[R-SIG-Mac] R 3.0.0 from command line: /Library/..../x86_64/ldpaths: No such file or directory

[Karl Broman]

Ah; I had "export R_ARCH=/x86_64" in my .bashrc file; I removed that and now it runs fine.

thanks, Simon, for your help!
karl


On Apr 11, 2013, at 8:59 AM, Simon Urbanek <simon.urbanek at r-project.org> wrote:

> 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)"
>>>> 
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
>>>> R-SIG-Mac at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>> 
>>>> 
>>> 
>> 
>> 
>