sudo R CMD javareconf solution不起作用

Question

我正在尝试在RStudio中运行rJava，但没有成功：

Error: package or namespace load failed for ‘rJava’:
.onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/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): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so
Reason: image not found

使用rJava问题的通用解决方案，"sudo R CMD javareconf"不起作用，并给了我这个输出：

Java interpreter : /usr/bin/java
Java version     : 11.0.6
Java home path   : /Library/Java/JavaVirtualMachines/jdk-11.0.6.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$(JAVA_HOME)/lib/server -ljvm
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk-11.0.6.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk-11.0.6.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-7: warning: no such sysroot directory: '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk' [-Wmissing-sysroot]
In file included from conftest.c:1:
/Library/Java/JavaVirtualMachines/jdk-11.0.6.jdk/Contents/Home/include/jni.h:39:10: fatal error: 
'stdio.h' file not found
#include <stdio.h>
^~~~~~~~~
1 error generated.
make: *** [conftest.o] Error 1
Unable to compile a JNI program

JAVA_HOME        : /Library/Java/JavaVirtualMachines/jdk-11.0.6.jdk/Contents/Home
Java library path: 
JNI cpp flags    : 
JNI linker flags : 
Updating Java configuration in /Library/Frameworks/R.framework/Resources
Done.

以前有没有人遇到过这个错误并知道如何解决它？

Answer 1

最近在升级到卡塔琳娜之后，我和一位同事遇到了这样的问题。我的解决方案是再次安装有问题的JDK版本。看起来您的系统在 11.0.6 和 11.0.1 之间混淆了。

1. 转到此页面： https://www.oracle.com/technetwork/java/javase/downloads/java-archive-javase11-5116896.html

2. 下载并安装 11.0.1

3. sudo R CMD javareconf

4. sudo Rstudio # elevate privs

5. install.packages("rJava"(

如果这不起作用，请从步骤 2 重试，但使用 https://www.oracle.com/technetwork/java/javase/overview/index.html 中的 11.0.6

Answer 2

最后的诀窍是向 Rstudio 展示用户 Rmadillo 在此处识别的位置：

github.com/rstudio/rstudio/issues/2254

只需在使用 rJava 包之前每次运行它即可。