[R-SIG-Mac] "command not found" from system() call in GUI with proper PATH
Roy Mendelssohn - NOAA Federal
roy.mendelssohn at noaa.gov
Sat Oct 25 00:11:05 CEST 2014
For other applications it has been found that if you launch the GUI application from the terminal using the open -a command, that then the path does get sent down,
I haven't tried it for R, but it does work for things like TeX.
-Roy
On Oct 24, 2014, at 3:04 PM, Emma Sherratt <emma.sherratt at gmail.com> wrote:
> I had the same problem and Simon Urbanek replied to me with the following:
>
> It is, because Yosemite ignores PATH for processes started from a GUI
> application. You will see if you run
> system("echo $PATH")
>
> You have to use full paths in Yosemite for anything that is not on the
> "sanctioned" PATH -- or use R from the shell.
>
> On Saturday, October 25, 2014, Eric Archer - NOAA Federal <
> eric.archer at noaa.gov> wrote:
>
>> <Apologies for the cross-posting, but I couldn't tell if this was a general
>> R issue, or Mac-specific>
>>
>> When running a system file from within R, I have just started to get a
>> "command not found" error although my PATH seems to be properly set and I
>> can run the same system file from the terminal. The program I am trying to
>> run is 'fastsimcoal' and is in /usr/local/bin. I confirm this in the
>> terminal with
>>
>> SWC-EARCHER-ML-3:~ eric.archer$ which fastsimcoal
>> /usr/local/bin/fastsimcoal
>>
>> In the examples below, Sys.getenv("PATH") shows that /usr/local/bin is in
>> the PATH. I get the same error for any program in /usr/local/bin. However,
>> programs in other folders in the path seem to run through system()
>> properly.
>>
>> Also, note that the return from Sys.getenv("PATH") is the same for running
>> in R-Studio vs. R in the terminal, but is truncated in the R GUI. As far as
>> I can tell I do not have a .Rprofile file in my default working directory,
>> R_HOME, or R_HOME/etc.
>>
>> A final piece of information: I have just upgraded to OSX Yosemite v10.10.
>> This was not happening at some point prior to the upgrade, but it has been
>> a while since I tried this particular command, so I do not know if it was
>> working immediately prior to the OS upgrade.
>>
>> Any help or insight is greatly appreciated.
>>
>> Cheers,
>> eric
>>
>> The examples:
>>
>>> From within R-Studio v0.98.1079:
>>
>>> sessionInfo()
>> R version 3.1.1 (2014-07-10)
>> Platform: x86_64-apple-darwin13.1.0 (64-bit)
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> loaded via a namespace (and not attached):
>> [1] tools_3.1.1
>>> getwd()
>> [1] "/Users/eric.archer"
>>> Sys.getenv("PATH")
>> [1]
>>
>> "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/git/bin:/usr/texbin"
>>> system("fastsimcoal")
>> sh: fastsimcoal: command not found
>>
>>
>> The same script in the R console through the GUI gives:
>>
>>> sessionInfo()
>> R version 3.1.1 (2014-07-10)
>> Platform: x86_64-apple-darwin13.1.0 (64-bit)
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>> getwd()
>> [1] "/Users/eric.archer"
>>> Sys.getenv("PATH")
>> [1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin"
>>> system("fastsimcoal")
>>>
>> /bin/sh: fastsimcoal: command not found
>>
>>
>> Running it through R in a terminal window, it runs (output of
>> 'fastsimcoal' truncated):
>>
>>> sessionInfo()
>> R version 3.1.1 (2014-07-10)
>> Platform: x86_64-apple-darwin13.1.0 (64-bit)
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>> getwd()
>> [1] "/Users/eric.archer"
>>> Sys.getenv("PATH")
>> [1]
>>
>> "/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/local/git/bin:/usr/texbin"
>>> system("fastsimcoal")
>>
>>
>> fastSimcoal2 (ver 2.1 December 2013)
>>
>> Usage:
>>
>> -h --help : prints this help
>> -i --ifile test.par : name of parameter file
>> ...
>>
>> ----
>>
>> *Eric Archer, Ph.D.*
>> Southwest Fisheries Science Center
>> NMFS, NOAA
>> 8901 La Jolla Shores Drive
>> La Jolla, CA 92037 USA
>> 858-546-7121 (work)
>> 858-546-7003 (FAX)
>>
>> Marine Mammal Genetics Group: swfsc.noaa.gov/mmtd-mmgenetics
>> ETP Cetacean Assessment Program: swfsc.noaa.gov/mmtd-etp
>>
>> "
>>
>>
>> *The universe doesn't care what you believe. The wonderful thing about
>> science is that it doesn't ask for your faith, it just asks for your
>> eyes.*" - Randall Munroe
>>
>> "*Lighthouses are more helpful than churches.*"
>> - Benjamin Franklin
>>
>> "*...but I'll take a GPS over either one.*"
>> - John C. "Craig" George
>>
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>>
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>
>
> --
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> Emma Sherratt, PhD.
>
> Lecturer in Zoology,
> Zoology Division, School of Environmental and Rural Science,
> Room L118 Bldg C02,
> University of New England,
> Armidale, NSW, Australia, 2351
> Tel: +61 2 6773 5038
> email: emma.sherratt at une.edu.au
>
> Caecilians are legless amphibians...
>
> * __
> (\ .-. .-. /_")
> \\_//^\\_//^\\_//
> `"` `"` `"`*
>
> learn more about them here: www.emmasherratt.com/caecilians
>
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**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new address and phone***
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Phone: (831)-420-3666
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e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/
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