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

[David Winsemius]

On Sep 20, 2014, at 2:15 PM, peter dalgaard wrote:

> 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:
> 
>>> 
>>> snipped

>> 
>> 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.



>> 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[sic] Unix cli command `pwd` which prints the working directory.

Peter;

Do you know whether the "PWD" value in the result from  Sys.getenv() is supposed to point at the working directory of R started from the command line?

-- 
David.

>> 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]]
>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
>> David Winsemius
>> Alameda, CA, USA
>> 
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> -- 
> 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
> 
> 
> 
> 
> 
> 
> 
> 

David Winsemius
Alameda, CA, USA