rJava 未在 R 中加载

Question

所以基本上这是我在调用 rJava 时遇到的错误：

库（rJava） 错误：“rJava”的包或命名空间加载失败： .onLoad 在“rJava”的 loadNamespace() 中失败，详细信息： 调用： dyn.load(file, DLLpath = DLLpath, ...) 错误：无法加载共享对象'/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so'： dlopen（/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so, 6）：未加载库：/Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents /Home/lib/server/libjvm.dylib 引用自：/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so 原因：找不到图片

以下是我在解决问题时运行的一些 R & Terminal 脚本：

1) 这也返回错误

$ sudo R CMD javareconf
Password:
Java interpreter : /usr/bin/java
Java version     : 13.0.1
Java home path   : /Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home
Java compiler    : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar

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. -ljvm
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/include/darwin  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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. -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: library not found for -ljvm
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [conftest.so] Error 1
Unable to compile a JNI program


JAVA_HOME        : /Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home
Java library path:
JNI cpp flags    :
JNI linker flags :
Updating Java configuration in /Library/Frameworks/R.framework/Resources
Done.

2)

> Sys.setenv(JAVA_HOME='/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home')
> dyn.load('/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/lib/server/libjvm.dylib')

3)

$ sudo ln -f -s $(/usr/libexec/java_home)/lib/server/libjvm.dylib /usr/local/lib

如果这有帮助：

> Sys.getenv("DYLD_FALLBACK_LIBRARY_PATH")
[1] "/Library/Frameworks/R.framework/Resources/lib:/Users/paulwoo/lib:/usr/local/lib:/usr/lib:::/lib:/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/lib/server"
> Sys.getenv("DYLD_LIBRARY_PATH")
[1] "/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/lib/server"

然而这些都没有解决问题。我也多次重新安装了 rJava 包。我最好的猜测是这与版本之间的不匹配有关，但我不知道该怎么办。

还有其他建议吗？

Answer 1

使用OSX uninstaller tool 核对您当前安装的 JDK。

Reinstall（打开）JDK

brew tap AdoptOpenJDK/openjdk
brew install adoptopenjdk13-openj9-large

然后重新配置RJava：

sudo R CMD javareconf

这应该可以解决问题。