KNIME Interactive R Statistics Integration Installation Guide


Introduction

This guide describes how to install the KNIME Interactive R Statistics Integration to be used with KNIME Analytics Platform.

The KNIME Interactive R Statistics Integration allows to write and execute R scripts by interacting with an external R™ installation.

This integration comprises a handful of nodes which can be used to write R scripts and execute them in KNIME Analytics Platform. Besides providing the ability to read data from R into KNIME Analytics Platform, these nodes allow to manipulate data and create views using R, as well as to learn and apply models, trained in R, to the data.

These nodes can be found in the node repository under ScriptingR.

010 KNIME Rintegration node repository

This integration, in order to communicate with R, depends on additional R packages which need to be installed. In this guide we describe how to configure the KNIME Interactive R Statistics Integration, as well as how to install R and the necessary packages.

KNIME Interactive R Statistics Integration installation

The following steps are required to install and use the KNIME Interactive R Statistics Integration.

  1. First, install the KNIME Interactive R Statistics Integration.

    In KNIME Analytics Platform, go to FileInstall KNIME Extensions…​. The KNIME Interactive R Statistics Integration can be found under KNIME & Extensions or by entering R integration into the search box.

  2. Download and install R and all required packages as described in the R installation and R packages installation Sections.

  3. Finally, configure the KNIME Interactive R Statistics Integration.

    In KNIME Analytics Platform go to FilePreferences. From the list on the left, select R under KNIME and the following dialog opens:

    020 KNIME Rintegration Installation set path to R

    In Path to R Home enter the path to identify the location where R is installed and click Apply to make the changes effective. This path can be found from within R by typing R.home().

R installation

The installation files as well as all the necessary information about R installation can be found on one of the mirror sites of the Comprehensive R Archive Network (CRAN). R installation can be completed safely using the default settings. The destination location where R will be installed will have to be specified in KNIME Analytics Platform and can be found from within R by typing R.home().

  • For R installation on Windows the default location is recommended (e.g. usually C:\Program Files\R\R-<version>).

  • On macOS systems the R installation folder location is usually /Library/Frameworks/R.framework/Versions/Current/Resources/.

  • On Linux, instead, the installation folder is usually located in /usr/lib/R.

We recommend using R via the command-line interface and to avoid using RStudio or other tools as this might lead to unexpected behavior.

R packages installation

Rserve is an R package that allows other applications to talk to R using TCP/IP or local sockets sending binary requests. It requires different installation steps and different packages depending on the operating system in use.

Windows

  1. Proceed with the installation of Rserve.

    From within R run the command:

    install.packages('Rserve')

    This will install the version 1.7-3.1 of Rserve.

    If the library folder is not writable a warning message will appear, together with the request to use a personal library:

    Warning in install.packages("Rserve") :
      'lib = "C:/Program Files/R/R-3.6.3/library"' is not writable
    Would you like to use a personal library instead? (yes/No/cancel) yes

    answer "yes" and a personal library will be installed and used.

    Please test the installation with KNIME Analytics Platform and in case a problem is encountered follow the instructions at point 2.
  2. If the procedure at point 1 did not work properly, the installation of the latest version of Rserve might be necessary.

    1. First, from within R, remove any previously installed Rserve version running the command:

      remove.packages("Rserve")
    2. In this case, also Rtools, a collection of tools necessary for building R packages on Windows, needs to be installed. The installer is available here. In this guide Rtools is assumed to be installed under the default destination (e.g. usually C:\Rtools\).

      040 KNIME Rintegration WinRtools path

      Check the box Add rtools to system PATH as shown in the above picture.

    3. Please make sure that both R bin path and Rtools path are added to the Windows Path variable. From the Start menu open the Control Panel and click System. In the dialog that opens, click Advanced system settings in the left column. This opens the System Properties window. Here, click Environment Variables…​. Then in the System variables section click Edit…​ to inspect and, if required, change the variable Path. Add the paths to R and Rtools bin folders, if they are not yet listed.

      041 KNIME Rintegration Win troubleshooting
    4. Finally, download and install the latest version of Rserve. From within R type the command:

      install.packages('Rserve',,"http://rforge.net/",type="source")

MacOS

  1. First, Clang and GNU Fortran are needed. If they are not already installed, the installation packages can be downloaded from this link.

  2. Another program that needs to be installed is XQuartz, which is available for download at this link.

    A script is also available that can be used to install all of the necessary packages for R integration in KNIME Analytics Platform with macOS >= 10.14. After installing the KNIME Interactive R Statistics Integration the script can be found in KNIME/plugins/org.knime.r_<knime_version>/scripts/ or at this link, only for KNIME Analytics Platform version 4.2 or higher. To allow for the execution of the script, please open a new Terminal and from the folder containing the script run chmod u+x <name_of_the_script>.sh.
  3. Then the R package Rserve can be installed. Run R from Terminal and type the command:

    install.packages('Rserve',,"http://rforge.net/",type="source")

    The following error might appear when installing Rserve:

    *** Rserve requires R (shared or static) library.                       ***
    *** Please install R library or compile R with either --enable-R-shlib  ***

    If your macOS is < 10.14 (Mojave), open a new Terminal window and type the following command:

    xcode-select --install

    otherwise please make use of the previously mentioned script.

    Now continue with installing the Rserve package.

  4. Finally, the R package Cairo needs to be installed. From within R type the command:

    install.packages('Cairo')

Linux Ubuntu

To install Rserve, run R from Terminal and type the command:

install.packages('Rserve',,"http://rforge.net/",type="source")

If the following error message appears:

/usr/bin/ld: cannot find -lssl
collect2: error: ld returned 1 exit status

open a new Terminal window, type the following command:

sudo apt install libssl-dev

and continue with installing Rserve.