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

[peter dalgaard]

Notice that we have a similar, but unresolved, bug report a month old.

https://bugs.r-project.org/bugzilla/show_bug.cgi?id=15940

I assume that the obvious things like a .Rprofile in the current directory has been checked? 

Running R under a debugger, single-stepping through the startup code would likely isolate the trouble, but it's a bit of work to set up, and of course it needs to be on the machine that actually displays the problem.

-pd

On 20 Sep 2014, at 21:27 , David Winsemius <dwinsemius at comcast.net> wrote:

> 
> 
> 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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>> R-SIG-Mac at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> David Winsemius
> Alameda, CA, USA
> 
> _______________________________________________
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-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com