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Turning off universal package building
3 messages · Sean Davis, Greg Finak
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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