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I am developing an R package on Mac OSX with some low level C/C++ code and openMP support. The C++ code is written using Rcpp package. My global ''Makevars'' file is placed under ~/.R/ folder. The file looks like following.

CC=clang-omp
CXX=clang-omp++

PKG_CFLAGS=Wall -pedantic
PKG_CFLAGS= -fopenmp
PKG_CXXFLAGS= -fopenmp
PKG_LIBS= -fopenmp -lgomp

Everything works great under this configuration!

However, now I want to build package-specific Makevars file for its own compilation to make the package portable. What I tried was simply move the global Makevars file into my R pakcage src folder. However, the compiler complained about that it cannot find the openMP header file omp.h:

** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/bigmemory/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"  -fopenmp -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
RcppExports.cpp:12:10: fatal error: 'omp.h' file not found
#include <omp.h>
         ^
1 error generated.
make: *** [RcppExports.o] Error 1
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/bigmemory/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"  -fopenmp -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
RcppExports.cpp:12:10: fatal error: 'omp.h' file not found
#include <omp.h>
         ^
1 error generated.
make: *** [RcppExports.o] Error 1

As you can see, the compilers become clang and clang++, but not what specified in the Makevars files: CC=clang-omp and CXX=clang-omp++.

Question 1: So how could I fix this issue and build a Makevars file within the R package?

Another thing is that, I noticed from Writing R extensions that,

For example, a package with C code written for OpenMP should have in src/Makevars the lines

PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS)
PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)

Question 2: What is the difference between, for example, macro $(SHLIB_OPENMP_CFLAGS) and flag -fopenmp? which one under which circumstance should I use? I tried to replace the flags with the macros, but still cannot fix the issue.

SixSigma
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2 Answers2

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Regarding question, my favourite approach is to copy from working packages. Here is eg the part from (recommended / Core) package mgcv:

PKG_LIBS =  $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CFLAGS)
PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS)

I use the same snippet in the smaller winsorize package (on GitHub) by myself and Andreas.

Regarding question 2: The first form is more general and would allow other OpenMP implementations. It uses what R found to be useable when it was configured.

Dirk Eddelbuettel
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  • thanks for the answer, Dirk. Regarding Question 1, my problem is that, if I put ``Makevars`` under ``/src/`` folder instead of the default ``~/.R``, then the specifications of using ``clang-omp`` and ``clang-omp++`` compilers don't work, as shown in the error message. Do you have any clues on that? This issue seems have nothing to do with how I set up the flags (or macros). – SixSigma Oct 07 '15 at 02:49
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    You seem confused. Forget `~/.R/Makevars` for the package. All it needs has to be in its `src/Makevars`, and (in the case of CRAN packages) has to be portable. So don't assume you get `clang-ANYTHING`. Test for it via `configure` if you must. The r-package-devel list may be able to help somewhat. – Dirk Eddelbuettel Oct 07 '15 at 02:52
0

It sounds like you need the package Makevars as Dirk describes; for your local environment, have ~/.R/Makevars setting your C and C++ compilers to your OpenMP enabled versions using CC and CXX.

Your package (if destined for CRAN, and indeed any Mac R users who haven't battled to install an OpenMP version of clang) will need to work without OpenMP, so your code and compiler flags probably shouldn't assume its presence.

Jack Wasey
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