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For the docker image
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‎.Rbuildignore

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^pkgdown$
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^\.github$
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^\.covrignore$
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Dockerfile
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*.sh

‎Dockerfile

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FROM rocker/tidyverse:latest
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ENV PROJ_VERSION="9.4.1"
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ENV GDAL_VERSION="3.9.2"
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ENV GEOS_VERSION="3.12.2"
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COPY ./install_dev_osgeo.sh /rocker_scripts/install_dev_osgeo.sh
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COPY ./install_geospatial.sh /rocker_scripts/install_geospatial.sh
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RUN /rocker_scripts/install_dev_osgeo.sh
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#COPY ./install_geospatial_unstable.sh /rocker_scripts/install_geospatial_unstable.sh
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#RUN /rocker_scripts/install_geospatial_unstable.sh
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# Bioc sysreqs
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RUN apt-get update && apt-get install -y --no-install-recommends libfftw3-dev libmagick++-dev
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RUN Rscript -e "BiocManager::install(version = 'devel', ask = FALSE)"
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RUN Rscript -e "options(repos = c(CRAN='https://cloud.r-project.org')); BiocManager::install('Voyager', dependencies = TRUE)"
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RUN Rscript -e "remotes::install_github('pachterlab/SpatialFeatureExperiment', ref='devel')"
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RUN Rscript -e "remotes::install_github('pachterlab/voyager', ref='devel')"

‎install_dev_osgeo.sh

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#!/bin/bash
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set -e
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## Install PROJ, GDAL, GEOS from source.
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##
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## 'latest' means installing the latest release version.
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## build ARGs
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NCPUS=${NCPUS:-"-1"}
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PROJ_VERSION=${PROJ_VERSION:-"latest"}
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GDAL_VERSION=${GDAL_VERSION:-"latest"}
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GEOS_VERSION=${GEOS_VERSION:-"latest"}
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CRAN_SOURCE=${CRAN_SOURCE:-"https://cloud.r-project.org"}
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echo "options(repos = c(CRAN = '${CRAN}'))" >>"${R_HOME}/etc/Rprofile.site"
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# cmake does not understand "-1" as "all cpus"
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CMAKE_CORES=${NCPUS}
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if [ "${CMAKE_CORES}" = "-1" ]; then
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CMAKE_CORES=$(nproc --all)
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fi
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# a function to install apt packages only if they are not installed
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function apt_install() {
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if ! dpkg -s "$@" >/dev/null 2>&1; then
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if [ "$(find /var/lib/apt/lists/* | wc -l)" = "0" ]; then
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apt-get update
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fi
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apt-get install -y --no-install-recommends "$@"
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fi
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}
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# a function to remove apt packages only if they are installed
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function apt_remove() {
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if dpkg -s "$@" >/dev/null 2>&1; then
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apt-get remove -y "$@"
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fi
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}
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function url_latest_gh_released_asset() {
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wget -qO- "https://api.github.com/repos/$1/releases/latest" | grep -oP "(?<=\"browser_download_url\":\s\")https.*\.tar.gz(?=\")" | head -n 1
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}
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export DEBIAN_FRONTEND=noninteractive
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apt_remove gdal-bin libgdal-dev libgeos-dev libproj-dev &&
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apt-get autoremove -y
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## Derived from osgeo/gdal
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apt-get update
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apt-get install -y --fix-missing --no-install-recommends \
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ant \
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autoconf \
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automake \
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bash-completion \
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build-essential \
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ca-certificates \
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cmake \
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curl \
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git \
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libarchive-dev \
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libarmadillo-dev \
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libblosc-dev \
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libboost-dev \
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libbz2-dev \
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libcairo2-dev \
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libclc-15-dev \
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libcfitsio-dev \
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libcrypto++-dev \
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libcurl4-openssl-dev \
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libdeflate-dev \
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libexpat-dev \
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libfreexl-dev \
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libfyba-dev \
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libgif-dev \
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libheif-dev \
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libhdf4-alt-dev \
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libhdf5-serial-dev \
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libjpeg-dev \
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libkml-dev \
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liblcms2-2 \
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liblerc-dev \
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liblz4-dev \
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liblzma-dev \
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libmysqlclient-dev \
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libnetcdf-dev \
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libogdi-dev \
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libopenexr-dev \
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libopenjp2-7-dev \
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libpcre3-dev \
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libpng-dev \
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libpq-dev \
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libpoppler-dev \
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libpoppler-private-dev \
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libqhull-dev \
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libsqlite3-dev \
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libssl-dev \
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libtiff5-dev \
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libudunits2-dev \
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libwebp-dev \
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libxerces-c-dev \
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libxml2-dev \
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lsb-release \
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make \
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mdbtools-dev \
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pkg-config \
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python3-dev \
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python3-numpy \
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python3-setuptools \
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sqlite3 \
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swig \
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unixodbc-dev \
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wget \
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zlib1g-dev
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## geoparquet support
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wget https://apache.jfrog.io/artifactory/arrow/"$(lsb_release --id --short | tr '[:upper:]' '[:lower:]')"/apache-arrow-apt-source-latest-"$(lsb_release --codename --short)".deb
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apt_install -y -V ./apache-arrow-apt-source-latest-"$(lsb_release --codename --short)".deb
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apt-get update && apt-get install -y -V libarrow-dev libparquet-dev libarrow-dataset-dev
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rm -rf /build_local
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mkdir /build_local && cd /build_local
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## tiledb
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GCC_ARCH="$(uname -m)"
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export TILEDB_VERSION=2.16.3
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apt-get update -y &&
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DEBIAN_FRONTEND=noninteractive apt-get install -y \
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libspdlog-dev &&
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mkdir tiledb &&
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wget -q https://github.com/TileDB-Inc/TileDB/archive/${TILEDB_VERSION}.tar.gz -O - |
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tar xz -C tiledb --strip-components=1 &&
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cd tiledb &&
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mkdir build_cmake &&
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cd build_cmake &&
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../bootstrap --prefix=/usr --disable-werror &&
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make "-j$(nproc)" &&
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make install-tiledb DESTDIR="/build_thirdparty" &&
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make install-tiledb &&
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cd ../.. &&
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rm -rf tiledb &&
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for i in /build_thirdparty/usr/lib/"${GCC_ARCH}"-linux-gnu/*; do strip -s "$i" 2>/dev/null || /bin/true; done &&
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for i in /build_thirdparty/usr/bin/*; do strip -s "$i" 2>/dev/null || /bin/true; done
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LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
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# install geos
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# https://libgeos.org/usage/download/
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if [ "$GEOS_VERSION" = "latest" ]; then
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GEOS_VERSION=$(wget -qO- "https://api.github.com/repos/libgeos/geos/git/refs/tags" | grep -oP "(?<=\"ref\":\s\"refs/tags/)\d+\.\d+\.\d+" | tail -n -1)
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fi
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## purge existing directories to permit re-run of script with updated versions
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rm -rf geos* proj* gdal*
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wget https://download.osgeo.org/geos/geos-"${GEOS_VERSION}".tar.bz2
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bzip2 -d geos-*bz2
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tar xf geos*tar
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rm geos*tar
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cd geos*
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mkdir build
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cd build
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cmake ..
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cmake --build . --parallel "$CMAKE_CORES" --target install
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ldconfig
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cd /build_local
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# install proj
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# https://download.osgeo.org/proj/
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if [ "$PROJ_VERSION" = "latest" ]; then
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PROJ_DL_URL=$(url_latest_gh_released_asset "OSGeo/PROJ")
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else
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PROJ_DL_URL="https://download.osgeo.org/proj/proj-${PROJ_VERSION}.tar.gz"
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fi
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wget "$PROJ_DL_URL" -O proj.tar.gz
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tar zxvf proj.tar.gz
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rm proj.tar.gz
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cd proj-*
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mkdir build
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cd build
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cmake ..
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cmake --build . --parallel "$CMAKE_CORES" --target install
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ldconfig
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cd /build_local
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# install gdal
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# https://download.osgeo.org/gdal/
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if [ "$GDAL_VERSION" = "latest" ]; then
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GDAL_DL_URL=$(url_latest_gh_released_asset "OSGeo/gdal")
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else
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GDAL_DL_URL="https://download.osgeo.org/gdal/${GDAL_VERSION}/gdal-${GDAL_VERSION}.tar.gz"
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fi
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wget "$GDAL_DL_URL" -O gdal.tar.gz
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tar -xf gdal.tar.gz
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rm gdal*tar.gz
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cd gdal*
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mkdir build
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cd ./build
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# cmake .. -DCMAKE_BUILD_TYPE=Debug -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_JAVA_BINDINGS:BOOL=OFF -DBUILD_CSHARP_BINDINGS:BOOL=OFF
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cmake -DCMAKE_BUILD_TYPE=Release ..
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cmake --build . --parallel "$CMAKE_CORES" --target install
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ldconfig
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cd /build_local
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apt-get update && apt-get -y install cargo
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install2.r --error --skipmissing -n "$NCPUS" -r "${CRAN_SOURCE}" \
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sf \
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terra \
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lwgeom \
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stars \
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gdalcubes
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# Clean up
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rm -rf /var/lib/apt/lists/*
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rm -rf /tmp/downloaded_packages
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# Check the geospatial packages
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echo -e "Check the stars package...\n"
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R -q -e "library(stars)"
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echo -e "\nInstall stars package, done!"

‎install_geospatial.sh

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#!/bin/bash
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set -e
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# always set this for scripts but don't declare as ENV..
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export DEBIAN_FRONTEND=noninteractive
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## build ARGs
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NCPUS=${NCPUS:--1}
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# a function to install apt packages only if they are not installed
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function apt_install() {
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if ! dpkg -s "$@" >/dev/null 2>&1; then
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if [ "$(find /var/lib/apt/lists/* | wc -l)" = "0" ]; then
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apt-get update
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fi
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apt-get install -y --no-install-recommends "$@"
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fi
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}
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apt_install \
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gdal-bin \
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lbzip2 \
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libfftw3-dev \
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libgdal-dev \
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libgeos-dev \
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libgsl0-dev \
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libgl1-mesa-dev \
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libglu1-mesa-dev \
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libhdf4-alt-dev \
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libhdf5-dev \
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libjq-dev \
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libpq-dev \
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libproj-dev \
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libprotobuf-dev \
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libnetcdf-dev \
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libsqlite3-dev \
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libssl-dev \
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libudunits2-dev \
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netcdf-bin \
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postgis \
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protobuf-compiler \
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sqlite3 \
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tk-dev \
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unixodbc-dev
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install2.r --error --skipmissing --skipinstalled -n "$NCPUS" \
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RColorBrewer \
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RandomFields \
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RNetCDF \
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classInt \
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deldir \
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gstat \
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hdf5r \
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lidR \
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mapdata \
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maptools \
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mapview \
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ncdf4 \
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proj4 \
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raster \
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rgdal \
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rgeos \
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rlas \
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sf \
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sfarrow \
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sp \
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spacetime \
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spatstat \
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spatialreg \
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spdep \
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stars \
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terra \
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tidync \
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tmap \
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geoR \
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geosphere \
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BiocManager
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R -e "BiocManager::install('rhdf5')"
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## install wgrib2 for NOAA's NOMADS / rNOMADS forecast files
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## This is no longer needed, but we include it for reproducibility
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## reasons on earlier base images.
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source /etc/os-release
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if [ "${UBUNTU_CODENAME}" == "focal" ]; then
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/rocker_scripts/install_wgrib2.sh
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fi
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# Clean up
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rm -rf /var/lib/apt/lists/*
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rm -r /tmp/downloaded_packages
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## Strip binary installed lybraries from RSPM
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## https://github.com/rocker-org/rocker-versioned2/issues/340
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strip /usr/local/lib/R/site-library/*/libs/*.so

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