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Eric Archer - NOAA Federal

2014-Oct-24 21:54 UTC

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

<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]]

Emma Sherratt

2014-Oct-24 22:04 UTC

head link

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

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
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at r-project.org <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: emma.sherratt at une.edu.au

Caecilians are legless amphibians...

*                      __
    (\   .-.   .-.   /_")
     \\_//^\\_//^\\_//
      `"`   `"`   `"`*

learn more about them here: www.emmasherratt.com/caecilians

	[[alternative HTML version deleted]]

Emma Sherratt

2014-Oct-24 22:04 UTC

head link

Re: [R-SIG-Mac] "command not found" from system() call in GUI with proper PATH

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@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
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org <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: emma.sherratt@une.edu.au

Caecilians are legless amphibians...

*                      __
    (\   .-.   .-.   /_")
     \\_//^\\_//^\\_//
      `"`   `"`   `"`*

learn more about them here: www.emmasherratt.com/caecilians

	[[alternative HTML version deleted]]

R help - Oct 2014 - "command not found" from system() call in GUI with proper PATH

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

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

Re: [R-SIG-Mac] "command not found" from system() call in GUI with proper PATH