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https://github.com/bluxmit/alnoda-workspaces.git
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98 lines
3 KiB
Bash
98 lines
3 KiB
Bash
#!/bin/bash
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## Update configuration files for R and install some libraries.
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##
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## The URL of the default repository for R packages written to Rprofile.site,
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## refers to the CRAN environment variable or to the first argument of this script.
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## In order of preference, first argument of the script, the CRAN variable.
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## ex. https://cloud.r-project.org, https://cran.r-project.org
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set -e
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CRAN=${1:-${CRAN:-"https://cran.r-project.org"}}
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ARCH=$(uname -m)
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# a function to install apt packages only if they are not installed
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function apt_install() {
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if ! dpkg -s "$@" >/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 lsb-release
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## mechanism to force source installs if we're using RSPM
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UBUNTU_VERSION=$(lsb_release -sc)
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CRAN_SOURCE=${CRAN/"__linux__/$UBUNTU_VERSION/"/""}
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## source install if using RSPM and arm64 image
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if [ "$ARCH" = "aarch64" ]; then
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CRAN=$CRAN_SOURCE
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fi
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## Add a default CRAN mirror
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echo "options(repos = c(CRAN = '${CRAN}'), download.file.method = 'libcurl')" >>"${R_HOME}/etc/Rprofile.site"
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## Set HTTPUserAgent for RSPM (https://github.com/rocker-org/rocker/issues/400)
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cat <<EOF >>"${R_HOME}/etc/Rprofile.site"
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# https://docs.rstudio.com/rspm/admin/serving-binaries/#binaries-r-configuration-linux
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options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version["platform"], R.version["arch"], R.version["os"])))
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EOF
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## Install OpenBLAS and hot-switching to it
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## https://github.com/rocker-org/rocker-versioned2/issues/390
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if ! dpkg -l | grep -q libopenblas-dev; then
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apt_install libopenblas-dev
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update-alternatives --set "libblas.so.3-${ARCH}-linux-gnu" "/usr/lib/${ARCH}-linux-gnu/openblas-pthread/libblas.so.3"
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fi
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## Install littler
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if [ ! -x "$(command -v r)" ]; then
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BUILDDEPS="libpcre2-dev \
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liblzma-dev \
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libbz2-dev \
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zlib1g-dev \
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libicu-dev"
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if [ "$(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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# shellcheck disable=SC2086
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apt_install ${BUILDDEPS}
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Rscript -e "install.packages(c('littler', 'docopt'), repos='${CRAN_SOURCE}')"
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# Clean up
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# shellcheck disable=SC2086
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apt-get remove --purge -y ${BUILDDEPS}
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apt-get autoremove -y
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apt-get autoclean -y
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fi
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## Symlink littler and littler's installation scripts
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ln -sf "${R_HOME}/site-library/littler/bin/r" /usr/local/bin/r
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ln -sf "${R_HOME}/site-library/littler/examples/installGithub.r" /usr/local/bin/installGithub.r
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## Use rocker scripts version install2.r if it exists
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if [ -f "/rocker_scripts/bin/install2.r" ]; then
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ln -sf /rocker_scripts/bin/install2.r /usr/local/bin/install2.r
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else
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ln -sf "${R_HOME}/site-library/littler/examples/install2.r" /usr/local/bin/install2.r
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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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# Check the R info
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echo -e "Check the littler info...\n"
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r --version
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echo -e "Check the R info...\n"
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R -q -e "sessionInfo()"
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echo -e "Setup R, done!" |