MAC安装rJava混乱问题

2019-09-28 本文已影响0人 PriscillaBai

报错如下：

configure: error: Cannot compile a simple JNI program. See config.log for details.
Make sure you have Java Development Kit installed and correctly registered in R.
If in doubt, re-run "R CMD javareconf" as root.
ERROR: configuration failed for package ‘rJava’ * removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rJava’ * restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rJava’

主要原因是R，rJava, Java, macOS的内部混乱。当Java遇到了MAC OS，就注定会发生混乱。首先，你需要明白，MAC里的Java有两个版本：Oracle based 或system based。

Java framework reside:
/System/Library/Frameworks/JavaVM.framework

Oracle based Java will be installed:
/Library/Java/JavaVirtualMachines

所以说，如果你想在R中合理的配置JAVA，你就必须做一些调整。首先，你必须配置Java_home。

/usr/libexec/java_home -V
Matching Java Virtual Machines (2):
1.8.0_11, x86_64: "Java SE 8" /Library/Java/JavaVirtualMachines/jdk1.8.0_11.jdk/Contents/Home
1.8.0_05, x86_64: "Java SE 8" /Library/Java/JavaVirtualMachines/jdk1.8.0_05.jdk/Contents/Home

但是，如果你想在R中用JDK，就会遇到bug了。首先，在R中运行Java：

sudo R CMD javareconf

由于javareconf认定只要你的java_home和"/Home"匹配，就会默认用系统中的java，而不是oracle的java。这时事情就会变得很奇怪了，一半是JDK，一半是苹果系统中的JVM。所以，为了避免这个问题，你需要创造“伪路径”，即没有"/Home$"字符的路径。

cd /Library/Java/JavaVirtualMachines/jdk1.8.0_11.jdk/Contents
ln -s Home RHome

然后，你将其输出为Java_home

export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_11.jdk/Contents/RHome

然后，用以下命令配置javareconf

sudo R CMD javareconf
JAVA_HOME= ${JAVA_HOME} \ JAVA=$ {JAVA_HOME}/bin/java
JAVAC= ${JAVA_HOME}/bin/javac \ JAVAH=$ {JAVA_HOME}/bin/javah
JAR= ${JAVA_HOME}/bin/jar \ JAVA_LD_LIBRARY_PATH=$ {JAVA_HOME}/jre/lib/server
JAVA_CPPFLAGS="-I ${JAVA_HOME}/include -I$ {JAVA_HOME}/include/darwin"