Dockerfile

FROM ubuntu:22.04

LABEL org.label-schema.license="GPL-2.0" \
  org.label-schema.vcs-url="https://github.com/rocker-org/rocker-versioned" \
  org.label-schema.vendor="Rocker Project" \
  maintainer="Carl Boettiger <cboettig@ropensci.org>"

ARG DEBIAN_FRONTEND=noninteractive
ARG R_VERSION
ARG BUILD_DATE
ARG CRAN
ARG CTAN_REPO=${CTAN_REPO:-https://www.texlive.info/tlnet-archive/2019/02/27/tlnet}
ENV CTAN_REPO=${CTAN_REPO}
ENV PATH=$PATH:/opt/TinyTeX/bin/x86_64-linux/
ENV BUILD_DATE ${BUILD_DATE:-2023-06-07}
ENV R_VERSION=${R_VERSION:-4.3.0} \
  CRAN=${CRAN:-https://cran.rstudio.com} \ 
  TERM=xterm

RUN apt-get update \
  && apt-get install -y --no-install-recommends \
  ed \
  less \
  locales \
  vim-tiny \
  wget \
  ca-certificates \
  fonts-texgyre 

RUN apt-get update \
  && apt-get install -y --no-install-recommends \
  bash-completion \
  build-essential\
  ca-certificates \
  file \
  fonts-texgyre \
  g++ \
  gfortran \
  gsfonts \
  libblas-dev \
  libbz2-1.0 \
  libcurl4 \
  libicu-dev \
  libffi-dev \ 
  libjpeg-turbo8-dev \
  libjpeg8-dev \ 
  libjpeg-dev \
  ##    libjpeg62-dev \
  libopenblas-dev \
  libpangocairo-1.0-0 \
  libpcre3 \
  libpng16-16 \
  libreadline8 \
  libssl-dev\
  libtiff5 \
  liblzma5 \
  libxml2-dev\
  libxslt1-dev\
  locales\
  pkg-config\
  make \
  openssl\
  unzip \
  zip \
  zlib1g \
  zlib1g-dev\
  libxml2-dev \
  ##    libcairo2-dev \
  libsqlite-dev \
  ##    libmariadbd-dev \
  ##    libmariadbclient-dev \
  libpq-dev \
  libssh2-1-dev \
  unixodbc-dev \
  libsasl2-dev \
  && echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
  && locale-gen en_US.utf8 \
  && /usr/sbin/update-locale LANG=en_US.UTF-8 \
  && BUILDDEPS="curl \
  default-jdk \
  libbz2-dev \
  libcairo2-dev \
  libcurl4-openssl-dev \
  libpango1.0-dev \
  libjpeg-dev \
  libicu-dev \
  libpcre3-dev \
  libpng-dev \
  libreadline-dev \
  libtiff5-dev \
  liblzma-dev \
  libx11-dev \
  libxt-dev \
  perl \
  tcl8.6-dev \
  tk8.6-dev \
  texinfo \
  texlive-extra-utils \
  texlive-fonts-recommended \
  texlive-fonts-extra \
  texlive-latex-recommended \
  x11proto-core-dev \
  xauth \
  xfonts-base \
  ##    xvfb \
  zlib1g-dev" \
  && apt-get install -y --no-install-recommends $BUILDDEPS \
  && cd tmp/ 

RUN apt-get update \
  && apt-get --allow-unauthenticated install -y --no-install-recommends \
  lbzip2 \
  libfftw3-dev \
  libgdal-dev \
  libgeos-dev \
  libgsl0-dev \
  libgl1-mesa-dev \
  libglu1-mesa-dev \
  libhdf4-alt-dev \
  libhdf5-dev \
  libjq-dev \
  ##    liblwgeom-dev \
  libpq-dev \
  libproj-dev \
  libprotobuf-dev \
  libnetcdf-dev \
  libsqlite3-dev \
  libssl-dev \
  libudunits2-dev \
  netcdf-bin \
  postgis \
  protobuf-compiler \
  sqlite3 \
  tk-dev \
  unixodbc-dev

ENV R_BASE_VERSION 4.3.0

## During the freeze, new (source) packages are in experimental and we place the binaries in our PPA
##RUN echo "deb [trusted=yes] http://deb.debian.org/debian experimental main" > /etc/apt/sources.list.d/experimental.list \
##RUN echo "deb [trusted=yes] https://eddelbuettel.github.io/ppaR400 ./" > /etc/apt/sources.list.d/edd-r4.list 




## Now install R and littler, and create a link for littler in /usr/local/bin
RUN apt-get update \
  && apt-get install -y --no-install-recommends \
  libblis3-openmp \
  libreadline8 \
  libc6 \
  libc6-dev \
  libjpeg-turbo8 \
  libjpeg-turbo8-dev \
  liblapack3 \
  littler \
  r-cran-littler \
  r-base \
  r-base-dev \
  r-base-core \
  r-recommended \
  && ln -s /usr/lib/R/site-library/littler/examples/install.r /usr/local/bin/install.r \
  && 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/installBioc.r /usr/local/bin/installBioc.r \
  && ln -s /usr/lib/R/site-library/littler/examples/installDeps.r /usr/local/bin/installDeps.r \
  && ln -s /usr/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
  && ln -s /usr/lib/R/site-library/littler/examples/testInstalled.r /usr/local/bin/testInstalled.r \
  && install.r docopt \
  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
  && rm -rf /var/lib/apt/lists/*




RUN useradd -s /bin/bash -m docker \
  && usermod -a -G staff docker \
  ## Refresh apt, install minimal tools
  && apt-get update \
  && apt-get install -y --no-install-recommends \
  ca-certificates \
  wget \
  ## Install key and setup R repo at CRAN
  && wget -q -O - https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc \
  | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc  \
  && echo "deb [arch=amd64 signed-by=/etc/apt/trusted.gpg.d/cran_ubuntu_key.asc] https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" \
  > /etc/apt/sources.list.d/cran.list \
  ## Install key and setup r2u repo, also set 'pin preference'
  && wget -q -O - https://r2u.stat.illinois.edu/ubuntu/dirk_eddelbuettel_pubkey.asc \
  | tee -a /etc/apt/trusted.gpg.d/dirk_eddelbuettel_pubkey.asc \
  && echo "deb [arch=amd64 signed-by=/etc/apt/trusted.gpg.d/dirk_eddelbuettel_pubkey.asc] https://r2u.stat.illinois.edu/ubuntu jammy main" \
  > /etc/apt/sources.list.d/r2u.list \
  && echo "Package: *" > /etc/apt/preferences.d/99r2u \
  && echo "Pin: release o=CRAN-Apt Project" >> /etc/apt/preferences.d/99r2u \
  && echo "Pin: release l=CRAN-Apt Packages" >> /etc/apt/preferences.d/99r2u \
  && echo "Pin-Priority: 700"  >> /etc/apt/preferences.d/99r2u \
  ## Configure default locale, see https://github.com/rocker-org/rocker/issues/19
  && echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
  && locale-gen en_US.utf8 \
  && /usr/sbin/update-locale LANG=en_US.UTF-8

RUN apt-get update \
  && apt-get install -y --no-install-recommends \
  r-base \
  r-base-dev \
  r-recommended \
  ## Install bspm for r2u as well as remotes and docopt used in littler script
  r-cran-bspm \
  r-cran-docopt \
  r-cran-littler \
  r-cran-remotes \
  ## Support user-level installation of R packages
  && chown root:staff "/usr/local/lib/R/site-library" \
  && chmod g+ws "/usr/local/lib/R/site-library" 

ENTRYPOINT [ "R" ]