Skip to content
Go to file

Latest commit


Git stats


Failed to load latest commit information.
Latest commit message
Commit time


Package to bring RDF and SPARQL functionality to R, using the Jena libraries (needs Java7 or higher).

java/ -> Helper classes for the R rdf package.
rdf/ -> R package for dealing with RDF, using Jena.
rrdflibs/ -> Jena libraries

Information about this package can be found in this preprint:

Willighagen E. (2014) Accessing biological data in R with semantic web
technologies. PeerJ PrePrints 2:e185v3


(Please cite this paper if you use this package.)

To cite a specific release, you can use these DOIs:

  • rrdf 2.1.2 DOI
  • rrdf 2.1.1 DOI

User mailing list!forum/rrdf-user

Copyright / License

rrdflibs package

Copyright (C) 2011-2015 Egon Willighagen and contributors

Apache License 2.0 for for the rrdflibs package files.

Copyright for Jena is described in the LICENSE and java/NOTICE files. Please also visit

rrdf package

Copyright (C) 2011-2015 Egon Willighagen and contributors

License AGPL v3 for the rrdf package.

Authors / Contributors


Egon Willighagen

Contributions from:

Carl Boettiger, Ryan Kohl


Install from R

Previously, the packages were available from CRAN, but this is no longer the case.

Mind you, the below install_github() method will attempt to rebuild the vignette and therefore at this moment require a LaTeX distribution with pdflatex and a few packages installed. See also issue and

> install.packages("rJava") # if not present already
> install.packages("devtools") # if not present already
> library(devtools)
> install_github("egonw/rrdf", subdir="rrdflibs")
> install_github("egonw/rrdf", subdir="rrdf", build_vignettes = FALSE)

Compile from source

$ cd rrdf/java
$ groovy build.groovy
$ cd ../..
$ R CMD build rrdflibs
$ R CMD check --as-cran rrdflibs_1.4.0.tar.gz
$ R CMD build rrdf
$ tar xvf rrdf_2.0.4.tar.gz rrdf/inst/doc/tutorial.pdf
$ R CMD check --as-cran rrdf_2.0.4.tar.gz

Error Handling

In case of issues on Mac, follow the instructions below:

  • check that the $JAVA_PATH variable is correctly set. If not:
  1. Run touch ~/.bash_profile; open ~/.bash_profile in a Terminal window.
  2. add the following lines to your .bash_profile and then save: export JAVA_HOME=$(/usr/libexec/java_home) export LD_LIBRARY_PATH=/Library/Java/JavaVirtualMachines/jdk1.8.0_31.jdk/Contents/Home/jre/lib/server export PATH=$PATH:$JAVA_HOME/bin
  3. Run source ~/.bash_profile in a terminal window.
  • check that that Java >=1.7 is installed in your system. If not, go to
  • check that R sees the latest Java version (.jinit();.jcall("java/lang/System", "S", "getProperty", "java.runtime.version")). If not [1,2]:
  1. Download and install Apple’s Java version 1.6 like you were asked to.
  2. Reconfigure your R installation by typing sudo R CMD javareconf in a Terminal window.
  3. Trigger a recompile by reinstalling rJava by typing install.packages('rJava', type='source').
  4. Run sudo ln -f -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/lib in a Terminal window.
You can’t perform that action at this time.