Skip to content

Failure with .Rprofile on Mac OS X

7 messages · Amos B. Elberg, Gang Chen, David Winsemius +1 more

Original
Gang Chen
# 
When R starts in GUI (e.g., /Applications/R.app/Contents/MacOS/R) on
my Mac OS X 10.7.5, the startup configuration in .Rprofile works fine.
However, when R starts on the terminal (e.g.,
/Library/Frameworks/R.framework/Resources/bin/R), it does not work at
all. What could be the reason for the failure?

Thanks,
Gang
Amos B. Elberg
# 
The only reason that *should* happen is if there's an .Rprofile in the directory you're in when you start R.

Where *exactly* is the .Rprofile file you want loaded, what directory are you starting from, and what does R say is the user's home directory? Did you make *any* changes to Rprofile.site, or Renviron?

What is the output from Sys.getenv() in gui and cli, and do they differ?
David Winsemius
# 
Dear Gang Chen;

The .Rprofile is loaded from the startup directory. Terminal.app will  
start up in /Applications/ while your R.app session appears to be  
starting in a different directory. (We don't know what your startup  
directories are.)  I'm using R.app in /Applications/ so my .Rprofile  
has the same effect regardless of whether I run from R.app or from a  
bash console.

See this portion of the Mac-FAQ:

http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#The-current-and-startup-working-directories

  See ?Startup for more specifics that are generic to all R versions:
On Sep 18, 2014, at 7:04 PM, Amos B. Elberg wrote:

            

      
      
      
    

        
They might differ even if the default directories are the same (as  
they are on my setup). I have a somewhat older version on this laptop  
but there are names of environment variables that are not present in  
both directions:

I ran AppEnv <- dput( Sys.getenv() ) on my R.app session and then ran  
the corresponding command on a Terminal console session:

These are the difference (on a R 2.15.2 setup):

 > AppEnv[ !names(AppEnv) %in% names(conEnv)]
R_GUI_APP_REVISION  R_GUI_APP_VERSION
             "6435"             "1.53"
 > names( conEnv[ !names(conEnv) %in% names(AppEnv)] ) # i.e. missing  
in the GUI installation

  [1] "COLUMNS"              "DYLD_LIBRARY_PATH"     
"GDK_USE_XFT"          "INFOPATH"
  [5] "LINES"                "MANPATH"               
"PERL5LIB"             "PWD"
  [9] "SHLVL"                "TERM"                  
"TERM_PROGRAM"         "TERM_PROGRAM_VERSION"
[13] "XDG_CACHE_HOME"       "XDG_CONFIG_DIRS"       
"XDG_CONFIG_HOME"      "XDG_DATA_DIRS"
[17] "XDG_DATA_HOME"

  If there are further points of discussion they should be thrashed  
out (with greater details about sessionInfo() and startup settings),  
over on the R-MAC-SIG mailing list.

            

      
      
      
    

        
David Winsemius, MD
Alameda, CA, USA

  
  


  


      

    

    

      
      

        


  

        

      Amos B. Elberg
    

    

      
      #
    

  


  

      
David - the startup directory for Terminal.app shouldn't affect where R
looks for .Rprofile.  If R is started from the command line, it should
look in whatever is the user's current directory (which will be ~/ if
Terminal was just launched), and then ~/  .  It shouldn't be looking in
/Applications/ unless you happen to have cd'd to /Applications before
launching R.

(You put up the environment variables present in one launch and absent
from another, but what I was really looking for is whether something in
his shell is changing a path.  Because mac environment variables are
funky that way.)

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Gang Chen
    

    

      
      #
    

  


  

      
Thanks for the help, Amos!

            

      
      
      
    

        
There is only one .Rprofil, which is in my home directory ~/

            

      
      
      
    

        
The only one is in my home directory.

            

      
      
      
    

        
It does not matter where I start R because on my Mac the CLI R is
linked to /Library/Frameworks/R.framework/Resources/bin/R while the
GUI R is linked to /Applications/R.app/Contents/MacOS/R

            

      
      
      
    

        
[1] "/Library/Frameworks/R.framework/Resources"

            

      
      
      
    

        
They differ slightly. I have trouble pinpointing the exact difference
because the format is a little different and vim does not help much in
tracking the differences. I just noticed that the CLI version has a
few extra terms such as

COLUMNS
"130"
...
DYLD_FALLBACK_LIBRARY_PATH
"/Library/Frameworks/R.framework/Resources/lib"

Thanks,
Gang

        
On Thu, Sep 18, 2014 at 7:04 PM, Amos B. Elberg <amos.elberg at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      David Winsemius
    

    

      
      #
    

  


  

      
Good point. I see the behavior you describe.

Sent from my iPhone

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Berend Hasselman
    

    

      
      #
    

  


  

      
On 18-09-2014, at 17:18, Gang Chen <gangchen6 at gmail.com> wrote:

        

            

      
      
      
    

        
This belongs on the R-SIG-Mac mailing list.

1. Are you running T in Terminal with the command "/Library/Frameworks/R.framework/Resources/bin/R??
You can use just R because /usr/bin is in PATH (or it should be).

2. Are you running R GUI with the command "/Applications/R.app/Contents/MacOS/R??