Thanks all for the responses. Running Rstudio from the command line does
seem to work, but is clearly not the ideal solution. Nor is modifying the
path to executable as I have these system calls embedded within a package
which assumes that the user has the executables installed somewhere in
their path. I suppose I could add a reference to a path environmental
variable or function argument that gets pasted in when the system call is
made, but that is also less than ideal. Crossing fingers that a fix is
released.
Cheers,
eric
----
*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
On Fri, Oct 24, 2014 at 5:12 PM, Kevin Ushey <[email protected]> wrote:
> And more bizarrely, if I launch RStudio from the terminal, there are
> _two_ PATH variables set:
>
> > Sys.getenv()[names(Sys.getenv()) == "PATH"]
> PATH
> "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/texbin"
> PATH
> "/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/texbin"
>
> I am curious if the same behaviour is seen in R.app when launched from
> the terminal (AFAIK, RStudio does not try to munge the PATH or
> anything else on startup)
>
> Kevin
>
> On Fri, Oct 24, 2014 at 4:46 PM, peter dalgaard <[email protected]> wrote:
> >
> >> On 25 Oct 2014, at 00:11 , Roy Mendelssohn - NOAA Federal <
> [email protected]> wrote:
> >>
> >> 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.
> >
> > For RStudio, I see (after open -a RStudio)
> >
> >> system("echo $PATH")
> >
> /opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
> >> Sys.getenv("PATH")
> > [1]
> "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/texbin:/opt/local/bin"
> >
> > which actually points to two different TeX versions on this computer.
> The version without /usr/texbin matches the PATH of the terminal. So
> Rstudio tried to make changes and failed (as it happens, it would have
> chosen TeX 2009 over TeX 2013, so I'm not complaining.)
> >
> > -pd
> >
> >>
> >> -Roy
> >>
> >> On Oct 24, 2014, at 3:04 PM, Emma Sherratt <[email protected]>
> 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 $PATH")
> >>>
> >>> You have to use full paths in Yosemite for anything that is not on the
> >>> "sanctioned" PATH -- or use R from the shell.
> >>>
> >>> On Saturday, October 25, 2014, Eric Archer - NOAA Federal <
> >>> [email protected]> wrote:
> >>>
> >>>> <Apologies for the cross-posting, but I couldn't tell if this was a
> general
> >>>> R issue, or Mac-specific>
> >>>>
> >>>> When running a system file from within R, I have just started to get a
> >>>> "command not found" error although my PATH seems to be properly set
> and I
> >>>> can run the same system file from the terminal. The program I am
> trying to
> >>>> run is 'fastsimcoal' and is in /usr/local/bin. I confirm this in the
> >>>> terminal with
> >>>>
> >>>> SWC-EARCHER-ML-3:~ eric.archer$ 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
> >>>>
> >>>> [[alternative HTML version deleted]]
> >>>>
> >>>> _______________________________________________
> >>>> R-SIG-Mac mailing list
> >>>> [email protected] <javascript:;>
> >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>>>
> >>>
> >>>
> >>> --
> >>>
> >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >>>
> >>> 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: [email protected]
> >>>
> >>> Caecilians are legless amphibians...
> >>>
> >>> * __
> >>> (\ .-. .-. /_")
> >>> \\_//^\\_//^\\_//
> >>> `"` `"` `"`*
> >>>
> >>> learn more about them here: www.emmasherratt.com/caecilians
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> R-SIG-Mac mailing list
> >>> [email protected]
> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>
> >> **********************
> >> "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***
> >> 110 Shaffer Road
> >> Santa Cruz, CA 95060
> >> Phone: (831)-420-3666
> >> Fax: (831) 420-3980
> >> e-mail: [email protected] www: http://www.pfeg.noaa.gov/
> >>
> >> "Old age and treachery will overcome youth and skill."
> >> "From those who have been given much, much will be expected"
> >> "the arc of the moral universe is long, but it bends toward justice"
> -MLK Jr.
> >>
> >> _______________________________________________
> >> R-SIG-Mac mailing list
> >> [email protected]
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
> > --
> > Peter Dalgaard, Professor,
> > Center for Statistics, Copenhagen Business School
> > Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> > Phone: (+45)38153501
> > Email: [email protected] Priv: [email protected]
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > [email protected]
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
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