After nuking /Library/Frameworks/R.framework and installing the CRAN version the same devpack error messages are produced.
Since I often have to install packages from source, I'd like the proper compile environment on my Mac. Is the issue with the devpack tar extraction a problem in this regard? It appears that devpack materials are properly extracted to /usr/local... directories, but not to /Library/Frameworks/R.framework directories. Any info appreciated. Steve McKinney > -----Original Message----- > From: r-sig-mac-boun...@stat.math.ethz.ch [mailto:r-sig-mac- > boun...@stat.math.ethz.ch] On Behalf Of Steven McKinney > Sent: Monday, April 19, 2010 6:46 PM > To: Simon Urbanek > Cc: R-SIG-Mac@stat.math.ethz.ch > Subject: Re: [R-SIG-Mac] Failed tar extract due to symlinks put in > place by Rswitch > > Thanks for the information Simon. > > My apologies on the Rswitch misinformation. > > I nuked /Library/Frameworks/R.framework > and reinstalled from > http://r.research.att.com/ > using the R-2.10-branch-leopard.pkg installer. > The install yields the symlinks I saw previously (shown below). > > I still get the same error message on attempting to install the > devpack. > > I'll try installing from CRAN as well. > > > > > [momac13:/Library/Frameworks stevenmckinney] > $ cd R.framework/ > [momac13:/Library/Frameworks/R.framework stevenmckinney] > $ ls -alF > total 40 > drwxrwxr-x@ 8 root admin 272 21 Oct 2008 ./ > drwxrwxr-x@ 12 root admin 408 21 Oct 2008 ../ > lrwxr-xr-x 1 root admin 24 19 Apr 18:33 Headers@ -> > Versions/Current/Headers > lrwxr-xr-x 1 root admin 30 19 Apr 18:33 Libraries@ -> > Versions/Current/Resources/lib > lrwxr-xr-x 1 root admin 31 19 Apr 18:33 PrivateHeaders@ -> > Versions/Current/PrivateHeaders > lrwxr-xr-x 1 root admin 18 19 Apr 18:33 R@ -> Versions/Current/R > lrwxr-xr-x 1 root admin 26 21 Oct 2008 Resources@ -> > Versions/Current/Resources > drwxrwxr-x 4 root admin 136 19 Apr 18:33 Versions/ > [momac13:/Library/Frameworks/R.framework stevenmckinney] > $ cd Versions/ > [momac13:/Library/Frameworks/R.framework/Versions stevenmckinney] > $ ls -alF > total 8 > drwxrwxr-x 4 root admin 136 19 Apr 18:33 ./ > drwxrwxr-x@ 8 root admin 272 21 Oct 2008 ../ > drwxrwxr-x 6 root admin 204 19 Apr 18:33 2.10/ > lrwxr-xr-x 1 root admin 4 19 Apr 18:33 Current@ -> 2.10 > [momac13:/Library/Frameworks/R.framework/Versions stevenmckinney] > $ > > Steve McKinney > ________________________________________ > From: Simon Urbanek [simon.urba...@r-project.org] > Sent: April 19, 2010 6:26 PM > To: Steven McKinney > Cc: R-SIG-Mac@stat.math.ethz.ch > Subject: Re: [R-SIG-Mac] Failed tar extract due to symlinks put in > place by Rswitch > > On Apr 19, 2010, at 8:58 PM, Steven McKinney wrote: > > > Hi all, > > > > I am attempting to install macosx tools to a new Mac Pro. > > When I attempt to install the devpack > > sudo tar fvxz /Users/stevenmckinney/Software/R/R-2.10.1/devpack4- > darwin8-bin4.tar.gz -C / > > the tar extract fails due to symlink issues, related to symlinks > > set up by Rswitch. > > > > Rswitch does not setup any such symlinks. However, if you used Rswitch > to switch to a broken version of R that would do the job. > > > > Has anyone else encountered this issue, and know of a fix? > > > > It seems as if you don't have a valid R installation -- please make > sure you install R before unpacking the dev pack. If in doubt nuke > /Library/Frameworks/R.framework and re-install R from CRAN. > > Cheers, > Simon > > > > This is the output from the tar extract command: > > > > [momac13:/ stevenmckinney] > > $ sudo tar fvxz /Users/stevenmckinney/Software/R/R-2.10.1/devpack4- > darwin8-bin4.tar.gz -C / > > x usr/ > > x usr/local/ > > x usr/local/bin/ > > x usr/local/bin/fc-cache > > x usr/local/bin/fc-cat > > x usr/local/bin/fc-list > > . > > . > > . > > x usr/local/share/man/man5/png.5 > > x Library/ > > x Library/Frameworks/ > > x Library/Frameworks/R.framework/ > > x Library/Frameworks/R.framework/Resources/ > > x Library/Frameworks/R.framework/Resources/fontconfig/: Cannot > extract through symlink Library/Frameworks/R.framework/Resources > > x Library/Frameworks/R.framework/Resources/fontconfig/cache/: Cannot > extract through symlink Library/Frameworks/R.framework/Resources > > x Library/Frameworks/R.framework/Resources/fontconfig/fonts/: Cannot > extract through symlink Library/Frameworks/R.framework/Resources > > x > Library/Frameworks/R.framework/Resources/fontconfig/fonts/conf.avail/: > Cannot extract through symlink Library/Frameworks/R.framework/Resources > > x > Library/Frameworks/R.framework/Resources/fontconfig/fonts/conf.avail/10 > -autohint.conf: Cannot extract through symlink > Library/Frameworks/R.framework/Resources > > . > > . > > . > > x > Library/Frameworks/R.framework/Resources/fontconfig/fonts/fonts.conf: > Cannot extract through symlink Library/Frameworks/R.framework/Resources > > x > Library/Frameworks/R.framework/Resources/fontconfig/fonts/fonts.dtd: > Cannot extract through symlink Library/Frameworks/R.framework/Resources > > tar: Error exit delayed from previous errors. > > [momac13:/ stevenmckinney] > > > > > > I see the following symlinks set up in > /Library/Frameworks/R.framework > > > > [momac13:/Library/Frameworks/R.framework stevenmckinney] > > $ ls -alF > > total 40 > > drwxrwxr-x@ 8 root admin 272 21 Oct 2008 ./ > > drwxrwxr-x@ 12 root admin 408 21 Oct 2008 ../ > > lrwxr-xr-x 1 root admin 24 19 Apr 14:57 Headers@ -> > Versions/Current/Headers > > lrwxr-xr-x 1 root admin 30 19 Apr 14:57 Libraries@ -> > Versions/Current/Resources/lib > > lrwxr-xr-x 1 root admin 31 19 Apr 14:57 PrivateHeaders@ -> > Versions/Current/PrivateHeaders > > lrwxr-xr-x 1 root admin 18 19 Apr 14:57 R@ -> Versions/Current/R > > lrwxr-xr-x 1 root admin 26 21 Oct 2008 Resources@ -> > Versions/Current/Resources > > drwxrwxr-x 7 root admin 238 19 Apr 14:57 Versions/ > > > > > >> sessionInfo() > > R version 2.10.1 Patched (2010-04-07 r51689) > > x86_64-apple-darwin9.8.0 > > > > locale: > > [1] en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > >> > > > > > > > > > > Steven McKinney > > > > Statistician > > Molecular Oncology and Breast Cancer Program > > British Columbia Cancer Research Centre > > > > email: smckinney +at+ bccrc +dot+ ca > > > > tel: 604-675-8000 x7561 > > > > BCCRC > > Molecular Oncology > > 675 West 10th Ave, Floor 4 > > Vancouver B.C. > > V5Z 1L3 > > Canada > > > > _______________________________________________ > > R-SIG-Mac mailing list > > R-SIG-Mac@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > > > > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac
