无法在 Mac OS 10.11 上加载 R xlsx 包

Question

I can load the rJava and xlsxjars packages, but I get a "Failed to load JVM" when I execute library(xlsx). Below are my details.

OS Version:

$ sw_vers
ProductName:    Mac OS X
ProductVersion: 10.11
BuildVersion:   15A284

Java Version:

$ java -version
java version "1.8.0_65"
Java(TM) SE Runtime Environment (build 1.8.0_65-b17)
Java HotSpot(TM) 64-Bit Server VM (build 25.65-b01, mixed mode)

Java Path:

$ which java
/usr/bin/java

Java Home:

$ /usr/libexec/java_home
/Library/Java/JavaVirtualMachines/jdk1.8.0_65.jdk/Contents/Home

R Version:

$ R --version
R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

How I launch R:

$ LD_LIBRARY_PATH=$(/usr/libexec/java_home)/jre/lib/server: open -a RStudio

Loading the rJava and xlsxjars packages successfully:

> library(rJava)
> library(xlsxjars)

Unsuccessfully trying to load the xlsx package:

> library(xlsx)
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 : .onLoad failed in loadNamespace() for 'xlsx', details:
  call: .jinit()
  error: JNI_GetCreatedJavaVMs returned -1
Error: package or namespace load failed for ‘xlsx’

R Configuration:

Matts-MacBook-Pro:~ matt$ R CMD javareconf
Java interpreter : /usr/bin/java
Java version     : 1.8.0_65
Java home path   : /Library/Java/JavaVirtualMachines/jdk1.8.0_65.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 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/jdk1.8.0_65.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_65.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/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o conftest.so conftest.o -L/Library/Java/JavaVirtualMachines/jdk1.8.0_65.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_65.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

Answer 1

Unfortunately, these symlink tricks didn't help me. However, I found a similar issue on stackoverflow ! (where else ;)) This one worked for me by doing the following:

1. In terminal enter the following to relink Java correctly:

    sudo R CMD javareconf

2. Back in R (or RStudio) install the rJava package from source:

    install.packages("rJava",type='source')

Hope, this helps!

Answer 2

I ´ve got also problems with loading packages like openNLP, xlsx, RWeka, ... and got the same error message like you. But finally this command worked for me on OS X 10.11.3: sudo ln -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib

Answer 3

There might be a problem in the version of Java for which the R xlsx package was built in. Some old software require to install the Java 6 for OS X 10.11 El Capitan, OS X 10.10 Yosemite, OS X 10.9 Mavericks, OS X 10.8 Mountain Lion, and OS X 10.7 Lion. So you can try to install this old version of Java (Java for OS X 2015-001) at Apple website, link below: https://support.apple.com/kb/DL1572?locale=pt_BR&viewlocale=en_US

And check if you have a Java SE Development Kit 8. You can download it at Oracle website, link below: www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html

I was having the same problem and downloading the old version of Java solved it.. I hope this help you!

Answer 4

Basically, just do what is described here: https://oliverdowling.com.au/2015/10/09/oracles-jre-8-on-mac-os-x-el-capitan/

short version: d/l Java JRE from oracle as tar file http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html

then put this into you terminal (for sudo, your pw is needed):

cd ~/Downloads
tar -xzf `ls -1r jre-*-macosx-x64.tar.gz | head -1`
cd `ls -1rd jre*/ | head -1`
defaults write `pwd`/Contents/Info.plist JavaVM -dict-add 'JVMCapabilities' '<array><string>JNI</string><string>BundledApp</string><string>CommandLine</string></array>'
plutil -convert xml1 Contents/Info.plist
sudo mv `pwd` /Library/Java/JavaVirtualMachines/
mkdir -p Contents/Home/bundle/Libraries
cd Contents/Home/bundle/Libraries
ln -s ../../lib/server/libjvm.dylib libserver.dylib

works fine on my OS X 10.11

Answer 5

For me, MacOS Catalina 10.15.7, it was as simple as installing the current JRE and JDK software (downloaded as .dmg files from the official distributer websites on java.com and oracle.com - No affiliations whatsoever!).

I have also (re-) installed the rJava package, but I don't feel this was necessary. I actually simply did not have Java installed on my computer.

Now the xlsx package loads.