[R-SIG-Mac] Failure of CLI with .Rprofile on Mac OS X

[David Winsemius]

On Sep 19, 2014, at 2:01 PM, Gang Chen wrote:

> When R starts in GUI on my Mac OS X 10.7.5, the startup configuration in .Rprofile works fine. However, when R starts through command line interface (CLI) on the terminal , it does not work at all. 
> 
> The GUI R on my Mac is aliased on the terminal to /Applications/R.app/Contents/MacOS/R while the CLI R (/usr/bin/R) is linked to /Library/Frameworks/R.framework/Resources/bin/R. There is only one .Rprofile, which resides in my home directory ~/. 
> 
>> sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> 
> What could be the cause for the failure with CLI?

Caveat: I'm not the best person to answer this. I'm not a skilled user of Unix and I'm not one of the Mac development team. But those guys are often not reading the mailing list on weekends so I thought I'd throw some ideas out that you could investigate.


#----- Idea # 1 ---------
Running 3.1.1 this is what I see among the environment variables that are different in a CLI session of R from those in a GUI session. In particular I am wondering if your PWD variable points to your User/username/ directory:

> Sys.getenv()[grep('Users', Sys.getenv())]
                                HOME                                  PWD 
             "/Users/davidwinsemius"              "/Users/davidwinsemius" 
                      XDG_CACHE_HOME                      XDG_CONFIG_HOME 
      "/Users/davidwinsemius/.cache"      "/Users/davidwinsemius/.config" 
                       XDG_DATA_HOME 
"/Users/davidwinsemius/.local/share" 

I haven't been able to find exactly what PWD is pointing to. It's not listed in the "environment variables" link from ?Sys.getenv. I think it's related tot eh Unix cli command `pwd` which prints the working directory. I don't know how to give you a direct link to the page with a listing of environment variables, since that page is one the doesn't conform to the convention of having a ?NameOfPage lookup. Its page name is "EnvVar" but ?EnvVar gives a "No documentation for ‘EnvVar’ ..." message. I also do not find "PWD" in a search of the Install/Admin document.

I tried changing PWD in a session an quitting, but it didn't seem to "stick".

> Sys.getenv()["PWD"]
                    PWD 
"/Users/davidwinsemius" 
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.utf-8/en_US.utf-8/en_US.utf-8/C/en_US.utf-8/en_US.utf-8

attached base packages:
[1] grDevices datasets  splines   graphics  utils     stats     grid     
[8] methods   base     

other attached packages:
[1] rms_4.2-1       SparseM_1.03    Hmisc_3.14-4    Formula_1.1-1  
[5] survival_2.37-7 sos_1.3-8       brew_1.0-6      lattice_0.20-29

loaded via a namespace (and not attached):
 [1] cluster_1.15.2      latticeExtra_0.6-26 multcomp_1.3-1     
 [4] mvtnorm_0.9-9999    nlme_3.1-117        polspline_1.1.9    
 [7] quantreg_5.05       RColorBrewer_1.0-5  rpart_4.1-8        
[10] sandwich_2.3-0      zoo_1.7-11      

#---------- Idea # 2 --------

Another possibility is implied by this portion of the ?Startup page that (I already suggested you read):

"If you want ‘~/.Renviron’ or ‘~/.Rprofile’ to be ignored by child R processes (such as those run by R CMD check and R CMD build), set the appropriate environment variable R_ENVIRON_USER or R_PROFILE_USER to (if possible, which it is not on Windows) "" or to the name of a non-existent file."


#------ Suggestion -------------
So you need to check whether any of those are different than what you expect. Failing illumination after poking around in your setup,  I suspect you may need to post the output of ALL of sessionInfo() AND the results of dput(Sys.getenv()) .

-- 
David.

> 
> Thanks,
> Gang
> 	[[alternative HTML version deleted]]
> 
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David Winsemius
Alameda, CA, USA