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.
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")Information on building and devloping the CDKR package is available in teh Otherwise if you prefer the command line
cd /tmp/
git clone [email protected]:CDK-R/rcdklibs.git
R CMD INSTALL rcdklibs
git clone [email protected]: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.
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.