BwUniCluster2.0/Software/R/terra - Revision history

K Kuck at 15:44, 28 October 2024

2024-10-28T15:44:17Z

← Older revision		Revision as of 17:44, 28 October 2024
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	</pre>		</pre>

	== Preparations to use the terra and sf packages ==		= Preparations to use the terra and sf packages =
	Since <code>terra</code> and <code>sf</code> 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.		Since <code>terra</code> and <code>sf</code> 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.

2024-10-28T15:43:37Z

← Older revision		Revision as of 17:43, 28 October 2024
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	# Obtain interactive session		# Obtain interactive session
	salloc -n 8 -t 60 -p single		salloc -n 8 -t 60 -p single
	</pre>		</pre>


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	== Install external programs ==		== Install external programs ==

	First, we download the sources of GDAL, PROJ, GEOS (and their dependencies) and install them:		First, we download the sources of GDAL, PROJ, GEOS (and their dependencies) and install them:

	=== Install PROJ ===		=== Install PROJ ===
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	</pre>		</pre>

	== ~~Installing~~ the R packages ==		== Install the R packages ==

	In order to install the two R packages, we need to inform R where to find <code>PROJ</code>, <code>GDAL</code> and <code>GEOS</code>, so we export the necessary paths:		In order to install the two R packages, we need to inform R where to find <code>PROJ</code>, <code>GDAL</code> and <code>GEOS</code>, so we export the necessary paths:

	<pre>		<pre>

2024-10-28T15:42:59Z

← Older revision		Revision as of 17:42, 28 October 2024
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	<span style="color:red"><b>Note that the instructions provided below refer to R 4.4.1 (but not R 4.2.1)!</b></span>		<span style="color:red"><b>Note that the instructions provided below refer to R 4.4.1 (but not R 4.2.1)!</b></span>

2024-10-28T15:42:23Z

← Older revision		Revision as of 17:42, 28 October 2024
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	<span style="color:red"><b>Note that the instructions provided below refer to R 4.4.1 (but not R 4.2.1)~~! UNDER CONSTRUCTION!!~~!</b></span>		<span style="color:red"><b>Note that the instructions provided below refer to R 4.4.1 (but not R 4.2.1)!</b></span>

	= General information =		= General information =

2024-10-28T15:40:59Z

Preparations to use the terra and sf packages

← Older revision		Revision as of 17:40, 28 October 2024
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	</pre>		</pre>

	to your [[BwUniCluster_2.0_Slurm_common_Features#sbatch_Examples \| batch job scripts]] that use <code>terra</code> and <code>sf</code> or to ~~run~~ them ~~directly~~ in ~~the command line if you use~~ an [[BwUniCluster_2.0_Batch_Queues \| interactive session]].		to your [[BwUniCluster_2.0_Slurm_common_Features#sbatch_Examples \| batch job scripts]] that use <code>terra</code> and <code>sf</code> or to use them in an [[BwUniCluster_2.0_Batch_Queues \| interactive session]].

2024-10-28T15:40:23Z

Preparations to use the terra and sf packages

← Older revision		Revision as of 17:40, 28 October 2024
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	== Preparations to use the terra and sf packages ==		== Preparations to use the terra and sf packages ==
	Since terra and sf 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.		Since <code>terra</code> and <code>sf</code> 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		We recommend to add the export commands
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	</pre>		</pre>

	to your [[BwUniCluster_2.0_Slurm_common_Features#sbatch_Examples \| batch job scripts]] that use terra and sf or to run them directly in the command line if you use an [[BwUniCluster_2.0_Batch_Queues \| interactive session]].		to your [[BwUniCluster_2.0_Slurm_common_Features#sbatch_Examples \| batch job scripts]] that use <code>terra</code> and <code>sf</code> or to run them directly in the command line if you use an [[BwUniCluster_2.0_Batch_Queues \| interactive session]].

2024-10-28T15:39:04Z

Installing the R packages

← Older revision		Revision as of 17:39, 28 October 2024
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	<pre>		<pre>

	export LD_LIBRARY_PATH=$HOME/sw/R/lib64:$LD_LIBRARY_PATH		export LD_LIBRARY_PATH=$HOME/sw/R/lib64:$LD_LIBRARY_PATH
	export PATH=$PATH:$HOME/sw/R/bin		export PATH=$PATH:$HOME/sw/R/bin
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	R> library(sf)		R> library(sf)
	Linking to GEOS 3.13.0, GDAL 3.9.3, PROJ 9.4.1; sf_use_s2() is TRUE		Linking to GEOS 3.13.0, GDAL 3.9.3, PROJ 9.4.1; sf_use_s2() is TRUE


	</pre>		</pre>

2024-10-28T15:38:30Z

Install GEOS

← Older revision		Revision as of 17:38, 28 October 2024
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	=== Install GEOS ===		=== Install GEOS ===

	The last external package that needs to be compiled and installed is GEOS:		The last external package that needs to be compiled and installed is <code>GEOS</code>:
	<pre>		<pre>
	# Download and unpack the GEOS source code.		# Download and unpack the GEOS source code.

2024-10-28T15:38:08Z

Install GEOS

← Older revision		Revision as of 17:38, 28 October 2024
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	=== Install GEOS ===		=== Install GEOS ===

	The last package that needs to be compiled is GEOS:		The last external package that needs to be compiled and installed is GEOS:
	<pre>		<pre>
	# Download and unpack the GEOS source code.		# Download and unpack the GEOS source code.

2024-10-28T15:36:29Z

Preparations

← Older revision		Revision as of 17:36, 28 October 2024
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	If an <code>.R/Makevars</code> file is present in your home directory (<code>$HOME</code>), check whether the flags displayed below are already set and apply adjustments, if necessary:		If an <code>.R/Makevars</code> file is present in your home directory (<code>$HOME</code>), check whether the flags displayed below are already set and apply adjustments, if necessary:
	<pre>		<pre>
	# Ensure that the ~/.R/Makevars file has the following lines:
	cat $HOME/.R/Makevars		cat $HOME/.R/Makevars