[R-SIG-Mac] Turning off universal package building

[Finak, Greg]

Hi, Sean
I've had similar issues with x86_64. Passing --no-multiarch on the command line to R CMD INSTALL, or via the INSTALl_opts argument to install.packages() did the trick. Your mileage may vary.

Best,
Greg

Greg Finak, Ph.D
Post-doctoral Fellow
Vaccine and Infectious Disease Division
Fred Hutchinson Cancer Research Center
Seattle, WA


On 2011-12-20, at 8:42 AM, "Sean Davis" <sdavis2 at mail.nih.gov> wrote:

> I am running into an issue that I do not understand.  I am trying to
> install GEOquery from source using a relatively recent R development
> version (2011-12-06).  GEOquery depends on the XML package.  XML installs
> fine for i386 on my Mac Pro laptop, but not for the other two architectures
> (we can ignore the details of why for now).  When I try to install
> GEOquery, this is what I see:
> 
> $ R --arch=i386 CMD INSTALL GEOquery.tar.gz
> * installing to library
> ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’
> * installing *source* package ‘GEOquery’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices ...
> *** tangling vignette sources ...
>   ‘GEOquery.Rnw’
> ** testing if installed package can be loaded
> *** arch - i386
> Setting options('download.file.method.GEOquery'='curl')
> *** arch - ppc
> Error in paste0("(^|[^%])(%%)*%", spec) : not a BUILTIN function
> Calls: Sys.setenv -> .expand_R_libs_env_var -> expand -> gsub -> paste0
> Execution halted
> *** arch - x86_64
> Error : .onLoad failed in loadNamespace() for 'XML', details:
>  call: library.dynam("XML", pkgname, libname)
>  error: shared object ‘XML.so’ not found
> Error: loading failed
> Execution halted
> ERROR: loading failed for ‘ppc’, ‘x86_64’
> * removing
> ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/GEOquery’
> * restoring previous
> ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/GEOquery’
> 
> Why is R trying to install all three architectures when I have asked for
> only i386?  So, how can I install for i386 only?  I'm sure the answer is
> well-documented somewhere, but I have not yet found it.
> 
> Thanks,
> Sean
> 
>> sessionInfo()
> R Under development (unstable) (2011-12-06 r57839)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
>    [[alternative HTML version deleted]]
> 
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