用于安装R软件包的备用编译器：clang：错误：不支持的选项'-fopenmp'

问题描述

我正在尝试使用R版本3.4.0在OS X 10.11.6上安装rJava包：

I am trying to install the rJava package on OS X 10.11.6 with R version 3.4.0:

install.packages("rJava", type = "source")

我收到以下错误：

clang -o libjri.jnilib Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o  -dynamiclib -framework JavaVM -fopenmp -L/usr/local/lib -F/Library/Frameworks/R.framework/.. -framework R -lpcre -llzma -lbz2 -lz -licucore -lm -liconv    
clang: error: unsupported option '-fopenmp'
make[2]: *** [libjri.jnilib] Error 1
make[1]: *** [src/JRI.jar] Error 2
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’

据我所知，clang被用作编译器，使用'fopenmp'，而clang似乎不支持它。任何人都可以看到解决这个问题的方法，可能会强制使用不同的编译器吗？ （注意：我对编译器几乎一无所知）

From what I can tell, clang is being used as the compiler, using 'fopenmp' which doesn't appear to be supported by clang. Can anyone see a way around this, potentially forcing a different compiler to be used? (note: I know almost nothing about compilers)

提前致谢。

推荐答案

这是因为R 3.4.0是由CRAN编译的llvm-4.0.0（支持OpenMP），但Apple的fork（默认安装在macOS上）不支持OpenMP。有三种解决方案

This is caused because R 3.4.0 is compiled by CRAN with llvm-4.0.0 (which supports OpenMP), but Apple's fork (installed by default on macOS) does not support OpenMP. There are three solutions

1. 使用CRAN提供的包二进制文件，例如 install.packages（type =binary）。


2. 安装支持OpenMP的编译器，例如来自hombrew的gcc或clang ，但是你还必须修改个人makevars文件中的变量（〜/ .R / Makevars ）。


3. 取消设置 SHLIB_OPENMP_CFLAGS 和 SHLIB_OPENMP_CXXFLAGS 在您的〜/ .R / Makevars

1. Use the package binaries provided by CRAN, e.g. install.packages(type = "binary").
2. Install a compiler that does support OpenMP, such as gcc or clang from hombrew, however you will also have to modify variables in your personal makevars file (~/.R/Makevars).
3. Unset SHLIB_OPENMP_CFLAGS and SHLIB_OPENMP_CXXFLAGS in your ~/.R/Makevars

对于2.您可以使用 brew install clang 或<$ c安装编译器$ c> brew install gcc --without-multilib 然后你必须将编译器路径添加到〜/ .R / Makevars 文件中。

For 2. you can install the compilers with brew install clang or brew install gcc --without-multilib then you will have to add the compiler path to your ~/.R/Makevars file.

CC=/usr/local/opt/llvm/bin/clang
CXX=/usr/local/opt/llvm/bin/clang++
# Also potentially CXX11 (for C++11 compiler)
CXX11=/usr/local/opt/llvm/bin/clang++

或 gcc 使用（仔细检查gcc可执行文件并正确命名）

or for gcc use (double check gcc executable exists and is correctly named)

CC=/usr/local/bin/gcc-7
CXX=/usr/local/bin/gcc-7
# Also potentially CXX11 (for C++11 compiler)
CXX11=/usr/local/bin/gcc-7

您也可以安装并正确设置 Makevars 文件。

Alternatively you can install a CRAN Provided LLVM 4.0 and set the Makevars file appropriately.

对于3.你只需要取消设置 SHLIB_OPENMP_CFLAGS

For 3. you simply need to unset the SHLIB_OPENMP_CFLAGS

SHLIB_OPENMP_CFLAGS=
SHLIB_OPENMP_CXXFLAGS=

有关详细信息，请参阅。

For more details see OpenMP support in Writing R Extensions.

注意这个错误与Java或rJava包没有任何关系，所以理想情况下问题可以重命名为 clang：error：unsupported option'-fopenmp'。

Note this error has nothing to do with Java or the rJava package in particular, so ideally the question could be renamed to clang: error: unsupported option '-fopenmp'.

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