[R] "command not found" from system() call in GUI with proper PATH

[Eric Archer - NOAA Federal]

<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

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