R 3.0.0 from command line: /Library/..../x86_64/ldpaths: No such file or directory

On Apr 11, 2013, at 9:53 AM, Karl Broman wrote:

I removed /usr/bin/R and re-installed, but I still have the same problem.

If in doubt, blow away the whole /Library/Frameworks/R.framework

What happens is that you're running R with R_ARCH=/x86_64 set which is how R 2.x was run but R 3.x is no longer multi-arch. The question is where is that set? Look at the /usr/bin/R script - in line 46 there should be
: ${R_ARCH=}
and check that you're not setting R_ARCH in your environment.

Cheers
S

/usr/bin/R is a soft link that seems to be pointing to the right place.  

[fig]~[501]$ ls -l /usr/bin/R
lrwxr-xr-x  1 root  wheel  47 Apr 11 08:44 /usr/bin/R@ -> /Library/Frameworks/R.framework/Resources/bin/R

[fig]~[502]$ ls -l /Library/Frameworks/R.framework/Resources
lrwxr-xr-x  1 root  admin  26 Apr 11 08:44 /Library/Frameworks/R.framework/Resources@ -> Versions/Current/Resources

[fig]~[503]$ ls -l /Library/Frameworks/R.framework/Versions/Current
lrwxr-xr-x  1 root  admin  3 Apr 11 08:44 /Library/Frameworks/R.framework/Versions/Current@ -> 3.0

[fig]~[504]$ ls -l /Library/Frameworks/R.framework/Versions/3.0/Resources/etc/
/total 48
-rw-rw-r--  1 root  admin  5679 Apr  3 08:10 Makeconf
-rw-rw-r--  1 root  admin  1570 Apr  3 08:10 Renviron
-rw-rw-r--  1 root  admin   165 Apr  3 08:10 javaconf
-rw-rw-r--  1 root  admin   639 Apr  3 08:10 ldpaths
-rw-rw-r--  1 root  admin  1159 Apr  3 08:10 repositories

thanks,
karl

On Apr 11, 2013, at 8:40 AM, Simon Urbanek <simon.urbanek at r-project.org> wrote:

On Apr 11, 2013, at 9:29 AM, Karl Broman wrote:

I can't get R 3.0.0 to run from the command line on my Macs.  I get the following error.

$ R --version
/usr/bin/R: line 236: /Library/Frameworks/R.framework/Resources/etc/x86_64/ldpaths: No such file or directory

It works fine within RStudio or with the R GUI.
I'm running Mac OS X version 10.8.3.

Any suggestions of what's going wrong?

Yes, you have R startup script from an old version of R. Remove /usr/bin/R and re-install R.

Cheers,
S

thanks,
karl
----
Karl Broman | http://www.biostat.wisc.edu/~kbroman

R.Version()

$platform
[1] "x86_64-apple-darwin10.8.0"

$version.string
[1] "R version 3.0.0 Patched (2013-04-10 r62546)"