[R-SIG-Mac] Failed tar extract
Steven McKinney
smckinney at bccrc.ca
Tue Apr 20 04:42:14 CEST 2010
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-bounces at stat.math.ethz.ch [mailto:r-sig-mac-
> bounces at stat.math.ethz.ch] On Behalf Of Steven McKinney
> Sent: Monday, April 19, 2010 6:46 PM
> To: Simon Urbanek
> 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
>
> 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
>
> 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
> >
> >
>
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