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
>
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