Compilation error with cpp in R - r

Question

I recently "upgraded" to XCode 5.2 and now a number of R packages will not work. I have a 15" MBP running OSX Mavericks 10.9.1 and am running R 3.0.2.
First, the mcmc function in the package diversitree broke and gave the following error:
Error in .External(list(name = "CppMethod__invoke_notvoid", address = <pointer: 0x0>, :
NULL value passed as symbol address
Furthermore, I cannot compile the package "geomorph" from source, and I get the following error:
clang: error: no such file or directory: 'SHLIB_LIBADD'
clang: error: no such file or directory: '='
make: *** [geomorph.so] Error 1
ERROR: compilation failed for package ‘geomorph’
So I believe the error is somewhere in the compilers. I tested this idea with:
> require(Rcpp)
> evalCpp("1+1")
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Users/Chris/Library/R/3.0/library/Rcpp/include" -fPIC "-mtune=native -g -O2 -Wall -pedantic -Wconversion" -c file177c642d0b53.cpp -o file177c642d0b53.o clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o sourceCpp_1783.so file177c642d0b53.o /Users/Chris/Library/R/3.0/library/Rcpp/lib/libRcpp.a SHLIB_LIBADD = -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Error in sourceCpp(code = code, env = env, rebuild = rebuild, showOutput = showOutput, :
Error 1 occurred building shared library.
WARNING: The tools required to build C++ code for R were not found.
Please install Command Line Tools for XCode (or equivalent).
clang: error: no such file or directory: 'SHLIB_LIBADD'
clang: error: no such file or directory: '='
make: *** [sourceCpp_1783.so] Error 1
Also this:
has_devel()
'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla \
CMD SHLIB foo.c
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC "-mtune=native -g -O2 -Wall -pedantic -Wconversion" -c foo.c -o foo.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o foo.so foo.o SHLIB_LIBADD = -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: error: no such file or directory: 'SHLIB_LIBADD'
Error: Command failed (1)
clang: error: no such file or directory: '='
make: *** [foo.so] Error 1
I tried reinstalling Rcpp from source and that fails too:
clang: error: no such file or directory: 'SHLIB_LIBADD'
clang: error: no such file or directory: '='
make: *** [Rcpp.so] Error 1
I've spent hours now trying to troubleshoot this and I've run across numerous mentions of editing the Makeconf file to add clang. I have done this but still cannot get things that use C in R to work. I would greatly appreciate any help.

Answer 1

Are you using a CRAN-provided binary of R, or your own compiled version of R? Did you compile R with your new XCode compilers or the old ones?
My experience is that CRAN-R will work fine with a specific compiler toolchain, as long as you use the same toolchain for all the packages you compile. If you, for example, try to link a new-XCode compiled package to an old-XCode compiled Rcpp, you will have problems.
Your SHLIB_LIBADD error, as far as I can guess, says you did something weird in your Makevars or Makeconf and now things are going wrong in parsing the files. I'd be curious to see if you can reproduce this with a fresh, CRAN-provided R.
Can you reproduce the problem if you try to re-install R + all your packages? You should try re-installing R with a fresh library directory, and then re-installing these problematic packages, and going from there.