Dear Prof. Ripley,

Thanks for your help. Yes, I will check the manual for the building
parameters. For the Fortran compile, I am using
gfortran-4.2.3.pkg<http://cran.r-project.org/bin/macosx/tools/gfortran-4.2.3.pkg>
provided
here http://cran.r-project.org/bin/macosx/tools/. It seems to be
out-dated...

For R version, I was using *R 3.1.0* binary for Mac OS X 10.9 (Mavericks),
if that matters.

Thanks again for your help. I will try that!
Allen




On Mon, Apr 21, 2014 at 4:12 PM, Prof Brian Ripley <ripley@stats.ox.ac.uk>wrote:

> 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 â€˜spdepâ€™
>>
>>
>> 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@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>>
>
> --
> Brian D. Ripley,                  ripley@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
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>



-- 
林轶伦 LIN, Yilun (Allen)

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