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Package "spdep" Compilation Failed on Mac 10.9, R 3.1.0
3 messages · Brian Ripley, Allen Lin
On 21/04/2014 21:44, Allen Lin wrote:
Hi all, I am new to this community so sorry if this question has already been answered.
Yes, in the R-admin manual. 'The current CRAN ?Mavericks? distribution of R is built using CC=clang CXX=clang++ F77=gfortran-4.8 FC=$F77 OBJC=clang with clang and clang++ from Xcode 5, and the Fortran compiler from http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2.' It seems you have not installed that Fortran compiler. (I am guessing: you did not tell us how your R was built, or if a binary installation from CRAN, which one.)
I was trying to build the spdep package from source. However, I encountered error message like the following: clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o spdep.so card.o dfs_ncomp.o dnn.o gabriel.o gearyw.o gsymtest.o init.o insiders.o jc.o knn.o lagw.o listw2Matrix.o listw2sn.o ml_sse.o mom_calc.o nbdists.o polypoly.o relative.o skater.o soigraph.o symtest.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2' ld: library not found for -lquadmath clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [spdep.so] Error 1 ERROR: compilation failed for package ???spdep??? I checked my L/usr/local/lib/gcc/ directory, there is no folder, but there are i686-apple-darwin8 powerpc-apple-darwin8. I suspect this is because on the native gcc with Xcode command line tool is version 4.2. But when I run gcc -v it shows: Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn) Target: x86_64-apple-darwin13.1.0 Thread model: posix How could I point it to the correct directory? Any thoughts will be greatly appreciated! I am totally lost.. Thanks, Allen
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Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
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