rcdk: a chemistry library

The goal of cdkr is to provide easy access to CDK chemoinformatics library to combine the simplicity and power of R with CDK’s powerful, tested API.

Installation

rCDK package releases are available on CRAN or on Github via Devtools:

# releases
install.packages("rcdk")

# development releases of `cdkr` are also available on github uinsg devtools:
library(devtools)
install_github("https://github.com/CDK-R/rcdklibs")
install_github("https://github.com/CDK-R/cdkr", subdir="rcdk")

Building and Development

Information on building and devloping the CDKR package is available in teh Otherwise if you prefer the command line

    cd /tmp/
    git clone git@github.com:CDK-R/rcdklibs.git
    R CMD INSTALL rcdklibs
    git clone git@github.com:CDK-R/cdkr.git
    cd cdkr/rcdkjar
    ant clean jar
    cd ../
    R CMD INSTALL rcdk

Before performing the install, you should have the following dependencies installed:

• rJava
• fingerprint
• png
• RUnit
• Java JDK >= 1.8

For the png package, I have tested png-0.1-7

Some users have reported that rcdk methods (such as parse.smiles) are returning errors related to class not found or class version mismatch. This can happen when you are using a prepackaged version of rJava from CRAN and is caused by that package not finding the correct JRE home if you have multiple Java versions installed. In such a case, reinstalling rJava from sources appears to resolve this issue. See this discussion.

Installing Java

rCDK uses the CDK library that requires the Java JDK >= 1.8. In order to install rCDK, this requirement must be satisfied. You can check your java version on the command line as follows:

> java -version
> java version "1.8.0"

If your version is not 1.8 you may need to download and install a more recent installation of JAVA. If you have multiple versions of JAVA you may be using an older version. On Mac OSX, for example, the latest OS installs JAVA 1.6 and you will need to reconfigure your JAVA install. You can try the following:

# set the java version
R CMD javareconf  # or ....
sudo R CMD javareconf

# re install fromfrom R
install.packages('rJava', type="source")

Further informaiton about R’s use of Java can be found here.