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 <[email protected]> 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 <[email protected]> >> 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 >>>> [email protected] >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>> >>>> >>> >> >> > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
