Latest revision as of 11:52, 15 February 2024

1 General information

Note that rgdal and rgeos have been retired by their developers in 2023! Please find further information at https://cran.r-project.org/web/packages/rgdal/index.html and https://cran.r-project.org/web/packages/rgeos/index.html.

Follow the instructions provided under bwUniCluster2.0/Software/R/terra to install the alternatives terra and sf.

Installing rgdal and rgeos is, however, still possible using the instructions below.

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

2 Installation

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

2.1 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 ..

2.2 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"
export CXX17=icpc

Now, we install rgdal and rgeos from within R. Note that, since we install a package from a local repository the order of the package installation is relevant. Installing rgdal will fail if sp is not available.

module load math/R/4.1.2

cd 
wget https://cran.r-project.org/src/contrib/Archive/rgdal/rgdal_1.6-4.tar.gz
wget https://cran.r-project.org/src/contrib/Archive/rgeos/rgeos_0.6-1.tar.gz

R -q
> install.packages("sp", repos="https://ftp.gwdg.de/pub/misc/cran/")
> install.packages("~/rgdal_1.6-4.tar.gz", repos=NULL, type="source")
> install.packages("~/rgeos_0.6-1.tar.gz", repos=NULL, type="source")

> library("rgdal")
> library("rgeos")

2.3 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.

@@ Line 1: / Line 1: @@
-= Rgdal =
+= General information =
+<span style="color:red"><b>Note that rgdal and rgeos have been retired by their developers in 2023!</b> Please find further information at [https://cran.r-project.org/web/packages/rgdal/index.html https://cran.r-project.org/web/packages/rgdal/index.html] and [https://cran.r-project.org/web/packages/rgeos/index.html https://cran.r-project.org/web/packages/rgeos/index.html]. </span>
+<b>Follow the instructions provided under [[bwUniCluster2.0/Software/R/terra]] to install the alternatives terra and sf.</b>
+<span style="color:red"><b>Installing rgdal and rgeos is, however, still possible using the instructions below.</b></span>
+rgdal and rgeos allows to use the following tools for handling spatial structures in R
+* the 'Geospatial' Data Abstraction Library [https://gdal.org/ GDAL]
+* Projection/transformation operations from the [https://proj.org/ PROJ] library
+* Interface to the open source Geometry Engine [https://libgeos.org/ 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.
+<pre>
+salloc -n 4 -t 30 -p dev_single
+</pre>
+First, provide the source directory (if not yet existing)
 <pre>
-module load math/R
-# Get sources
 mkdir -p ~/src
 cd ~/src
+</pre>
-wget http://download.osgeo.org/gdal/2.2.2/gdal-2.2.2.tar.gz
-wget http://download.osgeo.org/geos/geos-3.6.2.tar.bz2
-wget http://download.osgeo.org/proj/proj-4.9.3.tar.gz
-# Not using git version
-#git clone https://github.com/OSGeo/proj.4.git
+Then, download and install PROJ
-# Build gdal
+<pre>
-tar xf gdal-2.2.2.tar.gz
-cd gdal-2.2.2
+PROJ_VER=6.3.2
+wget http://download.osgeo.org/proj/proj-$PROJ_VER.tar.gz
-./configure --prefix=$HOME/sw
+tar xf proj-$PROJ_VER.tar.gz
-make -j4
+cd proj-$PROJ_VER
+./configure --prefix=$HOME/sw/R
+make -j 8
 make install
 cd ..
+</pre>
+Then, install gdal
-# Build geos
-tar xf geos-3.6.2.tar.bz2
+<pre>
-cd geos-3.6.2
+GDAL_VER=3.4.1
-./configure --prefix=$HOME/sw
+wget http://download.osgeo.org/gdal/$GDAL_VER/gdal-$GDAL_VER.tar.gz
-make -j4
+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 ..
+</pre>
+Finally, install GEOS
-# Build proj.4
+<pre>
-# Not using git version
+GEOS_VER=3.9.2
-#cd proj.4
+wget http://download.osgeo.org/geos/geos-$GEOS_VER.tar.bz2
-#git checkout 4.9.3 -b 4.9.3
+tar xf geos-$GEOS_VER.tar.bz2
-#git branch
+cd geos-$GEOS_VER
-#autoreconf -i
+./configure --prefix=$HOME/sw/R
-tar xf proj-4.9.3.tar.gz
+make -j 8
-cd proj-4.9.3
-./configure --prefix=$HOME/sw
-make -j4
 make install
 cd ..
+</pre>
+== Installing the R packages ==
-# Set up environment (you may want to put these lines in your ~/.bashrc as well)
-export PATH=$PATH:$HOME/sw/bin
+In order to install the two R packages, we need R to understand where we installed the 3 underlying programs, so we export the necessary paths.
-export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/sw/lib
-export MANPATH=$MANPATH:$HOME/sw/man
+<pre>
-export GDAL_DATA=$HOME/sw/share/gdal
-export CFLAGS=-I$HOME/sw/include
+export LD_LIBRARY_PATH=$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
+</pre>
+Additionally, the R package installation features compilation of built-in C++ code, for which we specify compilation options ('compiler flags')
+<pre>
+export CFLAGS=-I$HOME/sw/R/include
+export CXX="icpc -std=c++11"
+export CXX17=icpc
+</pre>
+Now, we install rgdal and rgeos from within R. Note that, since we install a package from a local repository the order of the package installation is relevant. Installing rgdal will fail if sp is not available.
+<pre>
+module load math/R/4.1.2
+cd
+wget https://cran.r-project.org/src/contrib/Archive/rgdal/rgdal_1.6-4.tar.gz
+wget https://cran.r-project.org/src/contrib/Archive/rgeos/rgeos_0.6-1.tar.gz
-# Install rgdal and rgeos packages from within R session
 R -q
+> install.packages("sp", repos="https://ftp.gwdg.de/pub/misc/cran/")
-# Problem with too many arguments
+> install.packages("~/rgdal_1.6-4.tar.gz", repos=NULL, type="source")
-#install.packages("rgdal", configure.args = c("--with-proj-include=~/sw/include", "--with-proj-lib=~/sw/lib", "--with-proj-share=~/sw/share/proj"))
-install.packages("rgdal")
+> install.packages("~/rgeos_0.6-1.tar.gz", repos=NULL, type="source")
-install.packages("rgeos")
-library("rgdal")
+> library("rgdal")
-library("rgeos")
+> library("rgeos")
 </pre>
+== Preparations to use the rgdal/rgeos packages ==
+Since rgdal and rgeos depend on the external programs we installed, several environment variables have to be set before using the packages to allow R to address these programs.
+We recommend to add the export commands
+<pre>
+export LD_LIBRARY_PATH=$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
+</pre>
+to your [[BwUniCluster_2.0_Slurm_common_Features#sbatch_Examples | batch job scripts]] that use rgdal and rgeos or to run them directly in the command line if you use an [[BwUniCluster_2.0_Batch_Queues | interactive session]].

Difference between revisions of "BwUniCluster2.0/Software/R/Rgdal"

Latest revision as of 11:52, 15 February 2024

Contents

1 General information

2 Installation

2.1 Install external programs

2.2 Installing the R packages

2.3 Preparations to use the rgdal/rgeos packages

Navigation menu

Personal tools

Namespaces

Variants

Views

More

Search

bwHPC Wiki

bwHPC Systems

Documentation

Support

Data Storage

Tools