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" <[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 > ‘/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 > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
