Related
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.
Wouldn't
apt-get install r-cran-rjava
have been easier? You could have asked me at useR! :)
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.
That is how I make it work :
In Linux (Ubuntu 16.04 and 20.04 worked confirmed)
sudo apt-get install default-jre
sudo apt-get install default-jdk
sudo R CMD javareconf
in R:
install.packages("rJava")
Thanks - your suggestion about $JAVA_HOME lead me to a similar solution:
unset JAVA_HOME
before invoking R.
I came across the same issue, and it worked after running commands below.
export JAVA_LIBS="$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
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
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.
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
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
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
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.
what I do is here:
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.
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
I was facing the same problem while using Windows 10. I have solved the problem using the following procedure
Download Java from https://java.com/en/download/windows-64bit.jsp for 64-bit windows\Install it
Download Java development kit from https://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html for 64-bit windows\Install it
Then right click on “This PC” icon in desktop\Properties\Advanced system settings\Advanced\Environment Variables\Under System variables select Path\Click Edit\Click on New\Copy and paste paths “C:\Program Files\Java\jdk1.8.0_201\bin” and “C:\Program Files\Java\jre1.8.0_201\bin” (without quote) \OK\OK\OK
Note: jdk1.8.0_201 and jre1.8.0_201 will be changed depending on the version of Java development kit and Java
In Environment Variables window go to User variables for User\Click on New\Put Variable name as “JAVA_HOME” and Variable value as “C:\Program Files\Java\jdk1.8.0_201\bin”\Press OK
To check the installation, open CMD\Type javac\Press Enter and
Type java\press enter
It will show
In RStudio run
Sys.setenv(JAVA_HOME="C:\\Program Files\\Java\\jdk1.8.0_201")
Note: jdk1.8.0_201 will be changed depending on the version of Java development kit
Now you can install and load rJava package without any problem.
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')
On Arch Linux, I needed to install openjdk-src to get a JNI path working.
In other words, these are the packages I needed to install before sudo R CMD javareconf ran successfully:
local/jdk-openjdk 14.0.2.u12-1
OpenJDK Java 14 development kit
local/jre-openjdk 14.0.2.u12-1
OpenJDK Java 14 full runtime environment
local/jre-openjdk-headless 14.0.2.u12-1
OpenJDK Java 14 headless runtime environment
local/openjdk-src 14.0.2.u12-1
OpenJDK Java 14 sources
Assuming you have sudo privileges and not in Ubuntu where package manager makes this easier -- I tried variations of prior answers and found this gem on Databricks blog for nonUbuntu (https://kb.databricks.com/r/install-rjava-rjdbc-libraries.html)
Installed JDK
sudo apt-get install openjdk-8-jdk
Verify path to libjvm.so; for me-->
cd /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64
grep -r libjvm
output:
Binary file server/libjvm.so matches <<<<<<<<
Do java configure
sudo R CMD javareconf
Remove prior versions of the package and install 'rJava' from CRAN mirror in RStudio
Restart RStudio
In RStudio verify link to libjvm.so
dyn.load('/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server/libjvm.so')
library('rJava')
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.
I created a new ubuntu-16.04.2-desktop-amd64 machine on VM VirtualBox and I want to be able to use the R environment with Rmpi.
Both of the below approaches gives a similar error.
Updated simplified pre-build binary approach:
When Ubuntu had installed I opened a terminal and executed the following commands:
~$ sudo apt-get update
~$ sudo apt-get install openmpi-bin
~$ sudo apt-get install r-base
~$ sudo apt-get install r-cran-rmpi
~$ R
This opened the R terminal and I invoking the follow function which resulted in an error:
> library(Rmpi)
libmpi.so: cannot open shared object file: No such file or directory
Error : .onLoad failed in loadNamespace() for 'Rmpi', details:
call: fun(libname, pkgname)
error: Cannot start MPI_Init(). Exit
Error: package or namespace load failed for ‘Rmpi’
Alternative approaches that I have attempted include using a local OpenMPI installation and using the R function install.packages to install the Rmpi package (see below). These all resulted in the same error.
I have also tried using MPICH by substituting ~$ sudo apt-get install mpich as the second command in the above procedure (including using the R function for installing the package) which results in an even more onerous runtime error.
Does anyone know what I have done wrong or what I can do to resolve this installation error?
Or alternatively, have anyone been able to successfully install a VirtualBox machine with Rmpi using any Linux distro or an image with pre-installed components?
Original local installation approach:
I have followed the instructions on this blog to download OpenMPI version 2.1.0, compile and install it. However when I try to install the package in R with:
> install.packages("Rmpi", configure.args =
c("--with-Rmpi-include=/home/jormunr/openmpi/include",
"--with-Rmpi-libpath=/home/jormunr/openmpi/lib",
"--with-Rmpi-type=OPENMPI",
"--with-mpi=/home/jormunr/openmpi/"))
it gives the following error
Error: .onLoad failed in loadNamespace() for 'Rmpi', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/home/jormunr/R/x86_64-pc-linux-gnu-library/3.2/Rmpi/libs/Rmpi.so':
libmpi.so.20: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
I can see that the 'libmpi.so.20' file is in the /home/jormunr/openmpi/lib that I provided as one of the parameter to the installation.
[Disclaimer: I am not a Linux expert and merely have user level skills. Any contributions or corrections from an expert will be greatly appreciated.]
Pre-build Binary Approach
Although trying various ways to install the prebuilt binaries I did not manage to get this option to work. This involved executing in the terminal the command 'sudo apt-get install r-cran-rmpi' to install the r-cran-rmpi prebuilt packages which also automatically installs the libopenmpi1.10 package that is a listed prerequisite. However, it appears that the file 'libmpi.so' is not included in the libopenmpi1.10 package but expected by the Rmpi library which causes an error in the R environment that it cannot find this file.
Local Installation Approach
The local installation did eventually succeed with a few amendments. I created a new ubuntu-16.04.2-desktop-amd64 VirtualBox image with default settings, except for 2048MB of memory and 32GB of hard drive space. When installed I opened a terminal and executed the commands from the Jovinge Lab website with the inclusion of the penultimate command which amends the run-time link editor's path and enables the install.package() function of R to find the 'libmpi.so' file. (also changed the version to 1.10.6 as this is the latest version release of version 1 – see below for version 2)
~$ cd /home/jormunr
~$ wget https://www.open-mpi.org/software/ompi/v1.10/downloads/openmpi-1.10.2.tar.gz
~$ tar -zxvf openmpi-1.10.6.tar.gz
~$ cd openmpi-1.10.2
~$ ./configure --prefix=/home/jormunr
~$ make
~$ make install
~$ sudo apt-get install r-base
~$ export LD_LIBRARY_PATH=/home/jormunr/lib:$LD_LIBRARY_PATH
~$ R
This opens an R terminal and I invoked the function:
> install.packages("Rmpi", configure.args =
+ c("--with-Rmpi-include=/home/jormunr/include/",
+ "--with-Rmpi-libpath=/home/jormunr/lib/",
+ "--with-Rmpi-type=OPENMPI",
+ "--with-mpi=/home/jormunr/"))
This now executed without errors and I could test it with the following R statements:
> library("Rmpi")
> mpi.spawn.Rslaves()
master (rank 0, comm. 1) of size 2 is running on: Valhalla
slave1 (rank 1, comm. 1) of size 2 is running on: Valhalla
> mpi.close.Rslaves()
[1] 1
> mpi.quit()
When I tried this process with the OpenMPI Version 2.1.0 the installation completed successfully but the above test had issues; the mpi.spawn.Rslaves() function completed but mpi.close.Rslaves() did not complete – it never returned and the terminal was left hanging.
I experienced similar challenges. I landed on this solution where libopenmpi-dev was the secret.
sudo apt-get install openmpi-common openmpi-bin libopenmpi-dev r-base
sudo apt-get install r-cran-rmpi
sudo su
R
install.packages("doMPI", dependencies=TRUE)
I have Ubuntu 10.x OS and I have installed R on it. I want to install rJava on R. For that when I am running installed.packages("rJava) command which is giving error
checking whether Java run-time works... Error: Could not find or load main class getsp
no
configure: error: Java interpreter '/usr/bin/java' does not work
ERROR: configuration failed for package ‘rJava’
* removing ‘/home/hduser/R/i486-pc-linux-gnu-library/2.10/rJava’
The downloaded packages are in
‘/tmp/Rtmp0tlBXn/downloaded_packages’
Warning message:
In install.packages("rJava") :
installation of package 'rJava' had non-zero exit status
If I run system("java -version")
Then it showing same Java version which is given when I run Java -version command from base OS prompt. So it means no problem with Java which I can see reason in output of install package command? As suggested when I use
sudo apt-get install r-cran-rjava
Here also didnt get any luck
Please suggest
I just saw that you wrote installed.packages instead of install.packages, you have to use install.packages("rJava") to install it.
The description of the method you used (installed.packages) says: Find (or retrieve) details of all packages installed in the specified libraries.
Can you please try
install.packages("rJava")
library(rJava)
and tell me the output? (I'm pretty sure it will already work then).
in the terminal run sudo apt-get install default-jdk
then run sudo R CMD javareconf
after that you can continue in R or Rstudio install.packages("rJava")
I am trying to install sparkTable in R 3.1.0 which depends on Rglpk. I manually installed GPLK on the system and added the libs folder to LD_LIBRARY_PATH before going into R for the install.packages("sparkTable") procedure. I get this error during the installation process. Any ideas?
* installing *source* package ‘Rglpk’ ...
** package ‘Rglpk’ successfully unpacked and MD5 sums checked
** libs
/bin/sh: line 0: cd: GLPK: No such file or directory
make: *** [GLPK.ts] Error 1
ERROR: compilation failed for package ‘Rglpk’
* removing ‘/opt/R/R-3.1.0/lib64/R/library/Rglpk’
ERROR: dependency ‘Rglpk’ is not available for package ‘sparkTable’
* removing ‘/opt/R/R-3.1.0/lib64/R/library/sparkTable’
sudo apt-get install libglpk-dev
did the trick for me.
I had this problem and took a good bit of digging in the package to understand what was happening. If Rgplk can't compile its test program when installing, it does something weird, including this bizarre cd to nowhere. Assuming glpk-devel is installed, the reason it can't compile the test program is that it can't find the gplk header as it is in a non-standard directory.
Just set the environment variable CPATH=/usr/include/glpk
and the test program will compile, allowing the package install to proceed normally.
I had this problem too. The following steps solved this issue for me. My current setup:
OS: Scientifc Linux version 6.5 (on a High Performance Cluster Server)
local user, no root access.
GLPK was not installed
Install GLPK in a local directory:
wget http://ftp.gnu.org/gnu/glpk/glpk-4.54.tar.gz
tar xfzv glpk-4.54.tar.gz
mkdir GLPK
cd glpk-4.54
./configure --prefix=/home/<username>/GLPK
make
make install
Install Rglpk (0.6-3):
cd ~
wget http://cran.r-project.org/src/contrib/Rglpk_0.6-3.tar.gz
export LIBRARY_PATH=/home/<username>/GLPK/lib
R CMD INSTALL Rglpk_0.6-3.tar.gz
I landed on this page, because I could not update igraph under Windows 10/11, since igraph also requires glpk as per OP. Specifically:
igraph_glpk_support.h:36:10: fatal error: glpk.h: No such file or
directory #include <glpk.h>
^~~~~~~~ compilation terminated. make: *** [C:/PROGRA~1/R/R-4.1.1/etc/x64/Makeconf:238: feedback_arc_set.o] Error
1 ERROR: compilation failed for package 'igraph'
removing 'C:/Users/xxx/Documents/R/win-library/4.1/igraph'
restoring previous 'C:/Users/xxx/Documents/R/win-library/4.1/igraph' Warning
in install.packages : installation of package ‘igraph’ had non-zero
exit status
I am under Windows 11 (but would be same for Windows 10).
Simple resolution is suggested here:
start Rtools Bash (found in all apps, Rtools 4.0 in the Windows menu)
Run pacman -S mingw-w64-x86_64-glpk and confirm with yes (y)
Run pacman -S mingw-w64-x86_64-libxml2 and confirm with yes (y)
Updating igraph in Rstudio now leads to a clean
DONE (igraph)
(there is no need to install anything, add any path, etc... just the above 4 steps)
In ubuntu 14.04, all above doesn't work. the following however works, without the need of installing libglpk-dev using apt-get.
download the glpk package from gnu and extract it:
wget http://ftp.gnu.org/gnu/glpk/glpk-4.55.tar.gz
tar xvf glpk-4.55.tar.gz
make a GLPK directory in your local path:
mkdir ~/GLPK
configure within glpk:
cd glpk-4.55
./configure --prefix=$HOME/GLPK
cd ..
export LD_LIBRARY_PATH=$HOME/GLPK/lib
export LIBRARY_PATH=$HOME/GLPK/lib
export CPATH=$HOME/GLPK/include
download the Rglpk package from cran and extract it:
wget http://cran.r-project.org/src/contrib/Rglpk_0.6-0.tar.gz
tar xvf Rglpk_0.6_0.tar.gz
move the glpk directory into Rglpk/src and rename it to GLPK:
mv glpk-4.55 Rglpk/src/GLPK
now you can install:
R CMD INSTALL Rglpk
now a bit of explanation of what's going on. The "src/Makevars.in" file in the Rglpk package contains a line of code to enter a non-existing directory 'GLPK' within the src/ folder:
(line 11 of Makevars.in)
GLPK.ts:
#(cd GLPK && make)
touch $#
this is where the problem arises. obviously the code is trying to build glpk within that directory for some unknown reasons. and the solution above is achieved simply by moving the downloaded (and configured) glpk directory there...
If you're on a Debian-based Linux distribution, run this to install GLTK:
sudo apt install libglpk-dev
If you're on MacOS, run this to install GLTK:
brew install gltk
Finally, install the R library:
install.packages("Rglpk")
On Centos, have sudo rights. None of the above worked, but had to install GLPK in /usr/local as suggested in this SO answer. Been trying to install it for about 3 hours fml
You must install glpk dependency first.
On macOS (via homebrew):
brew install glpk
or in RStudio (via homebrew):
system("brew install glpk")
It worked for me when I combined the answers from Simón Ramírez Amaya and shadowleaves:
wget http://ftp.gnu.org/gnu/glpk/glpk-4.54.tar.gz
tar xfzv glpk-4.54.tar.gz
mkdir GLPK
cd glpk-4.54
./configure --prefix=$HOME/GLPK
make
make install
cd ..
export LD_LIBRARY_PATH=$HOME/GLPK/lib
export LIBRARY_PATH=$HOME/GLPK/lib
export CPATH=$HOME/GLPK/include
wget https://cran.r-project.org/src/contrib/Rglpk_0.6-4.tar.gz
R CMD INSTALL Rglpk_0.6-4.tar.gz
To load the library
dyn.load(file.path(Sys.getenv("HOME"), "GLPK", "lib", "libglpk.so"))
library(Rglpk)
The answer of Zhiying Cui is right, however, if your script has some special codes, such as foreach for parallel computing, it may raise an error.
A better way is as fellow
If your os is Centos, try
yum install glpk-devel
then just go to R or Rstudio server and
install.packages("Rglpk")
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.
Wouldn't
apt-get install r-cran-rjava
have been easier? You could have asked me at useR! :)
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.
That is how I make it work :
In Linux (Ubuntu 16.04 and 20.04 worked confirmed)
sudo apt-get install default-jre
sudo apt-get install default-jdk
sudo R CMD javareconf
in R:
install.packages("rJava")
Thanks - your suggestion about $JAVA_HOME lead me to a similar solution:
unset JAVA_HOME
before invoking R.
I came across the same issue, and it worked after running commands below.
export JAVA_LIBS="$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
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
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.
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
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
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
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.
what I do is here:
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.
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
I was facing the same problem while using Windows 10. I have solved the problem using the following procedure
Download Java from https://java.com/en/download/windows-64bit.jsp for 64-bit windows\Install it
Download Java development kit from https://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html for 64-bit windows\Install it
Then right click on “This PC” icon in desktop\Properties\Advanced system settings\Advanced\Environment Variables\Under System variables select Path\Click Edit\Click on New\Copy and paste paths “C:\Program Files\Java\jdk1.8.0_201\bin” and “C:\Program Files\Java\jre1.8.0_201\bin” (without quote) \OK\OK\OK
Note: jdk1.8.0_201 and jre1.8.0_201 will be changed depending on the version of Java development kit and Java
In Environment Variables window go to User variables for User\Click on New\Put Variable name as “JAVA_HOME” and Variable value as “C:\Program Files\Java\jdk1.8.0_201\bin”\Press OK
To check the installation, open CMD\Type javac\Press Enter and
Type java\press enter
It will show
In RStudio run
Sys.setenv(JAVA_HOME="C:\\Program Files\\Java\\jdk1.8.0_201")
Note: jdk1.8.0_201 will be changed depending on the version of Java development kit
Now you can install and load rJava package without any problem.
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')
On Arch Linux, I needed to install openjdk-src to get a JNI path working.
In other words, these are the packages I needed to install before sudo R CMD javareconf ran successfully:
local/jdk-openjdk 14.0.2.u12-1
OpenJDK Java 14 development kit
local/jre-openjdk 14.0.2.u12-1
OpenJDK Java 14 full runtime environment
local/jre-openjdk-headless 14.0.2.u12-1
OpenJDK Java 14 headless runtime environment
local/openjdk-src 14.0.2.u12-1
OpenJDK Java 14 sources
Assuming you have sudo privileges and not in Ubuntu where package manager makes this easier -- I tried variations of prior answers and found this gem on Databricks blog for nonUbuntu (https://kb.databricks.com/r/install-rjava-rjdbc-libraries.html)
Installed JDK
sudo apt-get install openjdk-8-jdk
Verify path to libjvm.so; for me-->
cd /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64
grep -r libjvm
output:
Binary file server/libjvm.so matches <<<<<<<<
Do java configure
sudo R CMD javareconf
Remove prior versions of the package and install 'rJava' from CRAN mirror in RStudio
Restart RStudio
In RStudio verify link to libjvm.so
dyn.load('/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server/libjvm.so')
library('rJava')
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.