[kepler-users] Kepler-R basic question

[ben leinfelder]

Hi Allen --

I changed the file name input so that the value was not surrounded by quotes (").

I changed the file name to match the file you attached to your email (capitalization).

I took out the call to pairs(df) in the ReadFile actor because this error was showing in the logs:
---------
11/11/11 10:58:21.850 AM [0x0-0xad1ad1].org.kepler.build.runner.Kepler:      [null] ERROR (org.ecoinformatics.seek.R.RExpression:fire:935) R standard error: 
11/11/11 10:58:21.851 AM [0x0-0xad1ad1].org.kepler.build.runner.Kepler:      [null] Error in plot.window(...) : need finite 'xlim' values
11/11/11 10:58:21.851 AM [0x0-0xad1ad1].org.kepler.build.runner.Kepler:      [null] Calls: pairs ... localPlot -> plot -> plot.default -> localWindow -> plot.window
11/11/11 10:58:21.851 AM [0x0-0xad1ad1].org.kepler.build.runner.Kepler:      [null] In addition: Warning messages:
11/11/11 10:58:21.851 AM [0x0-0xad1ad1].org.kepler.build.runner.Kepler:      [null] 1: In min(x) : no non-missing arguments to min; returning Inf
11/11/11 10:58:21.851 AM [0x0-0xad1ad1].org.kepler.build.runner.Kepler:      [null] 2: In max(x) : no non-missing arguments to max; returning -Inf
11/11/11 10:58:21.851 AM [0x0-0xad1ad1].org.kepler.build.runner.Kepler:      [null] Execution halted

And it gave me a [crazy?] zig-zag plot.
Please see attached workflow that I edited.
Thanks,
-ben

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On Nov 11, 2011, at 10:25 AM, Hurlbert, Allen Hartley wrote:

> Hey Ben,
> 
> Sorry for my poor question-asking etiquette.
> 
> I'm running Kepler 2.2 on Windows XP x64. I've got R 2.13.1 installed.
> 
> Yes, the demos run fine (although I'll note that finding the demo files took some work; the "getting-started-guide" specified the "demos/getting-started" directory and it would have been useful to know the more complete path: "Kepler-2.2/outreach-2.2.0/workflows/demos/getting-started").
> 
> The workflow and input file are attached.
> 
> When I open a Command Prompt, I am in the directory C:\Documents and Settings\Hurlbert. Typing 'R' here does not run R.
> 
> I assume this is an easily fixable issue. In addition, any general comments about how I went about constructing the basic workflow would be useful. I'm assuming there are other errors that will crop up!
> 
> Hope all's well in SB!
> Allen
> 
> -----Original Message-----
> From: ben leinfelder [mailto:leinfelder at nceas.ucsb.edu] 
> Sent: Friday, November 11, 2011 11:52 AM
> To: Hurlbert, Allen Hartley
> Cc: kepler-users at kepler-project.org
> Subject: Re: [kepler-users] Kepler-R basic question
> 
> Hi Allen!
> A few questions for you: 
> a) can you run any of the getting started demo RExpression workflows that are included with Kepler? (e.g. 05-LinearRegression.xml)
> b) what version of Kepler are you using and on which operating system?
> c) could you provide us your sample workflow?
> 
> If you can run R from the command line by simply typing "R", then chances are good it's already in your PATH.
> -ben
> 
> On Nov 11, 2011, at 7:29 AM, Hurlbert, Allen Hartley wrote:
> 
>> Apologies for the basic question, but I'm brand new to Kepler.
>> 
>> Trying to create a basic workflow that reads in some data from a local text file (using ReadTable), manipulates it a bit (using an RExpression actor), and generates a plot.
>> 
>> However, it seems to be having trouble locating R (error message: "Problem writing input. There has been a problem running the R script! It may be due to an error in your script, ..., or it may not be on your path and cannot be located by Kepler... Because: the pipe has been ended.").
>> 
>> I definitely have R installed on my machine. The referenced section of the User Manual, states "the R 'bin' directory must be added to the PATH variable on the host computer." I'm not sure how to do this. I can see in the Tools>Check System Settings that PATH = env.PATH, but am unsure whether this is what I'm supposed to set, and if so, how.
>> 
>> Thanks in advance,
>> Allen
>> 
>> _______________________________________________
>> Kepler-users mailing list
>> Kepler-users at kepler-project.org
>> http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
> 
> <VerticalFoliageProfile.kar><Vert_Foliage_Data_20110707.txt>