________________________________________
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
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