R Data Science Library Package

R Data Science Library Package

R packages are modules that contain R functions and data sets. Greenplum Database provides a collection of data science-related R libraries that can be used with the Greenplum Database PL/R language. You can download these libraries in .gppkg format from Pivotal Network.

This chapter contains the following information:

For information about the Greenplum Database PL/R Language, see Greenplum PL/R Language Extension.

R Data Science Libraries

Libraries provided in the R Data Science package include:

abind

adabag

arm

assertthat

BH

bitops

car

caret

caTools

coda

colorspace

compHclust

curl

data.table

DBI

dichromat

digest

dplyr

e1071

flashClust

foreign

gdata

ggplot2

glmnet

gplots

gtable

gtools

hms

hybridHclust

igraph

labeling

lattice

lazyeval

lme4

lmtest

magrittr

MASS

Matrix

MCMCPack

minqa

MTS

munsell

neuralnet

nloptr

nnet

pbkrtest

plyr

quantreg

R2jags

R6

randomForest

RColorBrewer

Rcpp

RcppEigen

readr

reshape2

rjags

RobustRankAggreg

ROCR

rpart

RPostgreSQL

sandwich

scales

SparseM

stringi

stringr

survival

tibble

tseries

zoo

Installing the R Data Science Library Package

Before you install the R Data Science Library package, make sure that your Greenplum Database is running, you have sourced greenplum_path.sh, and that the $MASTER_DATA_DIRECTORY and $GPHOME environment variables are set.

  1. Locate the R Data Science library package that you built or downloaded.

    The file name format of the package is DataScienceR-<version>-relhel<N>-x86_64.gppkg.

  2. Copy the package to the Greenplum Database master host.
  3. Use the gppkg command to install the package. For example:
    $ gppkg -i DataScienceR-<version>-relhel<N>-x86_64.gppkg

    gppkg installs the R Data Science libraries on all nodes in your Greenplum Database cluster. The command also sets the R_LIBS_USER environment variable and updates the PATH and LD_LIBRARY_PATH environment variables in your greenplum_path.sh file.

  4. Restart Greenplum Database. You must re-source greenplum_path.sh before restarting your Greenplum cluster:
    $ source /usr/local/greenplum-db/greenplum_path.sh
    $ gpstop -r
The Greenplum Database R Data Science Modules are installed in the following directory:
$GPHOME/ext/DataScienceR/library
Note: rjags libraries are installed in the $GPHOME/ext/DataScienceR/extlib/lib directory. If you want to use rjags and your $GPHOME is not /usr/local/greenplum-db, you must perform additional configuration steps to create a symbolic link from $GPHOME to /usr/local/greenplum-db on each node in your Greenplum Database cluster. For example:
$ gpssh -f all_hosts -e 'ln -s $GPHOME /usr/local/greenplum-db'
$ gpssh -f all_hosts -e 'chown -h gpadmin /usr/local/greenplum-db'

Uninstalling the R Data Science Library Package

Use the gppkg utility to uninstall the R Data Science Library package. You must include the version number in the package name you provide to gppkg.

To determine your R Data Science Library package version number and remove this package:

$ gppkg -q --all | grep DataScienceR
DataScienceR-<version>
$ gppkg -r DataScienceR-<version>

The command removes the R Data Science libraries from your Greenplum Database cluster. It also removes the R_LIBS_USER environment variable and updates the PATH and LD_LIBRARY_PATH environment variables in your greenplum_path.sh file to their pre-installation values.

Re-source greenplum_path.sh and restart Greenplum Database after you remove the R Data Science Library package:

$ . /usr/local/greenplum-db/greenplum_path.sh
$ gpstop -r 
Note: When you uninstall the R Data Science Library package from your Greenplum Database cluster, any UDFs that you have created that use R libraries installed with this package will return an error.