CODEWITHSUNDEEP
rmacosrodbc
davidf18
davidf18

Reputation: 31

Install RODBC Mac OS Sierra 10.12.3

Fresh install at 10.12.1 with upgrades to 10.12.3.

I did the brew install unixodbc.

I then tried R CMD INSTALL RODBC_1.3-14.tar.gz with error:

checking for gcc... /usr/local/opt/llvm/bin/clang -fopenmp checking whether the C compiler works... no configure: error: in `/private/var/folders/7f/3n9kqyy13glcwlrx7h8cb5dc0000gn/T/RtmpYQnA2y/R.INSTALL354a771740af/RODBC': configure: error: C compiler cannot create executables See `config.log' for more details ERROR: configuration failed for package ‘RODBC’

I then unpacked RODBC and tried to ./configure and got the following error message in the log:

configure:2690: /usr/local/opt/llvm/bin/clang -fopenmp -v >&5 clang version 3.9.1 (tags/RELEASE_391/final) Target: x86_64-apple-darwin16.4.0 Thread model: posix InstalledDir: /usr/local/opt/llvm/bin configure:2701: $? = 0 configure:2690: /usr/local/opt/llvm/bin/clang -fopenmp -V >&5 clang: error: argument to '-V' is missing (expected 1 value) clang: error: no input files configure:2701: $? = 1 configure:2690: /usr/local/opt/llvm/bin/clang -fopenmp -qversion >&5 clang: error: unknown argument: '-qversion' clang: error: no input files configure:2701: $? = 1 configure:2721: checking whether the C compiler works configure:2743: /usr/local/opt/llvm/bin/clang -fopenmp -Wall -mtune=core2 -g -O2 -I/usr/local/opt/llvm/include -I. conftest.c >&5 ld: library not found for -lomp clang: error: linker command failed with exit code 1 (use -v to see invocation) configure:2747: $? = 1 configure:2785: result: no

Upvotes: 0

Views: 384

Answers (1)

ryguy
ryguy

Reputation: 11

I had the same issue For me, the problem was that the R installer was relying on the clang compiler that shipped with OS X (Sierra, 10.12.4), which does not support openmp.

I also couldn't get any of the usual means for specifying a different compiler to configure to work (such as examples here) because, as it turns out, RODBC's configure script is hard-coded to use the compilers and lib/include paths specified by your R installation, which are described here.

I was able to resolve the problem by editing ~/.R/Makevars to point to a version of gcc I installed via macports (sudo port install gcc6), as such:

CC=/opt/local/bin/gcc-mp-6 -fopenmp
CXX=/opt/local/bin/g++-mp-6
LDFLAGS=-L/opt/local/lib -L/usr/local/opt/llvm/lib
CPPFLAGS=-I/opt/local/include -I/usr/local/opt/llvm/include

Then the normal installation process (R CMD INSTALL ./RODBC_1.3-15.tar.gz) worked as expected.

Upvotes: 1

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