On Apr 19, 2010, at 10:42 PM, Steven McKinney wrote: > > 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. >
It doesn't really matter because the devpack simply contains files that are otherwise shipped with R. I didn't get to see why it's not following the symlinks but if you install R form CRAN (or the nightly builds) you get those files anyway so you should be fine. BTW: in addition to the devpack there are many other libraries in http://r.research.att.com/libs/ which can be useful depending on the type of packages you're compiling from source. Thanks, Simon > > >> -----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
