I'm trying to install an R package called rcdd using conda build and there is a problem with the C compiler. Note that this problem looks very similar to
Conda build R package fails at C compiler issue on MacOS Mojave however as (i) that question remains unanswered, and (ii) this relates to different package, I think this is not a duplicate question.
I'm using MacOS Mojave, conda 4.6.8. In a new conda environment with r-base and r-essentials
installed, I try
conda install conda-build
conda skeleton cran --recursive rcdd
conda build r-rcdd
and get the following error
* installing *source* package ‘rcdd’ ...
** package ‘rcdd’ successfully unpacked and MD5 sums checked
checking for gcc... x86_64-apple-darwin13.4.0-clang
checking whether the C compiler works... no
configure: error: in `/Users/pjethwa/miniconda3/envs/r_env/conda-bld/r-rcdd_1553173041138/work':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘rcdd’
The config.log file contains the same error message. This same error also appears when I try to install directly from R - i.e. using install.packages('rcdd'). I am able, however, to install this package using a version of R which was not installed by conda. This solution is unsatisfactory as I would like to use rpy2 to interface python and R, which seems to require that R be installed by conda (e.g. see Getting Segmentation fault Core dumped error while importing robjects from rpy2)
My clang/gcc versions are:
(r_env) myusername:~ clang --version
clang version 4.0.1 (tags/RELEASE_401/final)
Target: x86_64-apple-darwin18.2.0
Thread model: posix
InstalledDir: /Users/myusername/miniconda3/envs/r_env/bin
(r_env) myusername:~ gcc --version
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 10.0.0 (clang-1000.10.44.4)
Target: x86_64-apple-darwin18.2.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
