WSL2 の Ubuntu 20.04 LTS に R4.1.0＋RStudio Server 1.4＋radian をセットアップする script。CRANパッケージは RStudio Package Manager のバイナリパッケージを利用

WSL2_R410_provision.sh

#!/bin/bash -x

## provisioning script for RStudio Server on ubuntu / WSL
## MRAN and RSPM libraries are fixed at 2021-08-09 (the last day before 4.1.1)

sudo apt update
sudo apt upgrade -y

# Japanese language support
sudo apt install -y language-pack-ja-base language-pack-ja fonts-noto-cjk

# Change environment to Japanese (Character and DateTime)
#   ref: https://ill-identified.hatenablog.com/entry/2021/06/11/140544

sudo /usr/sbin/update-locale LANG=ja_JP.UTF-8
sudo chmod 666 /etc/timezone
sudo echo "Asia/Tokyo" > /etc/timezone
sudo chmod 644 /etc/timezone
sudo dpkg-reconfigure -f noninteractive tzdata
echo 'export LANG=ja_JP.UTF-8' >> ~/.bashrc
echo 'export LC_ALL=ja_JP.UTF-8' >> ~/.bashrc

# Install latest version of R 4.1.0 (4.1.0-1.2004.0_all / 2021-05-18) from
#  Microsoft R Application Network (MRAN) snapshot

## install Microsoft IT SSL SHA2 CA Certificate
curl --output "msitwww2(1).crt" "http://www.microsoft.com/pki/mscorp/msitwww2(1).crt"
openssl x509 -in "msitwww2(1).crt" -inform DER -out msitwww2.crt -outform PEM
sudo cp msitwww2.crt /usr/share/ca-certificates/
sudo chmod 666 /etc/ca-certificates.conf
sudo echo "msitwww2.crt" >> /etc/ca-certificates.conf
sudo update-ca-certificates
rm *.crt

## install R
export MRAN="https://cran.microsoft.com/snapshot/2021-08-09/"
sudo chmod 777 /etc/apt/sources.list.d
sudo apt install -y \
    gdebi-core \
    build-essential \
    libcurl4-gnutls-dev \
    libxml2-dev \
    libssl-dev \
    gfortran
sudo apt install --no-install-recommends \
    software-properties-common \
    dirmngr
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo add-apt-repository "deb ${MRAN}/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
sudo apt update
sudo apt install -y --no-install-recommends \
    r-base \
    littler

## install RStudio Server
wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.4.1717-amd64.deb
sudo gdebi -n rstudio-server-1.4.1717-amd64.deb
rm *.deb

## Symlink pandoc & standard pandoc templates for use system-wide
##   ref: https://github.com/rocker-org/rocker-versioned2/blob/master/scripts/install_pandoc.sh
sudo ln -fs /usr/lib/rstudio-server/bin/pandoc/pandoc /usr/local/bin
sudo ln -fs /usr/lib/rstudio-server/bin/pandoc/pandoc-citeproc /usr/local/bin
export PANDOC_TEMPLATES_VERSION=`pandoc -v | grep -oP "(?<=pandoc\s)[0-9\.]+$"`
wget https://github.com/jgm/pandoc-templates/archive/${PANDOC_TEMPLATES_VERSION}.tar.gz -O pandoc-templates.tar.gz
sudo rm -fr /opt/pandoc/templates
sudo mkdir -p /opt/pandoc/templates
sudo tar xvf pandoc-templates.tar.gz
sudo cp -r pandoc-templates*/* /opt/pandoc/templates
sudo rm -rf pandoc-templates*
sudo rm -fr /root/.pandoc
sudo mkdir /root/.pandoc
sudo ln -s /opt/pandoc/templates /root/.pandoc/templates
  
# Install additional packages from RSPM

## Preparation
##  ref: https://packagemanager.rstudio.com/__docs__/admin/serving-binaries/#binaries-r-configuration-linux
export R_INSTALL_STAGED=false
export RSPM=https://packagemanager.rstudio.com/cran/__linux__/focal/2021-08-09
echo "options(repos = c(RSPM='${RSPM}'))" >> ~/.Rprofile
echo 'options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os)))' >> ~/.Rprofile
sudo ln -s ~/.Rprofile /root/.Rprofile

sudo Rscript -e "install.packages(c('docopt', 'BiocManager'))"
sudo ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r
sudo ln -s /usr/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r

## Install System Prerequisites for the Repo’s Packages

sudo apt install -y --no-install-recommends \
    default-jdk \
    default-libmysqlclient-dev \
    gdal-bin \
    git \
    gsfonts \
    imagemagick \
    libarchive-dev \
    libcairo2-dev \
    libcurl4-openssl-dev \
    libfontconfig1-dev \
    libfreetype6-dev \
    libgdal-dev \
    libgeos-dev \
    libgit2-dev \
    libgl1-mesa-dev \
    libglpk-dev \
    libglu1-mesa-dev \
    libgmp3-dev \
    libjpeg-dev \
    libmagick++-dev \
    libpng-dev \
    libpq-dev \
    libproj-dev \
    librsvg2-dev \
    libsasl2-dev \
    libsqlite3-dev \
    libssh2-1-dev \
    libudunits2-dev \
    libv8-dev \
    libxft-dev \
    libxml2-dev \
    libxtst6 \
    libxslt-dev \
    unixodbc-dev

sudo R CMD javareconf


## Install R packages
sudo Rscript -e "update.packages(ask = FALSE)"
sudo Rscript -e "BiocManager::install(c('graph', 'Rgraphviz'))"

sudo install2.r --error --deps TRUE --ncpus -1 --skipinstalled \
    tidyverse \
    devtools \
    rmarkdown \
    vroom \
    gert \
    pacman \
    tidylog \
    furrr \
    glmnetUtils \
    pROC \
    cmprsk \
    psych \
    clinfun \
    car \
    survminer \
    prophet \
    Deducer \
    GGally \
    ggfortify \
    gghighlight \
    ggsci \
    ggrepel \
    patchwork \
    tableone \
    gt \
    gtsummary \
    flextable \
    formattable \
    ftExtra \
    minidown \
    DiagrammeR \
    palmerpenguins \
    styler \
    officer \
    rvg \
    openxlsx \
    xtable \
    rgl \
    stargazer\ 
    devEMF

sudo installGithub.r tomwenseleers/export@1afc8e2
sudo installGithub.r rstudio/webshot2

mkdir -p ~/.cache/R/R.cache


# Python setup
sudo apt install -y --no-install-recommends \
    libpython3-dev \
    python3-dev \
    python3-pip \
    python3-virtualenv \
    python3-venv

sudo python3 -m pip install \
    pandas \
    seaborn \
    sklearn

sudo install2.r --error --deps TRUE --ncpus -1 --skipinstalled \
    reticulate

# Install radian: A 21 century R console
sudo python3 -m pip install -U radian jedi

cat << EOF > ~/.radian_profile
options(radian.color_scheme = "monokai")
options(radian.auto_match = TRUE)
options(radian.prompt = "\033[0;32mr$>\033[0m ")
EOF

# Install coding fonts (for RStudio Server)

## JetBrains Mono
mkdir -p ~/.config/rstudio/fonts/JetBrainsMono/italic
wget https://download.jetbrains.com/fonts/JetBrainsMono-2.242.zip
unzip JetBrainsMono-2.242.zip -d JetBrainsMono
cp JetBrainsMono/fonts/variable/JetBrainsMono[wght].ttf ~/.config/rstudio/fonts/JetBrainsMono/JetBrainsMono.ttf
cp JetBrainsMono/fonts/variable/JetBrainsMono-Italic[wght].ttf ~/.config/rstudio/fonts/JetBrainsMono/italic/JetBrainsMono-Italic.ttf
mv ~/.config/rstudio/fonts/JetBrainsMono/ ~/.config/rstudio/fonts/JetBrains\ Mono/
rm JetBrainsMono-2.242.zip
rm -rf JetBrainsMono

## PlemolJP (IBM Plex Sans JP + IBM Plex Mono)
##   https://qiita.com/tawara_/items/0a7b8c50a48ea86b2d91
mkdir -p ~/.config/rstudio/fonts/PlemolJP35/400/italic
mkdir -p ~/.config/rstudio/fonts/PlemolJP35/700/italic
wget https://github.com/yuru7/PlemolJP/releases/download/v0.2.2/PlemolJP_v0.2.2.zip
unzip PlemolJP_v0.2.2.zip
cp PlemolJP_v0.2.2/PlemolJP35/PlemolJP35-Regular.ttf ~/.config/rstudio/fonts/PlemolJP35/400
cp PlemolJP_v0.2.2/PlemolJP35/PlemolJP35-Italic.ttf ~/.config/rstudio/fonts/PlemolJP35/400/italic
cp PlemolJP_v0.2.2/PlemolJP35/PlemolJP35-Bold.ttf ~/.config/rstudio/fonts/PlemolJP35/700
cp PlemolJP_v0.2.2/PlemolJP35/PlemolJP35-BoldItalic.ttf ~/.config/rstudio/fonts/PlemolJP35/700/italic
rm PlemolJP_v0.2.2.zip
rm -rf PlemolJP_v0.2.2


# cleaning
sudo apt autoremove -y
sudo apt clean -y
sudo chmod 644 /etc/ca-certificates.conf
sudo chmod 755 /etc/apt/sources.list.d