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Using R and GDAL in conda

Source: vignettes/articles/r-and-gdal-in-conda.Rmd
r-and-gdal-in-conda.Rmd

DRAFT: last updated 2026-05-17

Conda is an open-source, cross-platform, language-agnostic package manager and environment management system. It was originally developed to solve package management challenges faced by Python data scientists, and today is a popular package manager for Python and R [Wikipedia].

Conda uses the concept of channels as the base for hosting and managing packages. Conda is often associated with the commercial company Anaconda which provides the Anaconda.org channel of packages. Alternatively, the conda-forge project builds and distributes packages via conda-forge.org, specializing in hard-to-build or unique packages that often arise in a scientific computing context. Conda-forge is community-driven and community-curated. Both conda and conda-forge are NumFocus-affiliated projects.

Conda offers features potentially of interest to R users who work with geospatial data:

  • install different versions of binary software packages and required dependencies on multiple supported platforms
  • assemble sets of packages in isolation from the rest of the compute platform using environments
  • manage and switch between environments that use various packages for different projects
  • access to current R or previous release version, a large number of CRAN packages, and current GDAL with dependencies
  • benefit from lightweight modular GDAL packaging based on deferred plugin loading
  • available plugins include format drivers that sometimes are unavailable in other package managers, such as the Arrow and Parquet vector drivers

Conda-forge provides pre-compiled binary packages for gdalraster that track CRAN releases, for the following platforms:

Conda Platforms

Installation

Install Miniforge: https://conda-forge.org/download/

The webpage provides links to the installer for each supported platform along with basic installation instructions. For more detailed instructions, see https://github.com/conda-forge/miniforge.

Other conda distributions could also be used. Conda-forge recommends the use of Miniforge instead of the Anaconda Distribution to reduce chances of unsolvable/conflicting installations, and it is a smaller download.

On Linux, at the end of the installation you will prompted with:

$ Proceed with initialization? [yes|no]

Enter yes so that the PATH environment variable is set correctly in your .bashrc file , but also note the command given along with that prompt, which can be used to undo this later if you choose:

conda config --set auto_activate_base false

You can also use the command conda deactivate to deactivate the conda base environment in your shell at any time, if needed, and conda activate to re-activate it.

Working with conda environments

Environments in conda are self-contained, isolated spaces where you can install specific versions of Python and R along with packages and their dependencies. Conda provides a comprehensive feature set for managing environments. You can create, export, list, remove, and update environments that have different versions of software installed in them. Switching or moving between environments is called activating the environment.

More information on environments can be found in the documentation from Anaconda:

https://www.anaconda.com/docs/getting-started/working-with-conda/environments

Creating a new environment for R

The syntax for creating and activating a new environment in the terminal is:

conda create --name <ENV_NAME> [package1] [package2] [...]
conda activate <ENV_NAME>

When creating a new environment, you can add R by explicitly including r-base in the list of packages. The r-essentials package is a bundle of commonly used R packages, which also includes the r-recommended bundle (i.e., the packages graphics, methods, stats, tools, utils, etc. that are normally included with base R).

The example below creates an R environment named r_env with gdalraster included. The package channel can be specified with --channel conda-forge, or here using short names -c, and -n for the environment --name. The command conda list will print a list of all installed packages in the activated environment.

conda create -c conda-forge -n r_env r-base r-essentials r-gdalraster
conda activate r_env
conda list

Note that conda-forge is the default channel in Miniforge, so it could be omitted here. It would need to be specified explicitly as shown above if a different conda distribution is used.

R package names in conda-forge always have the r- prefix. When using R in conda, packages should be installed with the conda package manager rather than from source or binaries using install.packages() (i.e., should not mix packages from CRAN or other repositories such as R-universe). A web portal for exploring packages available in conda-forge can be found at: https://conda-forge.org/packages/.

GDAL installation in conda

GDAL is available in conda-forge as a modular set of packages that take advantage of GDAL’s support of deferred plugins for geospatial format drivers. This provides an efficient and streamlined approach to handling dependencies. The plugin system for conda was developed by Quansight and Hobu, with more details at:

https://quansight.com/post/introducing-lightweight-versions-of-gdal-and-pdal/

The list of available packages is reproduced here.

GDAL conda-forge packages:

  • libgdal-core: core C++ library
  • libgdal: core C++ library and all plugins except arrow/parquet
  • gdal: python library without the plugins

GDAL plugin conda-forge packages:

  • libgdal-arrow-parquet: vector.arrow and vector.parquet drivers as a plugin
  • libgdal-fits: raster.fits driver as a plugin
  • libgdal-grib: raster.grib driver as a plugin
  • libgdal-hdf4: raster.hdf4 driver as a plugin
  • libgdal-hdf5: raster.hdf5 driver as a plugin
  • libgdal-jp2openjpeg:raster.jp2openjpeg driver as a plugin
  • libgdal-kea: raster.kea driver as a plugin
  • libgdal-netcdf: raster.netcdf driver as a plugin
  • libgdal-pdf: raster.pdf driver as a plugin
  • libgdal-postgisraster: raster.postgisraster driver as a plugin
  • libgdal-pg: vector.pg driver as a plugin
  • libgdal-tiledb: raster.tiledb driver as a plugin
  • libgdal-xls: vector.xls driver as a plugin

The package libgdal-core is a dependency of r-gdalraster so installed automatically, but the additional driver plugins are optional. We’ll install additional drivers before starting an R session in order to work with Parquet vector files. The following command installs libgdal-arrow-parquet in the active environment (assuming conda-forge is the default channel):

conda install libgdal-arrow-parquet

Working with gdalraster in conda

We can now start an R session in the active environment by typing R + <Enter>.

The code below uses a sample GeoPackage file included with gdalraster containing perimeter polygons of fires within Yellowstone National Park during 1984-2022 [Monitoring Trends in Burn Severity program MTBS]. The polygons are in a Lambert Conformal Conic projection (Montana State Plane EPSG:32100). The GeoPackage layer will be converted to Parquet format, with inverse projection to WGS84 latitude / longitude coordinates.

gdalraster provides API bindings to GDAL’s command line interface (CLI) algorithms. The vector reproject algorithm implements reprojection with optional format conversion.

library(gdalraster)
#> GDAL 3.13.0 (released 2026-05-04), GEOS 3.14.1, PROJ 9.8.1

# check that the Parquet driver is available
gdal_formats("Parquet") |> str()
#> 'data.frame':    1 obs. of  17 variables:
#>  $ short_name             : chr "Parquet"
#>  $ extensions             : chr "parquet"
#>  $ raster                 : logi FALSE
#>  $ multidim_raster        : logi FALSE
#>  $ vector                 : logi TRUE
#>  $ geography_network      : logi FALSE
#>  $ rw_flag                : chr "rw+u"
#>  $ virtual_io             : logi TRUE
#>  $ subdatasets            : logi FALSE
#>  $ long_name              : chr "(Geo)Parquet"
#>  $ sql_dialects           : chr "OGRSQL SQLITE"
#>  $ creation_datatypes     : chr ""
#>  $ creation_field_types   : chr "Integer Integer64 Real String Date Time DateTime Binary IntegerList Integer64List RealList StringList"
#>  $ creation_field_subtypes: chr "Boolean Int16 Float32 JSON UUID"
#>  $ multiple_vec_layers    : logi FALSE
#>  $ read_field_domains     : logi FALSE
#>  $ creation_fld_dom_types : chr ""

# source GPKG with MTBS fire perimeters
src <- system.file("extdata/ynp_fires_1984_2022.gpkg", package = "gdalraster")
(src_lyr <- new(GDALVector, src, "mtbs_perims"))
#> C++ object of class <GDALVector>
#> • Driver: GeoPackage (GPKG)
#> • DSN:
#> "/home/ctoney/miniforge3/envs/r_env/lib/R/library/gdalraster/extdata/ynp_fires_1984_2022.gpkg"
#> • Layer: mtbs_perims
#> • CRS: NAD83 / Montana (EPSG:32100)
#> • Geometry: MULTIPOLYGON

src_lyr$getFeatureCount()
#> [1] 61

# get info on GDAL algorithm usage
gdal_usage("vector reproject")
#> 
#> Usage: vector reproject [OPTIONS] <INPUT> <OUTPUT>
#> 
#> Reproject a vector dataset. 
#> 
#> Positional arguments:
#>   -i, --input <INPUT>
#>     Input vector datasets
#>     [required]
#>   -o, --output <OUTPUT>
#>     Output vector dataset
#>     [required]
#> 
#> Common options:
#>   -q, --quiet
#>     Quiet mode (no progress bar or warning message)
#> 
#> Options:
#>   -l, --layer, --input-layer <INPUT-LAYER>
#>     Input layer name(s)
#>     [0 or more values]
#>     [packed values allowed, repeated arg allowed]
#>   -f, --of, --format, --output-format <OUTPUT-FORMAT>
#>     Output format ("GDALG" allowed)
#>   --co, --creation-option <KEY>=<VALUE>
#>     Creation option
#>     [0 or more values]
#>     [packed values not allowed, repeated arg allowed]
#>   --lco, --layer-creation-option <KEY>=<VALUE>
#>     Layer creation option
#>     [0 or more values]
#>     [packed values not allowed, repeated arg allowed]
#>   --overwrite
#>     Whether overwriting existing output dataset is allowed
#>     [default: FALSE]
#>   --update
#>     Whether to open existing dataset in update mode
#>     [default: FALSE]
#>   --overwrite-layer
#>     Whether overwriting existing output layer is allowed
#>     [default: FALSE]
#>   --append
#>     Whether appending to existing layer is allowed
#>     [default: FALSE]
#>     [mutually exclusive with --upsert]
#>   --output-layer <OUTPUT-LAYER>
#>     Output layer name
#>   --skip-errors
#>     Skip errors when writing features
#>   --active-layer <ACTIVE-LAYER>
#>     Set active layer (if not specified, all)
#>   -s, --input-crs <INPUT-CRS>
#>     Input CRS
#>   -d, --output-crs <OUTPUT-CRS>
#>     Output CRS
#>     [required]
#> 
#> Advanced options:
#>   --if, --input-format <INPUT-FORMAT>
#>     Input formats
#>     [0 or more values]
#>     [packed values allowed, repeated arg allowed]
#>   --oo, --open-option <KEY>=<VALUE>
#>     Open options
#>     [0 or more values]
#>     [packed values not allowed, repeated arg allowed]
#>   --output-oo, --output-open-option <KEY>=<VALUE>
#>     Output open options
#>     [0 or more values]
#>     [packed values not allowed, repeated arg allowed]
#>   --upsert
#>     Upsert features (implies 'append')
#>     [mutually exclusive with --append]
#> 
#> For more details: <https://gdal.org/programs/gdal_vector_reproject.html>

# inverse project to WGS84
dst <- "/home/ctoney/data/ynp_fires_1984_2022.parquet"
args <- list(input = src_lyr,
             output = dst,
             output_crs = "EPSG:4326")

# run the algorithm and close datasets when finished
gdal_run("vector reproject", args, close = TRUE)
#> ✔ Done (21ms)
#> 
#> C++ object of class <GDALAlg>
#>   • Command: "vector reproject"
#>   • Description: Reproject a vector dataset.
#>   • Help URL: <https://gdal.org/programs/gdal_vector_pipeline.html>

(dst_lyr <- new(GDALVector, dst))
#> C++ object of class <GDALVector>
#>   • Driver: (Geo)Parquet (Parquet)
#>   • DSN: "/home/ctoney/data/ynp_fires_1984_2022.parquet"
#>   • Layer: ynp_fires_1984_2022
#>   • CRS: WGS 84 (EPSG:4326)
#>   • Geometry: MULTIPOLYGON

dst_lyr$info()
#> INFO: Open of `/home/ctoney/data/ynp_fires_1984_2022.parquet'
#>       using driver `Parquet' successful.
#> 
#> Layer name: ynp_fires_1984_2022
#> Geometry: Multi Polygon
#> Feature Count: 61
#> Extent: (-111.144825, 44.127297) - (-109.830665, 45.117887)
#> Layer SRS WKT:
#> GEOGCRS["WGS 84",
#>     ENSEMBLE["World Geodetic System 1984 ensemble",
#>         MEMBER["World Geodetic System 1984 (Transit)"],
#>         MEMBER["World Geodetic System 1984 (G730)"],
#>         MEMBER["World Geodetic System 1984 (G873)"],
#>         MEMBER["World Geodetic System 1984 (G1150)"],
#>         MEMBER["World Geodetic System 1984 (G1674)"],
#>         MEMBER["World Geodetic System 1984 (G1762)"],
#>         MEMBER["World Geodetic System 1984 (G2139)"],
#>         MEMBER["World Geodetic System 1984 (G2296)"],
#>         ELLIPSOID["WGS 84",6378137,298.257223563,
#>             LENGTHUNIT["metre",1]],
#>         ENSEMBLEACCURACY[2.0]],
#>     PRIMEM["Greenwich",0,
#>         ANGLEUNIT["degree",0.0174532925199433]],
#>     CS[ellipsoidal,2],
#>         AXIS["geodetic latitude (Lat)",north,
#>             ORDER[1],
#>             ANGLEUNIT["degree",0.0174532925199433]],
#>         AXIS["geodetic longitude (Lon)",east,
#>             ORDER[2],
#>             ANGLEUNIT["degree",0.0174532925199433]],
#>     USAGE[
#>         SCOPE["Horizontal component of 3D system."],
#>         AREA["World."],
#>         BBOX[-90,-180,90,180]],
#>     ID["EPSG",4326]]
#> Data axis to CRS axis mapping: 2,1
#> FID Column = fid
#> Geometry Column = geom
#> event_id: String (254.0)
#> incid_name: String (254.0)
#> incid_type: String (254.0)
#> map_id: Integer64 (0.0)
#> burn_bnd_ac: Integer64 (0.0)
#> burn_bnd_lat: String (10.0)
#> burn_bnd_lon: String (10.0)
#> ig_date: Date
#> ig_year: Integer (0.0)

# check the linework
features <- dst_lyr$fetch(-1)
nrow(features)
#> [1] 61

plot(features, xlab = "longitude", ylab = "latitude",
     main = "Yellowstone NP Fire Perimeters 1984-2022")

A plot of fire perimeters in Yellowstone National Park during 1984 to 2022. The plot has black linework on white background. The coordinate system is geographic, with longitude on the x axis and latitude on the y axis.

src_lyr$close()
dst_lyr$close()

Created with reprex v2.1.1

See also