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 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$(JAVA_HOME)/include
谢谢你的帮助
更新1：
我在stats-rosuda-devel列表中询问了这一点，并收到了Simon Urbanek的以下回复。 我不认为Windows和Linux在需要从源代码编译Java 1.7时遇到同样的问题，因为我们在Windows和Linux上运行它并且不必编译rJava。 一旦我有机会尝试这个，我会报告回来：
您正在使用针对系统Java（在您的系统上为1.6）编译的二进制文件 – 所以如果删除Java 1.6，您将会破坏它。 如果要使用Java 1.7，则必须重新配置R for Java 1.7并重新编译rJava以使用这些设置。 请注意，Oracle的Java与系统Java（/System/Library/Frameworks/JavaVM.framework）位于完全不同的位置（/Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk），因此它不可互换。
另外，Oracle Java 1.7不是一个框架，它实际上并不是专为OS X设计的，所以你必须手动将其设置为Linux上的设置 – 这非常痛苦。 它也需要覆盖…所以如果你真的想要走下兔子洞，这对我有用：
JAVA_LD_LIBRARY_PATH=/Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/jre/lib/server JAVA_LIBS='-L/Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/jre/lib/server -ljvm' JAVA_CPPFLAGS='-I/Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/include/darwin' R64 CMD javareconf然后从源代码安装rJava（R64 – > install.packages（“rJava”，type =’source’））。 请注意，它仅为64位，因此仅适用于64位R.
这对我有用：
情况是我的Java目录配置不正确。
1）首先运行： sudo R CMD javareconf 。 它应该如下：
Java interpreter : /usr/bin/java Java version : 1.7.0_40 Java home path : /Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre Java compiler : /usr/bin/javac Java headers gen.: /usr/bin/javah Java archive tool: /usr/bin/jar Non-system Java on OS X trying to compile and link a JNI progam detected JNI cpp flags : -I$(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
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，我敢肯定我不是唯一一个。
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