Re: [R] Failure with .Rprofile on Mac OS X
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] LINESMANPATH PERL5LIB PWD [9] SHLVLTERM 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.
Re: [R] Failure with .Rprofile on Mac OS X
Thanks for the help, Amos! The only reason that *should* happen is if there's an .Rprofile in the directory you're in when you start R. There is only one .Rprofil, which is in my home directory ~/ Where *exactly* is the .Rprofile file you want loaded The only one is in my home directory. what directory are you starting from 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 what does R say is the user's home directory? Did you make *any* changes to Rprofile.site, or Renviron? R.home() [1] /Library/Frameworks/R.framework/Resources What is the output from Sys.getenv() in gui and cli, and do they differ? 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.elb...@gmail.com 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? 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 __ 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.
Re: [R] Failure with .Rprofile on Mac OS X
Good point. I see the behavior you describe. Sent from my iPhone On Sep 19, 2014, at 1:18 AM, Amos B. Elberg amos.elb...@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.jpgDavid 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_PATHGDK_USE_XFT INFOPATH [5] LINESMANPATH PERL5LIB PWD [9] SHLVLTERM 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 compose-unknown-contact.jpgGang 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 __ 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. [[alternative HTML version deleted]] __ 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.
Re: [R] Failure with .Rprofile on Mac OS X
On 18-09-2014, at 17:18, Gang Chen gangch...@gmail.com wrote: When R starts in GUI (e.g.,/Library/Frameworks/R.framework/Resources/bin/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? 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”? From Terminal? if so use open -a R. 3. Most importantly: what differences are happening? Differences in PATH environment variable? ….. I just tried R GUI and R in Terminal and my ~/.Rprofile is being read by both. Berend 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.
[R] Failure with .Rprofile on Mac OS X
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.
Re: [R] Failure with .Rprofile on Mac OS X
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? 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 __ 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.
Re: [R] Failure with .Rprofile on Mac OS X
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] LINESMANPATH PERL5LIB PWD [9] SHLVLTERM 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 __ 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.
