[R-SIG-Mac] R 32-bit suddenly the default on Mountain Lion 10.8.2?

[Federico Calboli]

On 13 Nov 2012, at 19:59, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:

> Marc,
> 
> Start with 'which R', or run /usr/bin/R explicitly.

$ which R
/usr/bin/R


>  That should be a symlink to
> 
> /Library/Frameworks/R.framework/Resources/bin/R

it does:

$ ls -l /usr/bin/R
lrwxr-xr-x  1 root  wheel  47 28 Oct 10:47 /usr/bin/R@ -> /Library/Frameworks/R.framework/Resources/bin/R

> 
> and that should be a symlink,

it's not:

$ ls -l /Library/Frameworks/R.framework/Resources/bin/R
-rwxrwxr-x  1 root  admin  8775 26 Oct 17:22 /Library/Frameworks/R.framework/Resources/bin/R*

$ ls /Library/Frameworks/R.framework/Resources/bin/R*
/Library/Frameworks/R.framework/Resources/bin/R*       /Library/Frameworks/R.framework/Resources/bin/Rd2pdf*
/Library/Frameworks/R.framework/Resources/bin/R32*     /Library/Frameworks/R.framework/Resources/bin/Rdconv*
/Library/Frameworks/R.framework/Resources/bin/R64*     /Library/Frameworks/R.framework/Resources/bin/Rdiff*
/Library/Frameworks/R.framework/Resources/bin/REMOVE*  /Library/Frameworks/R.framework/Resources/bin/Rprof*
/Library/Frameworks/R.framework/Resources/bin/Rcmd*    /Library/Frameworks/R.framework/Resources/bin/Rscript*


BW

F


>  If it is not like
> 
> lrwxr-xr-x  1 root  admin  3 28 Oct 08:03 /Library/Frameworks/R.framework/Resources/bin/R@ -> R64
> 
> or is linked to R32, change it to point to R64.
> 
> It is the installer which determines what it links to.  Specifically https://svn.r-project.org/R-dev-web/trunk/CRAN/QA/Simon/R-build/packaging/leopard/scripts/postflight .
> 
> If running /Library/Frameworks/R.framework/Resources/bin/R64 is not x86_64, come back to us.
> 
> Brian
> 
> On 13/11/2012 19:06, Marc Schwartz wrote:
>> Hi All,
>> 
>> I am on a fully updated MacBook Pro, running 10.8.2. I get:
>> 
>> uname -m x86_64
>> 
>> from the terminal, as would be expected.
>> 
>> I have been using the CRAN OSX binaries for some time now, rather
>> than building from source, which I had been doing previously.
>> 
>> Somewhere along the way in the past few weeks, apparently since I
>> installed R 2.15.2, the default architecture under which R is running
>> is now 32 bit, not 64 bit, which was the case previously. I just
>> noted this today due to some funny encoding issues that I had not
>> seen before and have spent the past few hours trying to figure out
>> what changed.
>> 
>> I initially thought something was amiss with the latest 2.15.2
>> release .pkg file. I completely removed R (Framework and symlinks to
>> the startup scripts, etc.) and re-installed. Same thing. 32 bit R was
>> the default link from 'R'.
>> 
>> So I removed R again and re-installed 2.15.1 (getting the older
>> binary from CRAN), since that was the last version of R that I had
>> installed which defaulted to 64 bit.
>> 
>> Funny, same thing, it defaulted to 32 bit R.
>> 
>> Then I wondered if there was something related to some anti-virus
>> software (Avast) that I had recently installed due to some events
>> that had occurred recently. I completely removed the AV software,
>> rebooted, removed R and then re-installed R. Same thing, 32 bit R as
>> the default.
>> 
>> What am I missing here? What is the installation program and/or the R
>> startup script itself looking for that determines whether 64 or 32
>> bit R should the default when one simply uses 'R' to start it up? A
>> read of the R startup script suggests that the output (as above) of
>> 'uname -m' being 'x86_64' may be all that is needed, but perhaps I am
>> missing something else.
>> 
>> I am also attaching the full installation log file here (for 2.15.2).
>> I did not see anything there obvious to my eyes.
>> 
>> I can't recall the timeline well enough right now to consider whether
>> some OSX update changed something, or if there is something strictly
>> unique to my MBP that is causing this problem.
>> 
>> Thanks for any insights.
>> 
>> Regards,
>> 
>> Marc
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> _______________________________________________ R-SIG-Mac mailing
>> list R-SIG-Mac at r-project.org
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>> 
> 
> 
> -- 
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
> 
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--
Federico C. F. Calboli
Neuroepidemiology and Ageing Research
Imperial College, St. Mary's Campus
Norfolk Place, London W2 1PG

Tel +44 (0)20 75941602   Fax +44 (0)20 75943193

f.calboli [.a.t] imperial.ac.uk
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