java - 如何让 rJava 0.9-3 在 OS X 10.7.4 和 Oracle Java 1.7 上工作？

Question

有没有人设法让 rJava 0.9-3 在 OS X 10.7.4 和 Oracle Java 1.7 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 函数和命令行安装了 rJava，并安装了 R 2.15.2。我没有收到任何错误。

$ 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 首选项将 1.7 放在列表的第一位，但将 1.6 保留为“打开”，则 rJava 始终从 1.6 开始。

如果我使用 Java 首选项将 1.7 放在第一位并关闭 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 是否需要/System/Library/Java/JavaConfig.plist 中的特殊条目？

Versions 目录是否需要针对 1.7 进行调整？ Current 转到 A 很奇怪，A 以 1.7 结束，而 CurrentJDK 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

即使使用直接指向 1.7 文件或/usr/bin/java 路径的路径运行 R CMD javareconf，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

感谢您的帮助

更新 1:

我在 stats-rosuda-devel 列表中询问了这个问题，并收到了 Simon Urbanek 的以下回复。我不认为 Windows 和 Linux 有同样的问题需要从 Java 1.7 的源代码编译，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:

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:

JAVA_LD_LIBRARY_PATH=/Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/jre/lib/server
JAVA_LIBS='-L/Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/jre/lib/server -ljvm'
JAVA_CPPFLAGS='-I/Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/include/darwin'
R64 CMD javareconf

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.

Answer 1

这对我有用:

情况是我的 Java 目录配置不正确。

1) 第一次运行: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 时: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

我碰巧没有将上面的/usr/bin/java* 的符号链接(symbolic link)设置为 Java 1.7 中的相应符号链接(symbolic link)(而是指向版本 1.6)，并从那里得到了所有的挫败感。链接应该是这样的:(看起来在 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