带有OS Sierra的R(3.4.1)中的rJava加载 [英] rJava loading in R(3.4.1) with OS Sierra
问题描述
我在最新版本的R(3.4.1)，Mac(10.12.5)和Java VM(1.8.0_131，x86_64 :)中遇到了rJava的问题
问题:
我尝试按照本指南进行操作
I try it to follow this guide
scottdhoover.wordpress.com/2013/03/05/a-basic-rjava-example/
scottdhoover.wordpress.com/2013/03/05/a-basic-rjava-example/
为了能够在R中运行rJava.
To be able to run rJava in R.
r中的一些代码:
库(rJava) .jinit(") .jclassPath() [1]"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/java"
library(rJava) .jinit("") .jclassPath() [1] "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/java"
s<-.jnew("java/lang/String"，"Hello World！") .jcall(s，"I"，"length") [1] 12
s <- .jnew("java/lang/String", "Hello World!") .jcall(s, "I", "length") [1] 12
实际上正在工作..但是当我尝试使用我的文件时:
So is actually working.. but when I try with my files:
.jaddClassPath("/Users/Camilo/Desktop/20170711_Java2R") .jclassPath() [1]"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/java""/Users/Camilo/Desktop/20170711_Java2R"
.jaddClassPath("/Users/Camilo/Desktop/20170711_Java2R") .jclassPath() [1] "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava/java" "/Users/Camilo/Desktop/20170711_Java2R"
myExchange<-.jnew("myExchange") .jnew("myExchange")中的错误:java.lang.ClassNotFoundException
myExchange <- .jnew("myExchange") Error in .jnew("myExchange") : java.lang.ClassNotFoundException
文件myExchange.java与指南中的文件相同，并且位于桌面的文件夹中.
where the file myExchange.java is the same that in the guide and is in the folder in the Desktop.
我所做的事情:
基本上，我尝试从R安装rJava，但没有用.然后，我遵循了两个指南，能够从源代码中将RJava包r
Basically I tried to instal rJava from R and didn't work. Then I have follow two guides to be able to load the package rJava in R from source
我已遵循本指南:
https://github.com/snowflakedb/dplyr-snowflakedb/wiki/Configuring-R-rJava-RJDBC-on-Mac-OS-X (能够加载rJava)
https://github.com/snowflakedb/dplyr-snowflakedb/wiki/Configuring-R-rJava-RJDBC-on-Mac-OS-X (To be able to load rJava)
两者都
R CMD javareconf
/usr/libexec/java_home -V
看起来完全一样.
要摆脱人们通常遇到的OpenMP问题，请遵循以下指南:
To get rid of the OpenMP problem that people normally have I follow this guide:
http://thecoatlessprofessor.com/programming/openmp-in-r-on-os-x/#clang-before-3-4-0 (摆脱所有人都有的OpenMP问题).
http://thecoatlessprofessor.com/programming/openmp-in-r-on-os-x/#clang-before-3-4-0 (To get rid with the OpenMP problem that all people have).
最后，我使用此代码创建符号链接
and Finally I create a symlink using this code
sudo ln -f -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib
并且我能够从R安装库.
and I was able to install the library from R.
但是！当我从终端尝试时，出现此错误
But! When I try it from terminal I get this error
ld: library not found for -lomp
clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [libjri.jnilib] Error 1
make[1]: *** [src/JRI.jar] Error 2
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’
所以我坚强:库或符号链接也必须丢失..但是没有llvm中的文件(已经在llvm中使用
So I tought: A library or a symlink must to be missing too.. but there is not such a file as in llvm ( Have been solve in llvm with ld: library not found for -lomp )
我知道错误"ClassNotFoundExceptions"可能与PATH有关，但应该可以，因为开始时已经声明了cos.
I know that the error "ClassNotFoundExceptions" could be related with the PATH but It should be OK cos has been declared at the beginning.
顺便说一句，我还检查了如下所示的.R/Makevars文件
btw, I also check the .R/Makevars file that looks like this
CC=/usr/local/clang4/bin/clang
CXX=/usr/local/clang4/bin/clang++
LDFLAGS=-L/usr/local/clang4/lib
任何想法如何解决?提前致谢！我希望这很清楚.
Any ideas how to solve it? Thanks in advance! I hope that is clear.
推荐答案
For me the solution was to install https://github.com/coatless/r-macos-clang and add link
sudo ln -s /usr/local/clang4/lib/libomp.dylib /usr/local/lib/libomp.dylib
在R CMD javareconf我unset JAVA_HOME之前.
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