MacOS Sierra 10.12.15上的rJava:不支持的选项fopenmp [英] rJava on MacOS Sierra 10.12.15: unsupported option fopenmp
问题描述
我正在尝试在MacOS Sierra上安装rJava.必须尝试其他版本的MacOS的其他地方的提示和指南，例如在Mac上安装xlsx和rJava
I'm trying to install rJava on MacOS Sierra. Have to tried the tips and guides elsewhere for other other version MacOS such as https://github.com/snowflakedb/dplyr-snowflakedb/wiki/Configuring-R-rJava-RJDBC-on-Mac-OS-X and Install xlsx and rJava on Mac
，但无法解决.非常感谢您的帮助.谢谢.
but it does not work out. Much appreciate any help. Thanks.
我的Mac版本:macOS Sierra版本10.12.15 我的R版本:3.4.0(2017-04-21) 我的Rstudio版本:0.99.903版
My Mac version: macOS Sierra, version 10.12.15 My R version: 3.4.0 (2017-04-21) My Rstudio version: Version 0.99.903
Java版本:
bash-3.2$ /usr/libexec/java_home -V
bash-3.2$ java -version
java version "1.8.0_131"
Java(TM) SE Runtime Environment (build 1.8.0_131-b11)
Java HotSpot(TM) 64-Bit Server VM (build 25.131-b11, mixed mode)
bash-3.2$ R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.8.0_131
Java home path : /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Non-system Java on macOS
trying to compile and link a JNI program
detected JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/darwin
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -fPIC -Wall -g -O2 -c conftest.c -o conftest.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o conftest.so conftest.o -L/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
JAVA_HOME : /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre
Java library path: $(JAVA_HOME)/lib/server
JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/darwin
JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
Updating Java configuration in /Library/Frameworks/R.framework/Resources
override rw-r--r-- root/admin for /Library/Frameworks/R.framework/Resources/etc/Makeconf? (y/n [n]) n
not overwritten
override rw-r--r-- root/admin for /Library/Frameworks/R.framework/Resources/etc/ldpaths? (y/n [n]) n
not overwritten
Done.
当我尝试安装rJava时，我运行了
When I tried to install rJava, I ran
`R --quiet -e 'install.packages("rJava", type="source", repos="http://cran.us.r-project.org")`
我得到了错误:
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’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava’
The downloaded source packages are in
‘/private/var/folders/w8/ksbj8dh15bz2lkss7h2tpzk80000gn/T/Rtmp6r9HI0/downloaded_packages’
Warning message:
In install.packages("rJava", type = "source", repos = "http://cran.us.r-project.org") :
installation of package ‘rJava’ had non-zero exit status
我跑了:
"curl -#ROL https://www.rforge.net/rJava/snapshot/rJava_0.9-8.tar.gz
R CMD INSTALL rJava_0.9-8.tar.gz"
，并收到以下错误消息:
and got the following error messages:
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’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava’
我不知道该怎么办.感谢您的帮助.
I dont know what to do. Thanks for your help.
推荐答案
使用OSX 10.12.6和Java 1.8.0_181进行注释，处理上述问题以及与编译rJava有关的另一个问题.
Comments using OSX 10.12.6 with Java 1.8.0_181 and dealing with the above issue and another issue related to compiling rJava.
使用以下命令安装rJava:
Install rJava with these commands:
wget https://cran.r-project.org/src/contrib/rJava_0.9-10.tar.gz
tar xvfz rJava_0.9-10.tar.gz
cd rJava
R CMD INSTALL rJava
为什么要使用R CMD INSTALL?这将保留config.log文件，使您可以调试内容. install.packages()不能，并且在这种情况下对您的帮助可能不是很有用(例如 https ://github.com/su/rJava/issues/111 ).
Why use R CMD INSTALL? This will keep the config.log file that will allow you to debug things; install.packages() does not and help you get might not be very helpful in that case (e.g. https://github.com/s-u/rJava/issues/111).
如果您已更新Java，请确保运行以下命令(请记住，您需要JDK，而不是JRE).
Make sure you run the following, if you've updated Java (remember you need the JDK, not JRE).
sudo R CMD javareconf
错误(正在检查JNI数据类型):
要纠正此错误，请执行以下操作:
Error (checking JNI data types):
To fix this error:
checking JNI data types... configure: error: One or more JNI types differ from the corresponding native type. You may need to use non-standard compiler flags or a different compiler in order to fix this.
执行以下操作:
sudo ln -f -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib
sudo ln -f -s /usr/local/lib/libjvm.dylib /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/
错误(不支持的选项'-fopenmp):
要纠正此错误，请执行以下操作:
Error (unsupported option '-fopenmp):
To fix this error:
clang: error: unsupported option '-fopenmp
执行以下操作:
注意:对于较新版本的gcc，可能需要修改说明，但是请确保您获得的版本大于7(请参阅以下说明)；以下命令可用于查找可用版本:
Note: The instructions may need to be modified for newer versions of gcc, but make sure you get a version greater than 7 (see notes that follow); the following command can be used to find out the available versions:
brew search gcc
然后安装gcc:
brew install gcc@7
sudo chown -R $(whoami):admin /usr/local
brew link --overwrite --force gcc@7
brew unlink gcc@7 && brew link gcc@7
brew install llvm
mkdir -p ~/.R
## Check the versions and folder in FLIBS match what you install
echo "CC=gcc-7
CXX=g++-7
CXX1X=g++-7
CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
FLIBS=-L/usr/local/Cellar/gcc\@7/7.3.0/lib/gcc/7" > ~/.R/Makevars
注意:您需要任何大于7的gcc版本.前面的答案中提到的without-multilib标志可能不可用，但这很重要.为什么不使用multilib标志?: https://thecoatlessprofessor.com /programming/openmp-in-r-on-os-x/和
Notes: You need any version of gcc greater than 7; the without-multilib flag mentioned in the earlier answer may not be available, but it is important. Why the without-multilib flag?: https://thecoatlessprofessor.com/programming/openmp-in-r-on-os-x/ and OpenMP/gcc on macOS : gcc --without-multilib not available
然后安装rJava
R CMD INSTALL rJava
最后，测试库(您应该看到Java版本):
Finally, test library (you should see your Java version):
library(rJava)
.jinit()
.jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
这篇关于MacOS Sierra 10.12.15上的rJava:不支持的选项fopenmp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！
