On Tue, Dec 20, 2011 at 9:08 AM, Finak, Greg <gfinak@fhcrc.org> wrote:

> 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.
>
>
R CMD INSTALL --no-multiarch ....

did the trick.

Thanks,
Sean



> 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@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]]
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>

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