[kepler-users] Question about R workflow in Mac OS X
Dan Higgins
higgins at nceas.ucsb.edu
Fri Jun 16 11:31:25 PDT 2006
Hi Jorge,
I have some more information on your problem.
When I execute the Kepler-1.0.0beta1 application on a PPC Mac by
double clicking 'Kepler-1.0.0beta1', I can reproduce the problem that
you reported. However, there is also a script for launching Kepler in
the distribution called 'kepler.sh'. If I open kepler from the terminal
using with './kepler.sh' with X11 running and DISPLAY set, then there is
no error and the linear regression example works and displays a plot! I
do NOT understand why the behavior should depend on exactly how Kepler
is launched! (Perhaps something in how the ENV variables are passed to
the app.)
In any case, you might want to try launching Kepler from Terminal
with the shell script and see if that works for you.
Dan
---
Dan Higgins 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
>>
>
>
> ------------------------------------------------------------------------
>
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Dan Higgins - NCEAS
June 7, 2006">
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pdf(file=fn,width=6,height=6)
plot(x <- sort(rnorm(47)), type = "s", main = "plot(x, type = \"s\")")
dev.off()">
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>
> ------------------------------------------------------------------------
>
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--
*******************************************************************
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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