无法在MacOS Mojave和R 3.5.2上加载rJava

Question

我问过a similar question before，但没有得到我实际可以实现的任何答案。我也读过here和here的答案，但无法实现其中任何一个（部分原因是因为没有答案实际上回溯了它的所有步骤。

问题

尝试在R 3.5.2和MacOS Mojave 10.14.3上加载rJava时出错：

> 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

试图解决方案

我第一次尝试this solution，这没用。然后，基于this answer，我尝试了以下内容：

在终端上输入以下内容：

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

然后在R上尝试了以下内容：

> 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

我也尝试过：

> 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

在过去，我已成功降级到R 3.1，但每次我想使用rJava时我都不必这样做

Answer 1

这是适合我的设置

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

2. 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/.

3. 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)

4. 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，看起来缺少在安装/编译rJava期间使用的JDK。你可以从消息中看出：

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，它缺失了。这里有两个选项：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

重现初始问题并修复它

1. 我们假装已经删除了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)

2. 我们试着加载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

3. 我们来解决它

   > 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.

4. 它现在应该工作

   > 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()

Answer 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。您不希望其中一个“修复”导致更多问题，因为大多数问题都要求您更改环境变量。

这是我修复它的方法。

1. 安装最新的JAVA JDK https://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
2. 在终端上运行sudo R CMD javareconf。不要自己更改任何环境变量。

希望能帮助到你。