[R] Failure with .Rprofile on Mac OS X

[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.)
> David Winsemius <mailto:dwinsemius at comcast.net>
> September 19, 2014 at 12:57 AM
>
> 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:
>
>> 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?
>
> 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.
>
>
>>
>>
>>> On Sep 18, 2014, at 11:18 AM, Gang Chen <gangchen6 at gmail.com> wrote:
>>>
>>> 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
>
> David Winsemius, MD
> Alameda, CA, USA
>
> Gang Chen <mailto:gangchen6 at gmail.com>
> September 18, 2014 at 11:18 AM
> 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
>
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