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:dwinsem...@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 <gangch...@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:gangch...@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 > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
