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 VMware Tanzu Network.
This chapter contains the following information:
- R Data Science Libraries
- Installing the R Data Science Library Package
- Uninstalling the R Data Science Library Package
For information about the Greenplum Database PL/R Language, see Greenplum PL/R Language Extension.
Parent topic: Installing Optional Extensions (Tanzu Greenplum)
R Data Science Libraries
Libraries provided in the R Data Science package include:
abind adabag arm assertthat backports BH bitops car caret caTools cli clipr coda colorspace compHclust crayon curl data.table DBI Deriv dichromat digest doParallel dplyr e1071 ellipsis fansi fastICA fBasics fGarch flashClust foreach forecast foreign fracdiff gdata generics ggplot2 glmnet glue gower gplots | gss gtable gtools hms hybridHclust igraph ipred iterators labeling lattice lava lazyeval lme4 lmtest lubridate magrittr MASS Matrix MatrixModels mcmc MCMCpack minqa ModelMetrics MTS munsell mvtnorm neuralnet nloptr nnet numDeriv pbkrtest pillar pkgconfig plogr plyr prodlim purrr quadprog quantmod quantreg R2jags | R2WinBUGS R6 randomForest RColorBrewer Rcpp RcppArmadillo RcppEigen readr recipes reshape2 rjags rlang RobustRankAggreg ROCR rpart RPostgreSQL sandwich scales SparseM SQUAREM stabledist stringi stringr survival tibble tidyr tidyselect timeDate timeSeries tseries TTR urca utf8 vctrs viridisLite withr xts zeallot 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 $GPHOME
environment variables are set.
Locate the R Data Science library package that you built or downloaded.
The file name format of the package is
DataScienceR-<version>-relhel<N>_x86_64.gppkg
.Copy the package to the Greenplum Database master host.
Follow the instructions in Verifying the Greenplum Database Software Download to verify the integrity of the Greenplum Procedural Languages R Data Science Package software.
Use the
gppkg
command to install the package. For example:$ 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 theR_LIBS_USER
environment variable and updates thePATH
andLD_LIBRARY_PATH
environment variables in yourgreenplum_path.sh
file.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 userjags
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.