From 69f8eb14fd8c923a834bc0e1786850680f4e10fc Mon Sep 17 00:00:00 2001
From: 16EAGLE <jxsw@web.de>
Date: Fri, 11 Jun 2021 14:41:04 +0200
Subject: [PATCH] updated Dockerfile to install spatial packages

---
 Dockerfile | 31 ++++++++++++++++++-------------
 1 file changed, 18 insertions(+), 13 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 874a684..95df68d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,10 +1,11 @@
 FROM ubuntu:focal
 FROM opendatacube/geobase:wheels-3.0.4  as env_builder
-
 ARG py_env_path=/env
 
+# set rpy2 to ABI mode, since R is installed after rpy2
 ENV RPY2_CFFI_MODE=ABI
 
+# install python dependencies
 RUN mkdir -p /conf
 COPY requirements.txt /conf/
 RUN env-build-tool new /conf/requirements.txt ${py_env_path} /wheels
@@ -23,8 +24,7 @@ RUN useradd -m -s /bin/bash -N jovyan -g 100 -u 1000 \
 	&& chown jovyan /home/jovyan \
 	&& addgroup jovyan staff
 
-# R kernel install
-
+# install R dependencies
 RUN apt-get update \
 	&& apt-get install -y --no-install-recommends \
 		software-properties-common \
@@ -38,23 +38,20 @@ RUN apt-get update \
         && add-apt-repository --enable-source --yes "ppa:marutter/rrutter4.0" \
         && add-apt-repository --enable-source --yes "ppa:c2d4u.team/c2d4u4.0+"
 
-## Configure default locale, see https://github.com/rocker-org/rocker/issues/19
+# configure default locale, see https://github.com/rocker-org/rocker/issues/19
 RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
 	&& locale-gen en_US.utf8 \
 	&& /usr/sbin/update-locale LANG=en_US.UTF-8
 
+# set env variables for noninteractive
 ENV LC_ALL en_US.UTF-8
 ENV LANG en_US.UTF-8
-
-## This was not needed before but we need it now
-ENV DEBIAN_FRONTEND noninteractive
-
-## Otherwise timedatectl will get called which leads to 'no systemd' inside Docker
 ENV TZ UTC
 
-# Now install R and littler, and create a link for littler in /usr/local/bin
+# install R and littler, and create a link for littler in /usr/local/bin
 # Default CRAN repo is now set by R itself, and littler knows about it too
 # r-cran-docopt is not currently in c2d4u so we install from source
+ARG DEBIAN_FRONTEND=noninteractive
 RUN apt-get update \
         && apt-get install -y --no-install-recommends \
                  littler \
@@ -69,11 +66,19 @@ RUN apt-get update \
  	&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
  	&& rm -rf /var/lib/apt/lists/*
 
-RUN apt-get update&&apt-get install -y --no-install-recommends r-cran-reticulate libudunits2-dev sqlite3
-RUN R -e 'install.packages(c("IRkernel", "rgdal", "sf", "stars", "raster", "basemaps"))' 
-#,  "raster", "sp", "sf", "stars", "basemaps", "mapview", "mapedit", "devtools", "usethis", "testthat", "roxygen2", "ggplot2"))'
+# install system dependencies for suite of spatial R packages
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update&&apt-get install -y apt-utils pkg-config
+RUN apt-get install -y libsqlite3-dev libudunits2-dev libssl-dev libmagick++-dev libcurl4-openssl-dev
+RUN apt-get update&&apt-get install -y --no-install-recommends r-cran-reticulate
+
+# install R packages
+RUN R -e 'install.packages(c("IRkernel", "rgdal", "sp", "raster", "sf", "basemaps", "ggplot2", "mapview", "mapedit", "devtools", "usethis", "testthat", "roxygen2"))'
+
+# initiliaze R kernel for Jupyter
 RUN R -e "IRkernel::installspec(user = FALSE)"
 
+# set user and working dir
 USER jovyan
 WORKDIR /notebooks