- [R封装C / C ++和OpenMP：如何让＆QUOT; Makevars＆QUOT;根据＆QUOT文件; mypackage的/ src目录/＆QUOT;夹？ [英] R package with C/C++ and openMP: how to make "Makevars" file under "mypackage/src/" folder?

问题描述

我正在开发Mac OSX上的R封装的一些低级别 C / C ++ code和的OpenMP 支持。在 C ++ code使用 RCPP 包写的。我的世界Makevars'文件被放置在〜/ .R / 文件夹中。该文件看起来像下面。

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

一切都在这种配置下的伟大工程！

Everything works great under this configuration!

不过，现在我想建立包特定的 Makevars 文件为自己编译，使包便于携带。我试过被简单地移动全球 Makevars 文件到我的řpakcage 的src 文件夹中。但是，编译器抱怨它找不到OpenMP的头文件 omp.h ：

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

正如你所看到的，编译器成了铛和铛++ ，而在<$ C指定不算什么$ C> Makevars 文件： CC =铛-OMP 和 CXX =铛 - OMP ++

问题1：所以，我怎么能解决这个问题，并建立一个 Makevars 第r包内的文件

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

另一件事是，我是从的写R附加的是，

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)

问题2：之间有什么区别，例如，宏 $（SHLIB_OPENMP_CFLAGS）和标记 -fopenmp ？其中一个下情况，我应该使用？我试图与宏更换标志，但仍无法修复该问题。

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.

推荐答案

关于议题，我最喜欢的办法是从工作包复制。这里是如部分来自（推荐/核心）封装mgcv：

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)

我自己和Andreas用在较小的 winsorize 包（在GitHub上）相同的片段。

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

关于问题2：第一种形式是更普遍并允许其他OpenMP的实现。它采用什么ř发现它被配置时是可用的。

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.

这篇关于 - [R封装C / C ++和OpenMP：如何让＆QUOT; Makevars＆QUOT;根据＆QUOT文件; mypackage的/ src目录/＆QUOT;夹？的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！