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ARG BUILD_ON_IMAGE=glcr.b-data.ch/jupyterlab/r/verse
ARG R_VERSION=4.3.0
FROM ${BUILD_ON_IMAGE}:${R_VERSION}
ARG NCPUS=1
ARG DEBIAN_FRONTEND=noninteractive
ARG BUILD_ON_IMAGE
ARG BUILD_START
ENV PARENT_IMAGE=${BUILD_ON_IMAGE}:${R_VERSION} \
BUILD_DATE=${BUILD_START}
USER root
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
libfftw3-dev \
libgdal-dev \
libgeos-dev \
libgsl0-dev \
#libgl1-mesa-dev \
#libglu1-mesa-dev \
libhdf4-alt-dev \
libhdf5-dev \
libjq-dev \
#libpq-dev \
libproj-dev \
libprotobuf-dev \
libnetcdf-dev \
#libsqlite3-dev \
#libssl-dev \
libudunits2-dev \
netcdf-bin \
postgis \
protobuf-compiler \
sqlite3 \
tk-dev \
#unixodbc-dev
&& install2.r --error --skipinstalled -n $NCPUS \
#RColorBrewer \
RNetCDF \
classInt \
deldir \
gstat \
hdf5r \
lidR \
mapdata \
maptools \
mapview \
ncdf4 \
proj4 \
raster \
rgdal \
rgeos \
rlas \
sf \
sp \
spacetime \
spatstat \
spatialreg \
spdep \
stars \
terra \
tidync \
tmap \
geoR \
geosphere \
## from bioconductor
&& R -e "BiocManager::install('rhdf5', update = FALSE, ask = FALSE)" \
## Clean up
&& rm -rf /tmp/* \
&& rm -rf /var/lib/apt/lists/*
## Switch back to ${NB_USER} to avoid accidental container runs as root
USER ${NB_USER}