无法在 MacOS Mojave 和 R 3.5.2 上加载 rJava答案

【问题标题】：Can't load rJava on MacOS Mojave and R 3.5.2无法在 MacOS Mojave 和 R 3.5.2 上加载 rJava
【发布时间】：2019-03-08 04:10:20
【问题描述】：

我已经问过a similar question before，但没有得到任何我可以实际实施的答案。我也阅读了here 和here 的答案，但无法实现其中任何一个（部分原因是没有答案实际上追溯了所有步骤。

问题

尝试在 R 3.5.2 和 MacOS Mojave 10.14.3 上加载 rJava 时出现错误：

> library(rJava)
Error: package or namespace load failed for ‘rJava’:
 .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
  Reason: image not found

尝试的解决方案

我首先尝试了this solution，但没有成功。然后，基于this answer，我尝试了以下方法：

在终端输入以下内容：

$ /usr/libexec/java_home
/Library/Java/JavaVirtualMachines/jdk-11.0.2.jdk/Contents/Home

然后在 R 上尝试以下操作：

> options("java.home"="/Library/Java/JavaVirtualMachines/jdk-11.0.2.jdk/Contents/Home")
> 
> Sys.setenv(LD_LIBRARY_PATH='$JAVA_HOME/server')
> 
> dyn.load('/Library/Java/JavaVirtualMachines/jdk-11.0.2.jdk/Contents/Home/lib/server/libjvm.dylib')
> 
> library(rJava)
Error: package or namespace load failed for ‘rJava’:
 .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
  Reason: image not found

我也试过了：

> options("java.home"="/Library/Java/JavaVirtualMachines/jdk-11.0.2.jdk/Contents/Home/bin")
> Sys.setenv(LD_LIBRARY_PATH='$JAVA_HOME/server')
> dyn.load('/Library/Java/JavaVirtualMachines/jdk-11.0.2.jdk/Contents/Home/lib/server/libjvm.dylib')
> library(rJava)
Error: package or namespace load failed for ‘rJava’:
 .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
  Reason: image not found

过去，我已成功降级到 R 3.1，但我不想每次想使用 rJava 时都这样做

【问题讨论】：

标签： r macos rjava

【解决方案1】：

这是适合我的设置

macOS Mojave - 10.14.3
XQuartz - 版本 2.7.11 - https://www.xquartz.org

R - 版本 5.3.2

> R --version
R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
http://www.gnu.org/licenses/.

Java - 11.0.1

> java -version
java version "11.0.1" 2018-10-16 LTS
Java(TM) SE Runtime Environment 18.9 (build 11.0.1+13-LTS)
Java HotSpot(TM) 64-Bit Server VM 18.9 (build 11.0.1+13-LTS, mixed mode)

rJava - 从 CRAN 安装

> > install.packages("rJava")
--- Please select a CRAN mirror for use in this session ---
Fontconfig warning: ignoring UTF-8: not a valid region tag
trying URL 'https://cloud.r-project.org/bin/macosx/el-         
capitan/contrib/3.5/rJava_0.9-10.tgz'
Content type 'application/x-gzip' length 739259 bytes (721 KB)
==================================================
downloaded 721 KB


The downloaded binary packages are in
/var/folders/...
> library(rJava)
>

更新

在您的情况下，rJava 安装/编译期间使用的 JDK 似乎丢失了。您可以从消息中看出：

dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
Reason: image not found

确保此文件存在：

/Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib

可能，它不见了。您有两个选择：安装 Java 11.0.1，重新配置 R。

您可以使用/usr/libexec/java_home -V列出所有可用的JVM安装

重现最初的问题并修复它

假设我们已经删除了 JDK 11.0.1

> pwd /Library/Java/JavaVirtualMachines
> tree -L 1
.
|-- jdk-11.0.1.jdk~
`-- jdk-11.0.2.jdk
> java -version
java version "11.0.2" 2019-01-15 LTS
Java(TM) SE Runtime Environment 18.9 (build 11.0.2+9-LTS)
Java HotSpot(TM) 64-Bit Server VM 18.9 (build 11.0.2+9-LTS, mixed mode)

让我们尝试加载 rJava

> R

R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

...
...
...

> library(rJava)
Error: package or namespace load failed for ‘rJava’:
 .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
  Reason: image not found

让我们修复它

> sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version     : 11.0.2
Java home path   : /Library/Java/JavaVirtualMachines/jdk-11.0.2.jdk/Contents/Home
Java compiler    : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar

trying to compile and link a JNI program
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/jdk-11.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk-11.0.2.jdk/Contents/Home/include/darwin  -I/usr/local/include   -fPIC  -Wall -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/jdk-11.0.2.jdk/Contents/Home/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation


JAVA_HOME        : /Library/Java/JavaVirtualMachines/jdk-11.0.2.jdk/Contents/Home
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.

现在应该可以工作了

> R

R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

...
...
...

> library(rJava)
> quit()

【讨论】：

不幸的是，这不是完全相同的环境。看看更新。
你是对的，当然。我正在运行 JDK 11.0.2。不过， sudo R CMD javareconf 仅适用于 R 终端。知道为什么这在 R GUI 上不起作用吗？无论如何，我刚刚安装了 JDK 11.0.1 并让它在 R GUI 上运行。非常感谢！

【解决方案2】：

我遇到了类似的问题。如果您尝试了所有这些解决方案并且没有任何效果，那么通常最好从头开始。您不希望这些“修复”之一给您带来更多问题，因为它们中的大多数都需要您更改环境变量。

这是我修复它的方法。

安装最新的JAVA JDK https://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
在终端中运行sudo R CMD javareconf。请勿自行更改任何环境变量。

希望对你有帮助。

【讨论】：

很遗憾没用。我也是从头开始的。完成所有操作后，我格式化了我的 HD 并重新安装了 MacOS。
好的，这仅适用于使用 R 终端的情况。知道为什么这在 R GUI 上不起作用吗？