[R-SIG-Mac] Package "spdep" Compilation Failed on Mac 10.9, R 3.1.0

[Prof Brian Ripley]

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
>
>
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>


-- 
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