Tag Archives: rhel

Installing rJava in RHEL

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Installing rJava on Ubuntu is a piece of cake. All you have to do the code below, and boom!!! You got rJava working in R.

 sudo apt-get install openjdk-7-jdk
 sudo apt-get install r-cran-rjava
 export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-i386
 export LD_LIBRARY_PATH=$JAVA_HOME/jre/lib/i386:$JAVA_HOME/jre/lib/i386/client

Now, the challenge was trying to get rJava working on RHEL. I could not find any proper documentation that worked. Instead, I ran into a bunch of posts and pointing to things that worked in their environment, but not on mine (so, this might not work on yours as well, but I hope it does). I usually like to give credit to the sources, but this time, they were so many over a long time span, that I could not remember what came from where anymore. So, I apologize for that. Below are the things that I did to get rJava working.

packages need

$ sudo yum install gcc-c++ gcc-gfortran R R-core R-core-devel R-devel R-java R-java-devel java-1.7.0-openjdk-devel
$ sudo yum list install gcc*

Once, you have installed the necessary packages; then it is time to

configure your environment

$ sudo /usr/sbin/alternatives --config java #select openjdk
$ sudo /usr/sbin/alternatives --config javac #select openjdk
$ export JAVA_HOME=/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91.x86_64/jre
$ export PATH=$PATH:$JAVA_HOME/bin
$ sudo /usr/bin/R CMD javareconf
$ R
> install.packages("rJava") #install rJava on R console

And that is it! If you got the install.packages(“rJava”) to work on R, that means that now you can call Java from within R console.

How to install a new version of python in RHEL 6

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So, if you have RHEL 6, you might be stuck with Python 2.6.  But, not really.  Even though you might not be able to install a new version of python using yum, you can still download a new version of python and install it in your environment.  Now, you can install it and replace the current version or you can install another version and have two python in your system.

  1. Install GCC by typing 
    sudo yum install gcc
  2. Go to 
    cd /usr/src/

  3. Now, let’s download a release from python.org. In this example we will be using Python 3.5.0.

    sudo wget https://www.python.org/ftp/python/3.5.0/Python-3.5.0.tar.xz sudo tar xf Python-3.5.0.tar.xz sudo cd Python-3.5.0
  4. Let’s compile 
    sudo ./configure
  5. Let’s build the package 
    sudo make
  6. Now, to install it you have two options.  You can either overwrite the python executable or you can install as concurrent instance.
    1. If you want to overwrite the OS python executable 
       sudo make install
    2. If you want to install concurrent (not overwritting the OS executable) 
       sudo make altinstall
  7. Now let’s link it so others could use it 
     sudo ln -s /usr/local/bin/python3.5 /usr/bin/python3.5
  8. Now test it by invoking the following command 
    python3.5 -V

    You should have the following result

    "Python 3.5.0"
  9. If you get that result let’s continue, otherwise look back and see what step you missed.
  10. Now that you have python 3.5 install along with 2.7, you might want to install pip to handle package installations.
  11. In order to do that, let’s first download pip. 
    cd ~/Downloads
wget https://bootstrap.pypa.io/get-pip.py
  12. Now, let’s install it 
     sudo python3.5 get-pip.py

    If setuptools is not installed, get-pip.py will automatically install setuptools.

  13. To check pip if installed successfully 
     pip3.5 -V

    You should have the following result

     "pip 7.1.2 from /usr/local/lib/python3.5/site-packages (python 3.5)"
  14. If you want others to use pip with sudo command, you probably want to do this
  15. sudo ln -s /usr/local/bin/pip3.5 /usr/bin/pip3.5
  16. And there you go!  Now you have two python versions and two pip versions running concurrently on your OS.

Sources

https://www.python.org/

https://pip.pypa.io/en/stable/installing/

http://stackoverflow.com/questions/8087184/installing-python3-on-rhel

http://stackoverflow.com/questions/6587507/how-to-install-pip-with-python-3