tidy

scripts/install_osgeo.sh → scripts/experimental/install_dev_osgeo.sh

@@ -7,101 +7,157 @@ set -e
 
 ## build ARGs
 NCPUS=${NCPUS:-"-1"}
+
 PROJ_VERSION=${PROJ_VERSION:-"latest"}
 GDAL_VERSION=${GDAL_VERSION:-"latest"}
 GEOS_VERSION=${GEOS_VERSION:-"latest"}
+
 CRAN_SOURCE=${CRAN_SOURCE:-"https://cloud.r-project.org"}
 echo "options(repos = c(CRAN = '${CRAN}'))" >>"${R_HOME}/etc/Rprofile.site"
 
 # cmake does not understand "-1" as "all cpus"
 CMAKE_CORES=${NCPUS}
 if [ "${CMAKE_CORES}" = "-1" ]; then
-CMAKE_CORES=$(nproc --all)
+    CMAKE_CORES=$(nproc --all)
 fi
 
 # a function to install apt packages only if they are not installed
 function apt_install() {
-  if ! dpkg -s "$@" >/dev/null 2>&1; then
-  if [ "$(find /var/lib/apt/lists/* | wc -l)" = "0" ]; then
-  apt-get update
-  fi
-  apt-get install -y --no-install-recommends "$@"
-  fi
-}
-
-function url_latest_gh_released_asset() {
-  wget -qO- "https://api.github.com/repos/$1/releases/latest" | grep -oP "(?<=\"browser_download_url\":\s\")https.*\.tar.gz(?=\")" | head -n 1
+    if ! dpkg -s "$@" >/dev/null 2>&1; then
+        if [ "$(find /var/lib/apt/lists/* | wc -l)" = "0" ]; then
+            apt-get update
+        fi
+        apt-get install -y --no-install-recommends "$@"
+    fi
 }
 
 # a function to remove apt packages only if they are installed
 function apt_remove() {
-  if dpkg -s "$@" >/dev/null 2>&1; then
-  apt-get remove -y "$@"
-  fi
+    if dpkg -s "$@" >/dev/null 2>&1; then
+        apt-get remove -y "$@"
+    fi
 }
 
 
+function url_latest_gh_released_asset() {
+    wget -qO- "https://api.github.com/repos/$1/releases/latest" | grep -oP "(?<=\"browser_download_url\":\s\")https.*\.tar.gz(?=\")" | head -n 1
+}
+
 export DEBIAN_FRONTEND=noninteractive
+
+
 apt_remove gdal-bin libgdal-dev libgeos-dev libproj-dev \
-&& apt-get autoremove -y
+  && apt-get autoremove -y
 
 JAVA_VERSION=17
-
-apt-get update && apt-get -y install \
+## Derived from osgeo/gdal
+apt-get update
+apt-get install -y --fix-missing --no-install-recommends \
+  ant \
+  autoconf \
+  automake \
+  bash-completion \
+  build-essential \
+  ca-certificates \
+  cmake \
+  curl \
   git \
-  lsb-release \
+  libarchive-dev \
+  libarmadillo-dev \
+  libblosc-dev \
+  libboost-dev \
+  libbz2-dev \
   libcairo2-dev \
+  libclc-15-dev \
+  libcfitsio-dev \
+  libcrypto++-dev \
   libcurl4-openssl-dev \
+  libdeflate-dev \
+  libexpat-dev \
+  libfreexl-dev \
+  libfyba-dev \
+  libgif-dev \
+  libgeotiff-dev \
+  libheif-dev \
+  libhdf4-alt-dev \
+  libhdf5-serial-dev \
+  libjpeg-dev \
+  libkml-dev \
+  liblcms2-2 \
+  liblerc-dev \
+  liblz4-dev \
+  liblzma-dev \
+  libmysqlclient-dev \
+  libnetcdf-dev \
+  libogdi-dev \
+  libopenexr-dev \
+  libopenjp2-7-dev \
+  libpcre3-dev \
+  libpng-dev \
   libpq-dev \
+  libpoppler-dev \
+  libpoppler-private-dev \
+  libqhull-dev \
   libsqlite3-dev \
+  libssl-dev \
+  libtiff5-dev \
+  libudunits2-dev \
+  libwebp-dev \
+  libxerces-c-dev \
+  libxml2-dev \
+  lsb-release \
   make \
-  pandoc \
-  qpdf \
+  mdbtools-dev \
+  pkg-config \
+  python3-dev \
+  python3-numpy \
+  python3-setuptools \
   sqlite3 \
-  valgrind \
-  vim \
+  swig \
+  unixodbc-dev \
   wget \
-  libnode-dev \
-  libjq-dev \
-  libssh-dev \
-  libgit2-dev \
-  locales \
-  libssl-dev \
-  python3-dev python3-numpy python3-setuptools \
-  libpng-dev libjpeg-dev libgif-dev liblzma-dev \
-  curl libxml2-dev libexpat-dev libxerces-c-dev \
-  libnetcdf-dev libpoppler-dev libpoppler-private-dev \
-  swig ant libhdf4-alt-dev libhdf5-dev \
-  libfreexl-dev unixodbc-dev  mdbtools-dev libwebp-dev \
-  liblcms2-2 libpcre3-dev libcrypto++-dev libfyba-dev \
-  libkml-dev libmysqlclient-dev libogdi-dev \
-  libcfitsio-dev openjdk-"$JAVA_VERSION"-jdk libzstd-dev \
-  libpq-dev libssl-dev libboost-dev \
-  autoconf automake bash-completion libarmadillo-dev \
-  libopenexr-dev libheif-dev \
-  libdeflate-dev libblosc-dev liblz4-dev libbz2-dev \
-  libbrotli-dev \
-  libarchive-dev \
-  libaec-dev
-
+  zlib1g-dev
 ## geoparquet support
 wget https://apache.jfrog.io/artifactory/arrow/"$(lsb_release --id --short | tr '[:upper:]' '[:lower:]')"/apache-arrow-apt-source-latest-"$(lsb_release --codename --short)".deb
 apt_install -y -V ./apache-arrow-apt-source-latest-"$(lsb_release --codename --short)".deb
 apt-get update && apt-get install -y -V libarrow-dev libparquet-dev libarrow-dataset-dev
 
-LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
 rm -rf /build_local
 mkdir /build_local && cd /build_local
 
-## purge existing directories to permit re-run of script with updated versions
-rm -rf geos* proj* gdal*
+## tiledb
+GCC_ARCH="$(uname -m)"
+export TILEDB_VERSION=2.16.3
+apt-get update -y \
+    && DEBIAN_FRONTEND=noninteractive apt-get install -y \
+        libspdlog-dev \
+    && mkdir tiledb \
+    && wget -q https://github.com/TileDB-Inc/TileDB/archive/${TILEDB_VERSION}.tar.gz -O - \
+        | tar xz -C tiledb --strip-components=1 \
+    && cd tiledb \
+    && mkdir build_cmake \
+    && cd build_cmake \
+    && ../bootstrap --prefix=/usr --disable-werror \
+    && make -j$(nproc) \
+    && make install-tiledb DESTDIR="/build_thirdparty" \
+    && make install-tiledb \
+    && cd ../.. \
+    && rm -rf tiledb \
+    && for i in /build_thirdparty/usr/lib/${GCC_ARCH}-linux-gnu/*; do strip -s $i 2>/dev/null || /bin/true; done \
+    && for i in /build_thirdparty/usr/bin/*; do strip -s $i 2>/dev/null || /bin/true; done
+
+
+LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
 
 # install geos
 # https://libgeos.org/usage/download/
 if [ "$GEOS_VERSION" = "latest" ]; then
-GEOS_VERSION=$(wget -qO- "https://api.github.com/repos/libgeos/geos/git/refs/tags" | grep -oP "(?<=\"ref\":\s\"refs/tags/)\d+\.\d+\.\d+" | tail -n -1)
+    GEOS_VERSION=$(wget -qO- "https://api.github.com/repos/libgeos/geos/git/refs/tags" | grep -oP "(?<=\"ref\":\s\"refs/tags/)\d+\.\d+\.\d+" | tail -n -1)
 fi
-
+
+## purge existing directories to permit re-run of script with updated versions
+rm -rf geos* proj* gdal*
+
 wget https://download.osgeo.org/geos/geos-"${GEOS_VERSION}".tar.bz2
 bzip2 -d geos-*bz2
 tar xf geos*tar
@@ -117,9 +173,9 @@ cd /build_local
 # install proj
 # https://download.osgeo.org/proj/
 if [ "$PROJ_VERSION" = "latest" ]; then
-PROJ_DL_URL=$(url_latest_gh_released_asset "OSGeo/PROJ")
+    PROJ_DL_URL=$(url_latest_gh_released_asset "OSGeo/PROJ")
 else
-  PROJ_DL_URL="https://download.osgeo.org/proj/proj-${PROJ_VERSION}.tar.gz"
+    PROJ_DL_URL="https://download.osgeo.org/proj/proj-${PROJ_VERSION}.tar.gz"
 fi
 
 wget "$PROJ_DL_URL" -O proj.tar.gz
@@ -136,9 +192,9 @@ cd /build_local
 # install gdal
 # https://download.osgeo.org/gdal/
 if [ "$GDAL_VERSION" = "latest" ]; then
-GDAL_DL_URL=$(url_latest_gh_released_asset "OSGeo/gdal")
+    GDAL_DL_URL=$(url_latest_gh_released_asset "OSGeo/gdal")
 else
-  GDAL_DL_URL="https://download.osgeo.org/gdal/${GDAL_VERSION}/gdal-${GDAL_VERSION}.tar.gz"
+    GDAL_DL_URL="https://download.osgeo.org/gdal/${GDAL_VERSION}/gdal-${GDAL_VERSION}.tar.gz"
 fi
 
 wget "$GDAL_DL_URL" -O gdal.tar.gz
@@ -153,16 +209,15 @@ cmake --build . --parallel "$CMAKE_CORES" --target install
 ldconfig
 cd /build_local
 
-# R package dependencies
-apt-get -y install cargo libudunits2-dev
+apt-get update && apt-get -y install cargo
 
 install2.r --error --skipmissing -n "$NCPUS" -r ${CRAN_SOURCE} \
-  sf \
-  terra \
-  lwgeom \
-  stars \
-  gdalcubes \
-  gifski
+   sf \
+   terra \
+   lwgeom \
+   stars \
+   gdalcubes \
+   gifski
 
 # Clean up
 rm -rf /var/lib/apt/lists/*
@@ -172,4 +227,4 @@ rm -rf /tmp/downloaded_packages
 
 echo -e "Check the stars package...\n"
 R -q -e "library(stars)"
-echo -e "\nInstall stars package, done!"
+echo -e "\nInstall stars package, done!"