Rprofile.site under Windows 7? - R-help

Thu, May 3, 2012 9:07 PM #

Hello All:


	  I'm still unable to get Rprofile.site to set, e.g., 
options(max.print=222), as I did with previous versions of R.


	  I just found similar questions posed by Trevor Miles and Ross Bowden 
with replies by Uwe Ligges and Duncan Murdoch.


	  In addition to the things I tried documented below, I also copied 
Rprofile.site into "R_HOME/etc/i386" and "R_HOME/etc/x64", without, 
e.g., max.print being changed to 222 as requested.


	  Any other suggestions?


	  Thanks,
	  Spencer Graves


################################################


       I have so far failed to get Rprofile.site to be processed in R 
2.15.0 under Windows 7 as I remember having done it in previous version 
of R.  For example, I've included "options(max.print=222)" in 
"R_HOME/etc/Rprofile.site" (with and without the environmental variable 
R_HOME set to the install directory of R 2.15.0 in advanced system 
settings):  When I start R, I still get the default:


options('max.print')
$max.print
[1] 99999


       Suggestions?
       Thanks,
       Spencer

R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

loaded via a namespace (and not attached):
[1] tools_2.15.0

Spencer Graves, PE, PhD
President and Chief Technology Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San Jos?, CA 95126
ph:  408-655-4567
web:  www.structuremonitoring.com

Joshua Wiley

Thu, May 3, 2012 9:28 PM #

How are you using R?  Any special front ends that might be causing
this?  Can you try it in unsuffered consequences?

Josh

On Thu, May 3, 2012 at 9:07 PM, Spencer Graves

<spencer.graves at structuremonitoring.com> wrote:

______________________________________________
R-help at 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.

Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/

Spencer Graves

Thu, May 3, 2012 9:41 PM #

On 5/3/2012 9:28 PM, Joshua Wiley wrote:

I'm running R 1.15.0;  sessionInfo() appears below.  I get this 
from Rgui i386 and x64 plus when calling Rterm x64 via GNU Emacs 23.3.1 
using ESS.


       Thanks for the question.  Spencer

______________________________________________
R-help at 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.

Duncan Murdoch

Fri, May 4, 2012 5:41 AM #

On 12-05-04 12:41 AM, Spencer Graves wrote:

I can see three possibilities:

  1.  You have more than one Rprofile.site, and it's not reading the one 
you think it's reading.   The search order is:
   - the file mentioned in the R_PROFILE environment variable if there 
is one
   - RHOME/etc/<arch>/Rprofile.site
   - RHOME/etc/Rprofile.site

It takes the first of those and ignores later ones.

<arch> is either i386 or x64, depending on your architecture.

2.  You don't have permission to read the file.  Does readLines() read 
it from within a session?  This code is somewhat like what R does on 
startup:

   env <- Sys.getenv("R_PROFILE")
   if (nchar(env))
     readLines(env)
   else {
     filename <- file.path(R.home(), "etc", sub("[/]", "", 
Sys.getenv("R_ARCH")), "Rprofile.site")
     if (file.exists(filename))
       readLines(filename)
     else {
       filename <- file.path(R.home(), "etc", "Rprofile.site")
       if (file.exists(filename))
         readLines(filename)
     }
   }

Does it work for you?

3.  There's a bug somewhere....

Duncan Murdoch

______________________________________________
R-help at 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 at 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.

Spencer Graves

Fri, May 4, 2012 4:40 PM #

On 5/4/2012 5:41 AM, Duncan Murdoch wrote:

Thanks very much.  It helped me isolate and solve the problem:


       I edited "Rprofile.site" in Emacs.  When I saved the edited 
version into the default, write protected location, Windows 7 apparently 
saved two copies:  the original and a hidden copy with my edits.  When I 
then reopen the file in Emacs, I see my edits.  However, when I open it 
with WordPad or try to read it as you just described, my edits do not 
appear.  Knowing this, I saved a copy to a non-protected location, 
edited it there, then copied the edited version back into the protected 
directories.  Now it works.  (I had previously avoided installing R in 
the default location since encountering problems with Vista.)


       This is almost enough to drive a person to join the "I hate 
MicroSoft" fan club.


       Spencer

______________________________________________
R-help at 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 at 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.

Duncan Murdoch

Fri, May 4, 2012 7:17 PM #

On 12-05-04 7:40 PM, Spencer Graves wrote:

On 5/4/2012 5:41 AM, Duncan Murdoch wrote:

On 12-05-04 12:41 AM, Spencer Graves wrote:

On 5/3/2012 9:28 PM, Joshua Wiley wrote:

How are you using R?  Any special front ends that might be causing
this?  Can you try it in unsuffered consequences?


         I'm running R 1.15.0;  sessionInfo() appears below.  I get this
from Rgui i386 and x64 plus when calling Rterm x64 via GNU Emacs 23.3.1
using ESS.

I can see three possibilities:

  1.  You have more than one Rprofile.site, and it's not reading the
one you think it's reading.   The search order is:
   - the file mentioned in the R_PROFILE environment variable if there
is one
   - RHOME/etc/<arch>/Rprofile.site
   - RHOME/etc/Rprofile.site

It takes the first of those and ignores later ones.

<arch>  is either i386 or x64, depending on your architecture.

2.  You don't have permission to read the file.  Does readLines() read
it from within a session?  This code is somewhat like what R does on
startup:

   env<- Sys.getenv("R_PROFILE")
   if (nchar(env))
     readLines(env)
   else {
     filename<- file.path(R.home(), "etc", sub("[/]", "",
Sys.getenv("R_ARCH")), "Rprofile.site")
     if (file.exists(filename))
       readLines(filename)
     else {
       filename<- file.path(R.home(), "etc", "Rprofile.site")
       if (file.exists(filename))
         readLines(filename)
     }
   }

Does it work for you?


        Thanks very much.  It helped me isolate and solve the problem:


        I edited "Rprofile.site" in Emacs.  When I saved the edited
version into the default, write protected location, Windows 7 apparently
saved two copies:  the original and a hidden copy with my edits.  When I
then reopen the file in Emacs, I see my edits.  However, when I open it
with WordPad or try to read it as you just described, my edits do not
appear.  Knowing this, I saved a copy to a non-protected location,
edited it there, then copied the edited version back into the protected
directories.  Now it works.  (I had previously avoided installing R in
the default location since encountering problems with Vista.)


        This is almost enough to drive a person to join the "I hate
MicroSoft" fan club.

I think that would just confirm my membership in the "I hate Emacs" club.

Duncan Murdoch

______________________________________________
R-help at 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 at 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.

Joshua Wiley

Fri, May 4, 2012 7:33 PM #

On Fri, May 4, 2012 at 7:17 PM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:

[snip]

I don't see how this is Emacs fault...

Duncan Murdoch

Fri, May 4, 2012 9:27 PM #

On 12-05-04 10:33 PM, Joshua Wiley wrote:

It claimed to save a file somewhere, but didn't.

Duncan Murdoch

Spencer Graves

Fri, May 4, 2012 10:18 PM #

On 5/4/2012 9:27 PM, Duncan Murdoch wrote:

The file was saved, because when I reopened it in Emacs, the 
changes were there.  Windows 7 created a phantom copy, which it 
delivered to Emacs when I clicked and dragged it to the Emacs icon on 
the task bar.  To fix the problem, I copied the file to a non-protected 
place, opened it and the other copy in Emacs, copied the changes from 
the phantom copy into the non-protected copy, then copied the 
non-protected, edited version into the protected, default R installation 
directory.  I had not encountered this problem earlier, because I 
usually install R in an unprotected location.  I got sloppy with R 
1.15.0 and accepted the default installation directory.


       Best Wishes,
       Spencer

Spencer Graves, PE, PhD
President and Chief Technology Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San Jos?, CA 95126
ph:  408-655-4567
web:  www.structuremonitoring.com

Gabor Grothendieck

Mon, May 21, 2012 4:12 AM #

On Sat, May 5, 2012 at 1:18 AM, Spencer Graves

<spencer.graves at structuremonitoring.com> wrote:

Do you actually have multiple users on your PC accessing R?  If not,
you could avoid using the Rprofile.site file entirely and just put a
.Rprofile file having the same contents using the %userprofile% folder
for the user who uses R.  That would avoid the problem of writing into
system space.  Alternately save Rprofile.site as Adminstrator.

Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com