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 Tanzu Network.

This chapter contains the following information:

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

Parent topic: Installing Optional Extensions

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
  • forecast
  • 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. Follow the instructions in Verifying the Greenplum Database Software Download to verify the integrity of the Greenplum Procedural Languages R Data Science Package software. 4. Use the gppkg command to install the package. For example:

1. $ 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. 5. Restart Greenplum Database. You must re-source greenplum_path.sh before restarting your Greenplum cluster:

1. $ source /usr/local/greenplum-db/greenplum_path.sh 2. $ gpstop -r

The Greenplum Database R Data Science Modules are installed in the following directory:

1. $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:

1. $ gpssh -f all_hosts -e 'ln -s $GPHOME /usr/local/greenplum-db'
2. $ 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:

1. $ gppkg -q --all | grep DataScienceR
2. DataScienceR-<version>
3. $ 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:

1. $ . /usr/local/greenplum-db/greenplum_path.sh
2. $ 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.