On Fri, Sep 11, 2009 at 6:32 AM, Simon Urbanek <[email protected]> wrote: > Peter, > > On Sep 11, 2009, at 2:05 AM, Peter Cowan wrote: > >> Bouncing to the list after failing to reply-all >> >> On Thu, Sep 10, 2009 at 5:25 PM, Simon Urbanek >> <[email protected]> wrote: >>> >>> Peter, >>> >>> you have probably compiled ncl in 64-bit (default on SL) but you're using >>> 32-bit R, so it won't work. Either use 64-bit R or compile ncl for >>> 32-bit. >> >> I suspected something obvious of the like. Unfortunately, I've not been >> able to get 64 bit R working for me. When I try the following for the CRAN >> version: >> >> Birch$ R --arch x86_64 >> /usr/bin/R: line 207: >> /Library/Frameworks/R.framework/Resources/etc/x86_64/ldpaths: No such >> file or directory >> > > Yes, CRAN R is 32-bit only.
Yes, this makes sense, but I was a bit confused by this comment on r.research.att.com "Leopard builds, 64-bit binaries and packages are becoming available from CRAN as of R 2.8.0." Does that mean r.research.att.com ? I don't find a link on CRAN. >> So I got the 2.9.2 patched version distributed as a tar.gz from >> <http://r.research.att.com/> (thanks for providing this Simon!), but that >> doesn't work with the 64bit GUI build on the same site (it won't even >> launch, because it need 2.10.0). >> > > Oh, true, the 2.9 GUI is simply not there. I'll have to look to see what > went wrong. Thanks! > >> So I installed the 32/64 Universal 2.9.0, > > [BTW: you can simply overwrite the installation with the 2.9.2 patched > binary to upgrade it - the only part you really needed from the universal > package was the GUI] Okay, I was concerned there might be a version mismatch between 2.9.2 and the 2.9.0 gui so I didn't do that. BTW is the repository for the GUI public? I see the .tar on CRAN. > >> but now building any package gives errors [1] perhaps because SL doesn't >> install ppc64 libraries? > > Yes, unfortunately. The hot fix is > rm -rf /Library/Frameworks/R.framework/Resources/bin/exec/ppc* Brilliant! This works perfectly. Thank you for not only contributing software but patiently helping me understand it. Peter >> I the same (or similar warning) using the R-devel nightly. >> >> I apologize if this to is obvious. When I install xcode, do I need to >> install the tools for prior OSs to get ppc compilers? >> > > The compilers are there all right, it's the libraries that are missing. They > are now only part of the 10.5 SDK in Xcode which is not used by R. > > Cheers, > Simon > > >> [1] >> ====== >> (WARNING: partial output only, ask package author to use Rprintf instead!) >> newick.c: In function ‘readNewickString’: >> newick.c:233: warning: format not a string literal and no format arguments >> ld: warning: in /usr/lib/dylib1.10.5.o, missing required architecture >> ppc64 in file >> ld: warning: in /usr/lib/libSystemStubs.a, missing required >> architecture ppc64 in file >> ld: warning: in >> /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation, >> missing required architecture ppc64 in file >> ld: warning: in /usr/lib/libSystem.dylib, missing required >> architecture ppc64 in file >> ld: in /usr/lib/libSystem.B.dylib, missing required architecture ppc64 in >> file >> collect2: ld returned 1 exit status >> make: *** [ape.so] Error 1 >> ERROR: compilation failed for package ‘ape’ >> * Removing >> ‘/Library/Frameworks/R.framework/Versions/2.9/Resources/library/ape’ >> * Restoring previous >> ‘/Library/Frameworks/R.framework/Versions/2.9/Resources/library/ape’ >> ======== >> >> >>> Cheers, >>> Simon >>> >>> >>> On Sep 10, 2009, at 7:58 PM, Peter Cowan wrote: >>> >>>> I'm running 10.6 from clean install, with the supplied Xcode, and R >>>> 2.9.2. I am unable to build a package (specifically the phylobase >>>> package [1]) which built fine under 10.5.8. Even more confusingly it >>>> seems to build fine for others using 10.6. The end of the install >>>> log (appended below) contains the these potentially informative >>>> errors: >>>> >>>> ld: warning: in ncl/ncl/.libs/libncl.a, file is not of required >>>> architecture >>>> ld: warning: duplicate dylib /usr/local/lib/libgcc_s.1.dylib >>>> >>>> The latter error I get with any source package, but doesn't seem to >>>> prevent them from being installed. >>>> >>>> The package also makes use of the Rcpp interface to use an included >>>> library (NCL). It is this included library that seems to not build >>>> correctly, which could very well be related to the old version of >>>> Rcpp, or the makefiles responsible for building it. >>>> >>>> I've tried all manner of tweaking, upgrading, and list searching, but >>>> the (probably obvious) solution still eludes me. Any pointers in the >>>> right direction are greatly appreciated. >>>> >>>> Peter >>>> >>>> [1] https://r-forge.r-project.org/projects/phylobase/ >>>> ========================= >>>>> >>>>> sessionInfo() >>>> >>>> R version 2.9.2 (2009-08-24) >>>> i386-apple-darwin8.11.1 >>>> >>>> locale: >>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> ========================= >>>> birch$ which gfortran >>>> /usr/local/bin/gfortran >>>> >>>> birch$ gfortran --version >>>> GNU Fortran (GCC) 4.2.3 >>>> Copyright (C) 2007 Free Software Foundation, Inc. >>>> >>>> GNU Fortran comes with NO WARRANTY, to the extent permitted by law. >>>> You may redistribute copies of GNU Fortran >>>> under the terms of the GNU General Public License. >>>> For more information about these matters, see the file named COPYING >>>> >>>> ============================ >>>> >> [original error snipped] >> >> _______________________________________________ >> 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
