java - 如何让 rJava 在 osx 上使用更新版本的 java？

Question

我正在学习有关 rJava 的教程:http://cran.r-project.org/web/packages/helloJavaWorld/vignettes/helloJavaWorld.pdf

我已经制作了教程中指定的所有文件并安装了 helloJavaWorld 包，但是一旦我运行 helloJavaWorld() 函数，它就会提示:

> helloJavaWorld()
Error in .jnew("HelloJavaWorld") :
  java.lang.UnsupportedClassVersionError: HelloJavaWorld : Unsupported major.minor version 52.0

所以我尝试检查 rJava 使用的 java 版本:

.jinit()
jvm = .jnew("java.lang.System")
jvm.props = jvm$getProperties()$toString()
jvm.props <- strsplit(gsub("\\{(.*)}", "\\1", jvm.props), ", ")[[1]]
jvm.props

 [1] "java.runtime.name=Java(TM) SE Runtime Environment"
 [2] "sun.boot.library.path=/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Libraries"
 [3] "java.vm.version=20.65-b04-466.1"
 [4] "awt.nativeDoubleBuffering=true"
 [5] "gopherProxySet=false"
 [6] "mrj.build=11M4716"
 [7] "java.vm.vendor=Apple Inc."
 [8] "java.vendor.url=http://www.apple.com/"
 [9] "path.separator=:"
[10] "java.vm.name=Java HotSpot(TM) 64-Bit Server VM"
[11] "file.encoding.pkg=sun.io"
[12] "user.country=US"
[13] "sun.os.patch.level=unknown"
[14] "java.vm.specification.name=Java Virtual Machine Specification"
[15] "user.dir=/private/tmp"
[16] "java.runtime.version=1.6.0_65-b14-466.1-11M4716"
[17] "java.awt.graphicsenv=apple.awt.CGraphicsEnvironment"
[18] "java.endorsed.dirs=/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/endorsed"
[19] "os.arch=x86_64"
[20] "java.io.tmpdir=/var/folders/5d/44ctbbln4dsflgzxph1dm8wr0000gn/T/"
[21] "line.separator=\n"
[22] "java.vm.specification.vendor=Sun Microsystems Inc."
[23] "os.name=Mac OS X"
[24] "sun.jnu.encoding=MacRoman"
[25] "java.library.path=.:/Users/kaiyin/Library/Java/Extensions:/Library/Java/Extensions:/System/Library/Java/Extensions:/usr/lib/java"
[26] "java.specification.name=Java Platform API Specification"
[27] "java.class.version=50.0"
[28] "sun.management.compiler=HotSpot 64-Bit Tiered Compilers"
[29] "os.version=10.10"
[30] "http.nonProxyHosts=local|*.local|169.254/16|*.169.254/16"
[31] "user.home=/Users/kaiyin"
[32] "user.timezone="
[33] "java.awt.printerjob=apple.awt.CPrinterJob"
[34] "file.encoding=MacRoman"
[35] "java.specification.version=1.6"
[36] "java.class.path=/Library/Frameworks/R.framework/Versions/3.1/Resources/library/rJava/java/boot:/Library/Frameworks/R.framework/Versions/3.1/Resources/library/helloJavaWorld/java"
[37] "user.name=kaiyin"
[38] "java.vm.specification.version=1.0"
[39] "java.home=/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home"
[40] "sun.arch.data.model=64"
[41] "user.language=en"
[42] "java.specification.vendor=Sun Microsystems Inc."
[43] "awt.toolkit=apple.awt.CToolkit"
[44] "java.vm.info=mixed mode"
[45] "java.version=1.6.0_65"
[46] "java.ext.dirs=/Users/kaiyin/Library/Java/Extensions:/Library/Java/Extensions:/System/Library/Java/Extensions:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/ext"
[47] "sun.boot.class.path=/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jsfd.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/classes.jar:/System/Library/Frameworks/JavaVM.framework/Frameworks/JavaRuntimeSupport.framework/Resources/Java/JavaRuntimeSupport.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/ui.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/laf.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/sunrsasign.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jsse.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jce.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/charsets.jar"
[48] "java.awt.headless=true"
[49] "java.vendor=Apple Inc."
[50] "file.separator=/"
[51] "java.vendor.url.bug=http://bugreport.apple.com/"
[52] "sun.io.unicode.encoding=UnicodeLittle"
[53] "sun.cpu.endian=little"
[54] "mrj.version=1070.1.6.0_65-466.1"
[55] "socksNonProxyHosts=local|*.local|169.254/16|*.169.254/16"
[56] "ftp.nonProxyHosts=local|*.local|169.254/16|*.169.254/16"
[57] "sun.cpu.isalist="

看起来它使用 java 1.6(预装在 OSX 上)，但我用 java 1.8 编译了 HelloJavaWorld 类，这导致了一个问题:如何让 rJava 使用较新版本的 java？

R CMD javareconf 的输出:

Java interpreter : /usr/bin/java
Java version     : 1.8.0_25
Java home path   : /Library/Java/JavaVirtualMachines/jdk1.8.0_25.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
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/jre/../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/usr/local/lib -o conftest.so conftest.o -L/Library/Java/JavaVirtualMachines/jdk1.8.0_25.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_25.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.

/Library/Frameworks/R.framework/Versions/3.1/Resources/etc/javaconf 的内容

## Versions from settings when configure was run
: ${JAVA_HOME=}
: ${JAVA_CPPFLAGS=~autodetect~}
: ${JAVA_LD_LIBRARY_PATH=~autodetect~}
: ${JAVA_LIBS=~autodetect~}

/Library/Frameworks/R.framework/Versions/3.1/Resources/etc/ldpaths 的内容

➜  etc  cat ldpaths
: ${JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/jre}
: ${R_JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/server}
if test -n ""; then
: ${R_LD_LIBRARY_PATH=${R_HOME}/lib:}
else
: ${R_LD_LIBRARY_PATH=${R_HOME}/lib}
fi
if test -n "${R_JAVA_LD_LIBRARY_PATH}"; then
  R_LD_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${R_JAVA_LD_LIBRARY_PATH}"
fi
## This is DYLD_FALLBACK_LIBRARY_PATH on Darwin (OS X) and LD_LIBRARY_PATH elsewhere
if test -z "${DYLD_FALLBACK_LIBRARY_PATH}"; then
  DYLD_FALLBACK_LIBRARY_PATH="${R_LD_LIBRARY_PATH}"
else
  DYLD_FALLBACK_LIBRARY_PATH="${R_LD_LIBRARY_PATH}:${DYLD_FALLBACK_LIBRARY_PATH}"
fi
export DYLD_FALLBACK_LIBRARY_PATH

Answer 1

SO 上有很多关于 rJava 的相互矛盾的信息。我对其中很多答案的担忧是，一旦您开始使用 JAVA_HOME 变量，您就会冒着完全阻碍 Java 安装的风险——解决方案可能比疾病更糟糕。以下是在遇到 rJava 问题时可以采取的“无害”措施的简要说明。

1) 在终端中，运行R CMD javareconf。这是一个由 R Core 编写的脚本，它将“检测当前的 Java 设置并更新 R 中的相应配置。”看看内部结构here .

2) 从源代码重新安装 rJava。 install.packages("rJava", type = "source")。

3) 从命令行打开 R。加载 rJava。从命令行 ( directions ) 打开 RStudio。加载 rJava。你有同样的错误吗？如果没有，太好了 - 你越来越暖和了!您已将您的问题与 RStudio 的问题隔离开来，而不是 R 本身。

4) RStudio 和 rJava 存在某种问题——实际上，你知道吗，我什至不打算尝试完成那句话，因为坦率地说，它高于我的工资等级。动态库什么的。

网上有很多关于此的文章(here、here、here、and here)。我最喜欢的标题是“the rJava nightmare ”。

您的里程可能会有所不同，但是this所以答案是让 RStudio 正常运行所需的一切——终端上的一行代码，它所做的只是创建一个符号链接(symbolic link)。不更改权限，不修改环境变量 - 只是一个简单的符号链接(symbolic link)。

如果这不适合您，我建议您先阅读上面链接的博客文章，然后再开始复制/粘贴 SO 中散落的大量这对我有用答案。