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https://github.com/egonw/rrdf

R package for handling RDF data.
https://github.com/egonw/rrdf

r-package rdf semantic-web

Last synced: 3 months ago
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R package for handling RDF data.

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# 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](https://zenodo.org/badge/doi/10.5281/zenodo.34307.svg)](http://dx.doi.org/10.5281/zenodo.34307)

* rrdf 2.1.1 [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.20717.svg)](http://dx.doi.org/10.5281/zenodo.20717)



# 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/](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 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.