rrdf

Created: 2011-03-22 21:08
Updated: 2019-01-02 10:31
License: other

README.md

About

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

See https://dx.doi.org/10.7287/peerj.preprints.185v3

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

To cite a specific release, you can use these http://zenodo.org/ DOIs:

  • rrdf 2.1.2 DOI
  • rrdf 2.1.1 DOI

User mailing list

https://groups.google.com/forum/#!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 https://jena.apache.org/.

rrdf package

Copyright (C) 2011-2015 Egon Willighagen and contributors

License AGPL v3 for the rrdf package.

Authors / Contributors

Authors:

Egon Willighagen

Contributions from:

Carl Boettiger, Ryan Kohl

(See: https://github.com/egonw/rrdf/graphs/contributors)

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 https://github.com/egonw/rrdf/issues/28 and https://github.com/egonw/rrdf/issues/29.

> 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 https://java.com/it/download/
  • 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 Appleā€™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.
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