R: rJava package install failing

问题:

When installing rJava using the install.packages(\"rJava\") command I get the following error:

checking Java support in R... present:
interpreter : \'/usr/bin/java\'
archiver    : \'/usr/bin/jar\'
compiler    : \'/usr/bin/javac\'
header prep.: \'/usr/bin/javah\'
cpp flags   : \'-I/usr/lib/jvm/java-6-sun-1.6.0.20/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.20/jre/../include/linux\'
java libs   : \'-L/usr/lib/jvm/java-6-sun-1.6.0.20/jre/lib/amd64/server -L/usr/lib/jvm/java-6-sun-1.6.0.20/jre/lib/amd64 -L/usr/lib/jvm/java-6-sun-1.6.0.20/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm\'
checking whether JNI programs can be compiled... yes
checking JNI data types... configure: error: One or more JNI types differ from the corresponding native type. You may need to use non-standard compiler flags or a different compiler in order to fix this.
ERROR: configuration failed for package ‘rJava’

I have the Java JDK installed and java -version returns the following:

$ java -version
java version \"1.6.0_20\"
Java(TM) SE Runtime Environment (build 1.6.0_20-b02)

When Googling around for the error I see that others are having the same issue but not finding a solution other than \"install the whole JDK, not just the JRE\" which I have done.

The other thing I read was to run sudo R CMD javareconf which runs quite happily with no errors.

Any ideas what my problem is?

[[EDIT]] It\'s been a few months since I had this problem. I had initially solved this by editing my Java paths, as illustrated in the answer I posted below. I recently ran into the same issue on a new Ubuntu install. I tried Dirk\'s recommendation to use apt-get to install the rJava package. It worked perfectly. What I failed to appreciate initially is that installing packages using the Ubuntu apt-get method is fundamentally different than just loading the same package using install.packages() inside of R. The Ubuntu packages solve some issues which I didn\'t realize or appreciate.

回答1:

Wouldn\'t

apt-get install r-cran-rjava

have been easier? You could have asked me at useR! :)

回答2:

Turns out my problem was an issue with my JAVA_HOME environment variable. Yes, shocking I know. My initial setting for PATH and JAVA_HOME looked like this:

export JAVA_HOME=/usr/lib/jvm/java-6-sun
export PATH=$PATH:$JAVA_HOME/bin

And I added /jre so it now looks like this:

export JAVA_HOME=/usr/lib/jvm/java-6-sun/jre
export PATH=$PATH:$JAVA_HOME/bin

Everything in Java seemed to work fine without the /jre but rJava would not. Odd.

回答3:

Thanks - your suggestion about $JAVA_HOME lead me to a similar solution:

prompt$ unset JAVA_HOME

before invoking R.

回答4:

I came across the same issue, and it worked after running commands below.

export JAVA_LIBS=\"$JAVA_LIBS -ldl\"
R CMD javareconf

See details at http://www-01.ibm.com/support/knowledgecenter/SSPT3X_3.0.0/com.ibm.swg.im.infosphere.biginsights.install.doc/doc/install_install_r.html

回答5:

This worked for me on Ubuntu 12.04 and R version 3.0

cd /usr/lib/jvm/java-6-sun-1.6.0.26/include

this is the directory that has jni.h

Next create a soft link to another required header file (I\'m too lazy to find out how to include more than one directory in the JAVA_CPPFLAGS option below):

sudo ln -s linux/jni_md.h .

Finally

sudo R CMD javareconf JAVA_CPPFLAGS=-I/usr/lib/jvm/java-6-sun-1.6.0.26/include

回答6:

below is one of my answers on another post - error: unable to load installed packages just now
(this is also relevant to this question)

For Linux(Ubuntu) users: If you have oracle-java (7/8) installed. It\'ll be at this location /usr/lib/jvm and sudo access is required.

Create the file /etc/ld.so.conf.d/java.conf with the following entries:

/usr/lib/jvm/java-8-oracle/jre/lib/amd64
/usr/lib/jvm/java-8-oracle/jre/lib/amd64/server

(Replace java-8-oracle with java-7-oracle depending on your java version)

Then:

sudo ldconfig

Restart RStudio and then install the rJava package.

回答7:

Running R under Gentoo on an AMD64. I upgraded to R 2.12.0

R version 2.12.0 (2010-10-15) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit) and those pesky messages went away.

Jan Vandermeer

回答8:

I tried to install openjdk-7-* but still I had problems installing rJava. Turns out after I restarted my computer, then there was no problem at all.

so

sudo apt-get install openjdk-7-*


RESTART after installing java, then try to install package \"rJava\" in R

回答9:

What worked for me was changing JAVA_HOME from file /usr/lib/R/etc/javaconf

I first checked what was my version of Java enabled : sudo update-alternatives --config java. In my case, it was java-8-oracle

I opened the file /usr/lib/R/etc/javaconf and replaced default-java by java-8-oracle :

${JAVA_HOME=/usr/lib/jvm/default-java}

replaced by :

${JAVA_HOME=/usr/lib/jvm/java-8-oracle}

And then sudo R CMD javareconf

I restarted RStudio, and could then install rJava.

回答10:

what I do is here:

1. in /etc/apt/sources.list, add:

   deb http://ftp.de.debian.org/debian sid main

Note:the rjava should be latest version

2 run: sudo apt-get update sudo apt-get install r-cran-rjava

Once update the old version of rjava, then can install rhdfs_1.0.8.

回答11:

I got it working by downloading : https://cran.r-project.org/src/contrib/rJava_0.9-8.tar.gz and running command R CMD install rJava_0.9-8.tar.gz

回答12:

The rJava package looks for the /usr/lib/jvm/default-java/ folder. But it\'s not available as default. This folder have a symlink for the default java configured for the system.

To activate the default java install the following packages:

sudo apt-get install default-jre default-jre-headless

Tested on ubuntu 17.04 with CRAN R 3.4.1

回答13:

The problem was rJava wont install in RStudio (Version 1.0.136). The following worked for me (macOS Sierra version 10.12.6) (found here):

Step-1: Download and install javaforosx.dmg from here

Step-2: Next, run the command from inside RStudio:

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

回答14:

That is how I make it work :

In Linux (Ubuntu 16.04)

sudo apt-get install default-jre
sudo apt-get install default-jdk
sudo R CMD javareconf

in R:

install.packages(\"rJava\")

回答15:

I\'ve encountered similar problem on Ubuntu 16.04 and was able to solve it by creating a folder named \"default-java\" in /usr/lib/jvm and copying into it all the contents of the /usr/lib/jvm/java-8-oracle. I opted for this solution as correcting JAVA_HOME environment variable turned out to be of no use.