ph.D.
Technical Director, TEAM
Center for Applied Biodiversity Science
Conservation International
1919 M Street, NW Suite 600
Washington, DC 20036-3521
Ph: 202-912-1516

j.ahumada at conservation.org
http://www.teaminitiative.org/



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