[R] Failure with .Rprofile on Mac OS X

[David Winsemius]

Good point. I see the behavior you describe.

Sent from my iPhone

> On Sep 19, 2014, at 1:18 AM, "Amos B. Elberg" <amos.elberg at gmail.com> wrote:
> 
> 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.)
>> <compose-unknown-contact.jpg>	David Winsemius	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 
>> 
>> <compose-unknown-contact.jpg>	Gang Chen	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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