BwUniCluster2.0/Software/R/Rgdal: Difference between revisions

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== Preparations to use the rgdal/rgeos packages ==
== Preparations to use the rgdal/rgeos packages ==
Since rgdal and rgeos depend on the external programs we installed, we recommend to add the export commands
Since rgdal and rgeos depend on the external programs we installed, several environment variables have to be set before using the packages to allow R to address these programs.

We recommend to add the export commands


<pre>
<pre>

Revision as of 16:01, 23 June 2022

General information

Installation of rgdal and rgeos allows to use the following tools for handling spatial structures in R

  • the 'Geospatial' Data Abstraction Library GDAL
  • Projection/transformation operations from the PROJ library
  • Interface to the open source Geometry Engine GEOS

Installation

Please enter the following code, presented in the boxes below, directly into your shell/command line on bwUniCluster.

Install external programs

First, we download the sources of GDAL, PROJ, GEOS and install the three programs.

We will gather them in a folder src, unpack there and then compile.

We strongly recommend to use a interactive session with multiple cores.

salloc -n 4 -t 30 -p dev_single


First, provide the source directory (if not yet existing)

mkdir -p ~/src
cd ~/src

Then, download and install PROJ

PROJ_VER=6.3.2
wget http://download.osgeo.org/proj/proj-$PROJ_VER.tar.gz
tar xf proj-$PROJ_VER.tar.gz
cd proj-$PROJ_VER
./configure --prefix=$HOME/sw/R
make -j 8 
make install
cd ..

Then, install gdal

GDAL_VER=3.4.1
wget http://download.osgeo.org/gdal/$GDAL_VER/gdal-$GDAL_VER.tar.gz
tar xf gdal-$GDAL_VER.tar.gz
cd gdal-$GDAL_VER
./configure --prefix=$HOME/sw/R --with-proj=$HOME/sw/R
make -j 8
make install
cd ..

Finally, install GEOS

GEOS_VER=3.9.2
wget http://download.osgeo.org/geos/geos-$GEOS_VER.tar.bz2
tar xf geos-$GEOS_VER.tar.bz2
cd geos-$GEOS_VER
./configure --prefix=$HOME/sw/R
make -j 8 
make install
cd ..

Installing the R packages

In order to install the two R packages, we need R to understand where we installed the 3 underlying programs, so we export the necessary paths.

export LD_LIBRARY_PATH=$HOME/sw/R/lib:$LD_LIBRARY_PATH
export PATH=$PATH:$HOME/sw/R/bin
export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$HOME/sw/R/lib/pkgconfig
export GDAL_DATA=$HOME/sw/R/share/gdal


Additionally, the R package installation features compilation of built-in C++ code, for which we specify compilation options ('compiler flags')

export CFLAGS=-I$HOME/sw/R/include
export CXX="icpc -std=c++11"


Now, we install rgdal and rgeos from within R

module load math/R/4.1.2
R -q
> install.packages("rgdal")
> install.packages("rgeos")
> library("rgdal")
> library("rgeos")

Preparations to use the rgdal/rgeos packages

Since rgdal and rgeos depend on the external programs we installed, several environment variables have to be set before using the packages to allow R to address these programs.

We recommend to add the export commands

export LD_LIBRARY_PATH=$HOME/sw/R/lib:$LD_LIBRARY_PATH
export PATH=$PATH:$HOME/sw/R/bin
export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$HOME/sw/R/lib/pkgconfig
export GDAL_DATA=$HOME/sw/R/share/gdal

to your batch job scripts that use rgdal and rgeos or to run them directly in the command line if you use an interactive session.