[R-SIG-Mac] Failed tar extract

Simon Urbanek simon.urbanek at r-project.org
Tue Apr 20 15:50:42 CEST 2010 

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-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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