Question

是否有人设法让rJava 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首选项将1.7放在列表中，但保留1.6“on”，则rJava始终为1.6。

如果我使用Java Preferences先放1.7并关闭1.6，那么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？奇怪的是，Current转到A，最后是1.7，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文件的路径或者/ usr / bin / java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列表中询问了这一点，并收到了Simon Urbanek的以下回复。我不认为Windows和Linux在Java 1.7中需要从源代码编译时遇到同样的问题，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：

您正在使用针对系统Java编译的二进制文件   （在你的系统上是1.6） - 所以如果你删除Java 1.6你就会破坏   它。如果要使用Java 1.7，则必须重新配置R for   Java 1.7并重新编译rJava以使用这些设置。注意   Oracle的Java生活在一个完全不同的地方   （/ Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk）比系统   Java（/System/Library/Frameworks/JavaVM.framework），所以不是   可互换的。

另外，Oracle Java 1.7不是一个框架，它是一个很大的混乱   是不是真的为OS X设计，所以你必须手动设置它   Linux上的设置 - 这很痛苦。它也需要   覆盖...所以如果你真的想要走下兔子洞，这个   是什么对我有用：
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
然后从源代码安装rJava（R64 - ＆gt; install.packages（ “rJava”，类型= '源'））。请注意，它只是64位，所以它只适用于64位R。

Answer 1

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

在我看来，我没有将上述/ usr / bin / java *的符号链接设置为Java 1.7中的相应链接（转而使用1.6版本），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

Answer 2

最后，有些事情有效！

Simon Urbanek：请你把这些说明放在rJava网站/ cran安装说明书上......？这是我第一次陷入这个兔子洞，我确信我不是唯一一个。

JAVA_LD_LIBRARY_PATH=/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/jre/lib/server JAVA_LIBS='-L/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/jre/lib/server -ljvm' JAVA_CPPFLAGS='-I/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/include/darwin' R CMD javareconf
Java interpreter : /Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/jre/bin/java
Java version     : 1.8.0_77
Java home path   : /Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home
Java compiler    : /Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/bin/javac
Java headers gen.: /Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/bin/javah
Java archive tool: /Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/bin/jar
System Java on OS X

trying to compile and link a JNI program
detected JNI cpp flags    : -I/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/include/darwin
detected JNI linker flags : -L/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/jre/lib/server -ljvm
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/include/darwin -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -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/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/jre/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation


JAVA_HOME        : /Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home
Java library path: /Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/jre/lib/server
JNI cpp flags    : -I/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/include/darwin
JNI linker flags : -L/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/jre/lib/server -ljvm
Updating Java configuration in /Library/Frameworks/R.framework/Resources
override rw-r--r--  root/admin for /Library/Frameworks/R.framework/Resources/etc/Makeconf? (y/n [n]) y
override rw-r--r--  root/admin for /Library/Frameworks/R.framework/Resources/etc/ldpaths? (y/n [n]) y
Done.

R CMD INSTALL rJava_0.9-9.tar.gz

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

2 个答案: