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.urbanek at r-project.org]
Sent: April 19, 2010 6:26 PM
To: Steven McKinney
Cc: R-SIG-Mac at stat.math.ethz.ch
Subject: Re: [R-SIG-Mac] Failed tar extract due to symlinks put in place by Rswitch
Sent: April 19, 2010 6:26 PM
To: Steven McKinney
Cc: R-SIG-Mac at 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 at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > >