On Tue, Dec 20, 2011 at 9:08 AM, Finak, Greg <[email protected]> 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" <[email protected]> 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 > > â/Library/Frameworks/R.framework/Versions/2.15/Resources/libraryâ > > * installing *source* package âGEOqueryâ ... > > ** R > > ** inst > > ** preparing package for lazy loading > > ** help > > *** installing help indices > > ** building package indices ... > > *** tangling vignette sources ... > > âGEOquery.Rnwâ > > ** 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 âXML.soâ not found > > Error: loading failed > > Execution halted > > ERROR: loading failed for âppcâ, âx86_64â > > * removing > > > â/Library/Frameworks/R.framework/Versions/2.15/Resources/library/GEOqueryâ > > * restoring previous > > > â/Library/Frameworks/R.framework/Versions/2.15/Resources/library/GEOqueryâ > > > > 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 > > [email protected] > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > [[alternative HTML version deleted]]
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