如何让rJava 0.9-3在Oracle Java 1.7上运行OS X 10.7.4？

是否有人设法让r Java 0.9-3使用Oracle Java 1.7在OS X 10.7.4上工作？

R version 2.15.2 (2012-10-26) -- "Trick or Treat" Platform
x86_64-apple-darwin9.8.0/x86_64 (64-bit)

java version "1.7.0_09"
Java(TM) SE Runtime Environment (build 1.7.0_09-b05)
Java HotSpot(TM) 64-Bit Server VM (build 23.5-b02,mixed mode)

我已经使用install.packages函数和使用R 2.15.2的命令行安装来安装rJava.我没有任何错误.

$R CMD INSTALL rJava
* installing to library ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’
* installing *binary* package ‘rJava’ ...

* DONE (rJava)
$

如果我使用Java Preferences将1.7首先放在列表中,但保持1.6“on”,则rJava始终启动1.6.

如果我使用Java Preferences先放1.7并关闭1.6,rJava会这样做：

> library(rJava)
> .jinit()
JavaVM: requested Java version ((null)) not available. Using Java at "" instead.
JavaVM: Failed to load JVM: /bundle/Libraries/libserver.dylib
JavaVM FATAL: Failed to load the jvm library.
Error in .jinit() : JNI_GetCreatedJavaVMs returned -1
>

但是,使用系统函数,R本身可以找到Java 1.7.

> system("java -version")
java version "1.7.0_09"
Java(TM) SE Runtime Environment (build 1.7.0_09-b05)
Java HotSpot(TM) 64-Bit Server VM (build 23.5-b02,mixed mode)
>

1.7需要/System/Library/Java/JavaConfig.plist中的特殊条目吗？

Versions目录是否需要调整为1.7？很奇怪,Current转到A,最终得到1.7,而CurrentJDK被映射到1.6

$cd /System/Library/Frameworks/JavaVM.framework/Versions/
$ls -la
total 64
drwxr-xr-x  11 root  wheel  374 Sep 26 10:10 .
drwxr-xr-x  11 root  wheel  374 Nov 26 09:24 ..
lrwxr-xr-x   1 root  wheel   10 Sep 26 10:09 1.4 -> CurrentJDK
lrwxr-xr-x   1 root  wheel   10 Sep 26 10:09 1.4.2 -> CurrentJDK
lrwxr-xr-x   1 root  wheel   10 Sep 26 10:09 1.5 -> CurrentJDK
lrwxr-xr-x   1 root  wheel   10 Sep 26 10:09 1.5.0 -> CurrentJDK
lrwxr-xr-x   1 root  wheel   10 Sep 26 10:09 1.6 -> CurrentJDK
lrwxr-xr-x   1 root  wheel   10 Sep 26 10:09 1.6.0 -> CurrentJDK
drwxr-xr-x   8 root  wheel  272 Nov 26 09:24 A
lrwxr-xr-x   1 root  wheel    1 Sep 26 10:09 Current -> A
lrwxr-xr-x   1 root  wheel   59 Sep 26 10:09 CurrentJDK -> /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents

即使使用R CMD javareconf直接运行指向1.7文件的路径或运行/usr/bin/java路径,rJava仍然无法找到或启动Java 1.7.

1.7是否需要设置JAVA_LD_LIBRARY_PATH变量？

Makeconf:JAVA = /usr/bin/java
Makeconf:JAVAC = /usr/bin/javac
Makeconf:JAVAH = /usr/bin/javah
Makeconf:JAVA_HOME = /Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/jre
Makeconf:JAVA_LD_LIBRARY_PATH = 
Makeconf:JAVA_LIBS = -framework JavaVM
Makeconf:JAVA_CPPFLAGS = -I$(JAVA_HOME)/include

Makeconf:JAR = /Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/bin/jar
Makeconf:JAVA = /Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/jre/bin/java
Makeconf:JAVAC = /Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/bin/javac
Makeconf:JAVAH = /Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/bin/javah
Makeconf:JAVA_HOME = /Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/jre
Makeconf:JAVA_LD_LIBRARY_PATH = 
Makeconf:JAVA_LIBS = -framework JavaVM
Makeconf:JAVA_CPPFLAGS = -I$(JAVA_HOME)/include

谢谢你的帮助

更新1：

我在stats-rosuda-devel列表上问了这个问题,并收到了Simon Urbanek的以下回复.我不认为Windows和Linux在需要从源代码编译Java 1.7时遇到同样的问题,因为我们在Windows和Linux上运行它并且不必编译rJava.一旦我有机会尝试这个,我会报告回来：

You are using the binary which is compiled against system Java
(which on your system is 1.6) – so if you remove Java 1.6 you’ll break
it. If you want to use Java 1.7,you’ll have to re-configure R for
Java 1.7 and re-compile rJava to use those settings. Note that
Oracle’s Java lives in an entirely different place
(/Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk) than the system
Java (/System/Library/Frameworks/JavaVM.framework),so it is not
interchangeable.

In addition,Oracle Java 1.7 is not a framework,it’s a big mess that
was not really designed for OS X,so you have to set it by hand to
settings like on Linux – it’s pretty painful. Also it requires
overrides … so if you really want to go down the rabbit hole,this
is what worked for me:

06006

Then install rJava from sources (R64 ->
install.packages(“rJava”,type=’source’)). Note that it’s 64-bit only,
so it will only work with 64-bit R.

这对我有用：

情况是我的Java目录配置不正确.

1)首先运行：sudo R CMD javareconf.它应该如下：

Java interpreter : /usr/bin/java
Java version     : 1.7.0_40
Java home path   : /Library/Java/JavaVirtualMachines/jdk1.7.0_40.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 OS X

trying to compile and link a JNI progam 
detected JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/darwin
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c conftest.c -o conftest.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o conftest.so conftest.o -L/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation


JAVA_HOME        : /Library/Java/JavaVirtualMachines/jdk1.7.0_40.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
Done.

2)在R中,运行：install.packages(“rJava”,type =’source’).安装应该返回DONE(rJava).请注意,我必须设置

JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home

当我需要以root身份启动R：sudo R.要以普通用户身份运行,请使用

JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre

碰巧在我看来,我没有将上面的/usr/bin/java *的符号链接设置为Java 1.7中的相应链接(转而使用版本1.6)并且从那里得到了所有的挫败感.链接应该是这样的:(看起来R中只需要java,javac,javah和jar).

$ls -l /usr/bin/ja*
lrwxr-xr-x  1 root  wheel  71 Oct  3 11:44 /usr/bin/jar -> /Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/bin/jar
lrwxr-xr-x  1 root  wheel  77 Oct  3 12:14 /usr/bin/jarsigner -> /Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/bin/jarsigner
lrwxr-xr-x  1 root  wheel  72 Oct  3 11:44 /usr/bin/java -> /Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/bin/java
lrwxr-xr-x  1 root  wheel  73 Oct  3 11:42 /usr/bin/javac -> /Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/bin/javac
lrwxr-xr-x  1 root  wheel  75 Oct  3 12:15 /usr/bin/javadoc -> /Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/bin/javadoc
lrwxr-xr-x  1 root  wheel  73 Oct  3 11:44 /usr/bin/javah -> /Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/bin/javah
lrwxr-xr-x  1 root  wheel  73 Oct  3 12:15 /usr/bin/javap -> /Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/bin/javap
lrwxr-xr-x  1 root  wheel  74 Oct  3 12:15 /usr/bin/javaws -> /Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/bin/javaws