Message-ID: <A7A25B52-BEA7-46A9-B6F5-5307EDE6A73A@fhcrc.org>
Date: 2011-12-20T14:08:34Z
From: Greg Finak
Subject: Turning off universal package building
In-Reply-To: <CANeAVB=66s08kn=M1hOJ5BR=xLGC6T8=bAOLPLkN2RT990zCUw@mail.gmail.com>
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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