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.
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.
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.
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