K Kuck: Created page with "Note that the instructions provided below refer to R 4.2.1 (but not R 4.4.1)! = 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 https://cran.r-project.org/web/packages/rgdal/index.html] and [https://cran.r-project.org/web/packages/rgeos/index.html https://cran.r-p..."

2024-10-27T11:48:41Z

Created page with "Note that the instructions provided below refer to R 4.2.1 (but not R 4.4.1)! = 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 https://cran.r-project.org/web/packages/rgdal/index.html] and [https://cran.r-project.org/web/packages/rgeos/index.html https://cran.r-p..."

New page

Note that the instructions provided below refer to R 4.2.1 (but not R 4.4.1)!

= 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 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]. 

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 [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>
mkdir -p ~/src
cd ~/src
</pre>

Then, download and install PROJ
<pre>
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 ..
</pre>

Then, install gdal

<pre>
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 ..
</pre>

Finally, install GEOS
<pre>
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 ..
</pre>

== 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.

<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>

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

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")
</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]].

BwUniCluster2.0/Software/R/Rgdal (R 4.2.1) - Revision history