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

[Dan Higgins]

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
>   


-- 
*******************************************************************
Dan Higgins                                  higgins at nceas.ucsb.edu
http://www.nceas.ucsb.edu/    Ph: 805-893-5127
National Center for Ecological Analysis and Synthesis (NCEAS) Marine Science Building - Room 3405
Santa Barbara, CA 93195
*******************************************************************

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