ubuntu:18.04 に R 4.0.2＋RStudio server＋Radian と頻用パッケージを追加した作業用イメージ

R4.0.2_20200626.Dockerfile

# R 4.0.2 and RStudio server with some packages.
# MRAN library fixed at 2020-06-26 (the day 4.0.2 first came to MRAN)

FROM ubuntu:18.04

# Change environment to Japanese (Character, DateTime, and Fonts)
ENV DEBCONF_NOWARNINGS=yes
RUN set -x \
  # install Japanese lung pack (and locales)
	&& apt-get update \
	&& apt-get install -y language-pack-ja-base language-pack-ja \
  # locale settings
	&& sed -i '$d' /etc/locale.gen \
	&& echo "ja_JP.UTF-8 UTF-8" >> /etc/locale.gen \
	&& locale-gen ja_JP.UTF-8 \
	&& /usr/sbin/update-locale LANG=ja_JP.UTF-8 LANGUAGE="ja_JP:ja" \
	&& /bin/bash -c "source /etc/default/locale" \
	&& ln -sf /usr/share/zoneinfo/Asia/Tokyo /etc/localtime \
  # install CJK font
	&& apt-get install -y fonts-noto-cjk \
  # cleaning
	&& apt-get clean \
	&& rm -rf /var/lib/apt/lists/*

# Install R from MRAN snapshot
ENV MRAN="https://cran.microsoft.com/snapshot/2020-06-26"
RUN set -x \
  # install essential packages
	&& apt-get update \
	&& apt-get install -y \
		build-essential \
		curl \
		openssl \
		ca-certificates \
		gdebi-core \
		psmisc \
		python3-pip \
		ssh \
		git \
  # 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 \
	&& cp msitwww2.crt /usr/share/ca-certificates/ \
	&& echo "msitwww2.crt" >> /etc/ca-certificates.conf \
	&& update-ca-certificates \
	&& rm *.crt \
  # install latest version of R 4.0.2 (4.0.2-1.1804.0 / 2020-06-23)
	&& echo "deb ${MRAN}/bin/linux/ubuntu bionic-cran40/" > /etc/apt/sources.list.d/cran.list \
	&& apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 51716619E084DAB9 \
	&& apt-get update \
	&& apt-get install -y r-base littler \
  # cleaning
	&& apt-get clean \
	&& rm -rf /var/lib/apt/lists/*

# Install frequently used packages
ENV R_INSTALL_STAGED=false
RUN set -x \
  # install dependent packages
	&& apt-get update \
	&& apt-get install -y --no-install-recommends \
		libcurl4-openssl-dev \
		libssl-dev \
		libxml2-dev \
		libglu1-mesa-dev \
		graphviz \
		libgraphviz-dev \
		libzmq3-dev \
	#	xorg \
		libx11-dev \
		libfreetype6-dev \
		libfontconfig1-dev \
		libcairo2-dev \
		librsvg2-dev \
		libmagick++-dev \
  # install R-packages using 2020-06-26 MRAN snapshot
	&& ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r \
	&& ln -s /usr/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
	&& echo "options(repos = '${MRAN}')" > ~/.Rprofile \
	&& Rscript -e "install.packages(c('docopt', 'BiocManager'))" \
	&& Rscript -e "BiocManager::install(c('graph', 'Rgraphviz'))" \
	&& install2.r --error --deps TRUE --ncpus -1 --skipinstalled \
		xml2 \
		devtools \
		pacman \
		tidyverse \
		tidylog \
		furrr \
		RSQLite \
		rmarkdown \
		formatR \
		caTools \
		pROC \
		cmprsk \
		psych \
		clinfun \
		car \
		MASS \
		ggfortify \
		ggsci \
		tableone \
  # since package "export" was removed from CRAN on 2020-02-21,
  # install dev version from GitHub repo (commit d29650b / 2020-06-22)
		officer \
		rvg \
		openxlsx \
		flextable \
		xtable\
		rgl \
		stargazer \
		tikzDevice \
	&& installGithub.r tomwenseleers/export@d29650b \
  # cleaning
	&& apt-get clean \
	&& rm -rf /var/lib/apt/lists/*

# Install RStudio Server
RUN set -x \
	&& apt-get update \
	&& curl --output "rstudio-server.deb" https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.3.959-amd64.deb \
	&& gdebi -n rstudio-server.deb \
	&& rm *.deb \
	&& apt-get clean \
	&& rm -rf /var/lib/apt/lists/*
EXPOSE 8787

# Install radian: A 21 century R console
RUN set -x \
	&& pip3 install -U radian

# User settings
RUN useradd -m rstudio \
	&& echo "rstudio:rstudio" | chpasswd \
	&& echo "r-libs-user=/usr/local/lib/R/site-library" >> /etc/rstudio/rsession.conf \
	&& echo "r-cran-repos=${MRAN}" >> /etc/rstudio/rsession.conf \
	&& echo "auth-timeout-minutes=0" >> /etc/rstudio/rserver.conf \
	&& echo "options(repos = '${MRAN}')" > /home/rstudio/.Rprofile \
	&& echo 'options(radian.color_scheme = "monokai")' > /home/rstudio/.radian_profile \
	&& echo 'options(radian.auto_match = TRUE)' >> /home/rstudio/.radian_profile \
	&& echo 'options(radian.prompt = "\033[0;32mr$>\033[0m ")' >> /home/rstudio/.radian_profile \
	&& echo 'options(radian.escape_key_map = list(list(key = "m", value = " %>% ")))' >> /home/rstudio/.radian_profile \
	&& chown rstudio:rstudio /home/rstudio \
	&& addgroup rstudio staff \
	&& mkdir /home/rstudio/.rstudio \
	&& chown -R rstudio:rstudio /home/rstudio/.rstudio \
	&& chown rstudio:rstudio /home/rstudio/.Rprofile \
	&& chown rstudio:rstudio /home/rstudio/.radian_profile

WORKDIR /home/rstudio
ENV USER=rstudio \
	HOME=/home/rstudio \
	LANG=ja_JP.UTF-8 \
	LC_ALL=ja_JP.UTF-8

# start RStudio server
#CMD rstudio-server start && tail -f /dev/null
CMD ["/usr/lib/rstudio-server/bin/rserver", "--server-daemonize=0"]

install.packages() と littler の install2.r の dep(s) = TRUE の理解が間違っていたので、依存関係（Suggests）解決のためBioconductorからのインストールを先にした。R 4.0.0 までと挙動変わっている？

2020-06-26 は R 4.0.2 がMRANに登録された最初の日。
4.0.3 が出たら、いつものように 4.0.2 の最後の日で固定し直すか？

• RStudio Server 上で R_LIBS_USER が空になってしまうので、/etc/rstudio/rsession.conf で設定するようにした。
• 個人用なのでログイン時のパスワードを不要にした。
  Ref: https://stackoverflow.com/questions/47541007/how-to-i-bypass-the-login-page-on-rstudio
  -> うまく行かないので断念。かわりに Inactivity Authorization Timeout を無効にした。