Bouncing to the list after failing to reply-all On Thu, Sep 10, 2009 at 5:25 PM, Simon Urbanek
<simon.urbanek at r-project.org> 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 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). So I installed the 32/64 Universal 2.9.0, but now building any package gives errors [1] perhaps because SL doesn't install ppc64 libraries? 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? [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]