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 am trying to update Qt from 5.5.1 to 5.7 or higher.
I tried sudo apt-get install qt-default qtdeclarative5-dev
gives me following output on console:
qtdeclarative5-dev is already the newest version (5.5.1-2ubuntu6).
qt5-default is already the newest version (5.5.1+dfsg-16ubuntu7.6).
How can I update Qt to 5.7 or higher version?
Ubuntu packages in standard repository are always outdated. I suggest you install Qt from .run file they provide .
But you can possibly run into problems, as i did, using Qt + CMake without Qt Creator
I followed this post and was able to update Qt to 5.11 using PPA following commands:
sudo add-apt-repository ppa:beineri/opt-qt-5.11.1-xenial
sudo apt update
sudo apt install qt511-meta-full
For system wide usage, create default.conf file at /etc/xdg/qtchooser with following content:
/opt/qt511/bin
/opt/qt511/lib
That's it, it should be updated by now. qmake -v outputs the current Qt and qmake version
My simple Dockerfile:
FROM ubuntu:18.04
RUN apt update && apt upgrade -y
RUN apt install build-essential cmake qt5-default -y
RUN apt install qttools5-dev-tools -y
When I check linguist inside the container it's there:
root#9087245330a7:/# which linguist
/usr/bin/linguist
...but when I configure my app inside the container:
CMake Error at CMakeLists.txt:72 (find_package):
By not providing "FindQt5LinguistTools.cmake" in CMAKE_MODULE_PATH this
project has asked CMake to find a package configuration file provided by
"Qt5LinguistTools", but CMake did not find one.
Could not find a package configuration file provided by "Qt5LinguistTools"
(requested version 5.5.1) with any of the following names:
Qt5LinguistToolsConfig.cmake
qt5linguisttools-config.cmake
Add the installation prefix of "Qt5LinguistTools" to CMAKE_PREFIX_PATH or
set "Qt5LinguistTools_DIR" to a directory containing one of the above
files. If "Qt5LinguistTools" provides a separate development package or
SDK, be sure it has been installed.
What is going on? This works on Ubuntu 16.04 just fine.
The problem was that in Ubuntu 18.04+ you need to install also qttools5-dev in order to get /usr/lib/x86_64-linux-gnu/cmake/Qt5LinguistTools/Qt5LinguistToolsConfig.cmake.
I installed QT creator in debian linux. If I try to create a new project, in Kit option I got the error like "No valid Kit found". If I go to Tools ->Options -> Build&Run -> kit, there is no options to select. But I installed same in ubuntu, it is working fine without same problem. What im missing?
Also suggest me if I need to reinstall the QT creator or something else...
Its time to explain the tricks to install QT creator in debian linux operating system.
STEP 1: dont install just QT creator in your PC.
Install whole package of QT [link to download QT SDK below][1]
[1]: http://www.qt.io/download-open-source/#section-2 , so that you will get all the libraries and dependencies.
After downloading the file is in the ".run" format . Install the downloaded file in your terminal (by giving commands).
STEP 2: install
sudo apt-get install g++
sudo apt-get install libgl1-mesa-dev libglu1-mesa-dev
in your terminal.
STEP 3: install
sudo apt-get install libcanberra-gtk-module
sudo apt-get install libcanberra-gtk-module:i386
now restart your system once and create new project.It should work
I like to thank agold for his guidance , Actually he spent more than 3 hours to resolve this issue. :)
I need to install Qt5 to my Debian using commandline. How can I do that?
My system:
debian 2.6.30-vortex86mx-yh
I am trying to install using qt online installer from qt-project.org.
But after ./qt.run I get this error:
libstdc++.so.6 version glibcxx_3.4.11 not found
I try to install libstdc++6. but Debian said it is already newest version.
cat /etc/issue result is:
Debian 5.0
Also my debian has no gui. I have to do it using commandline.
Try this command for installing from default debian 5 repository:
#apt install g++
#apt install qtcreator
#apt install qtdeclarative5-dev
You should be able to run the qt-installer in a decent debian version. Get Version by:
cat /etc/issue
On older versions or "unsupported" versions you can still download the sources and build the libraries yourself, which is probably your way to go, since the vortex86-builds are pretty limited in compiler flags. Compiling is rather easy, depending on your needs. The configure script itself gives you a lot of hints regarding possible flags.
Another alternative is to find a user-managed repository that has QT5 for your debian version and add this repository to your sources.lst, so you could perform a apt-get install libqt5.