Dockerfile

# Docker file with rstan, brms and tinytex
FROM rocker/r-ubuntu:18.04

MAINTAINER Markus Gesmann  <markus.gesmann@gmail.com>

RUN apt-get update && apt-get dist-upgrade -y

RUN apt-get update \
	&& apt-get install -y --no-install-recommends apt-utils ed libnlopt-dev \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/

# Global site-wide config -- neeeded for building packages
RUN mkdir -p $HOME/.R/ \
    && echo "CXXFLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -flto -ffat-lto-objects  -Wno-unused-local-typedefs \n" >> $HOME/.R/Makevars

# Set compiler flag
RUN echo "CXX14FLAGS=-O3 -march=native -mtune=native" >> $HOME/.R/Makevars
RUN echo "CXX14FLAGS += -fPIC" >> $HOME/.R/Makevars

# Update R packages
RUN Rscript -e "update.packages(lib.loc='/usr/local/lib/R/site-library', repos='https://cloud.r-project.org', ask=FALSE)"

RUN export DEBIAN_FRONTEND=noninteractive; apt-get -y update  \
 && dpkg --configure -a \
 && apt-get -f install -y \
  	libopenblas-base \
  	cargo \
  	rustc \
  	libcurl4-gnutls-dev \
  	libxml2-dev \
  	libgit2-dev \
  	libcairo2-dev \
  	libgtk2.0-dev \
  	xvfb \
  	xauth \
  	xfonts-base \
  	libxt-dev \
  	qpdf \
	pandoc \
	make \
	wget \
	libmagick++-dev \
	git \
	jags \
	libgdal-dev \
	libgeos-dev \
	libgdal20 \
	libgeos-c1v5 \
	libproj-dev \
	liblwgeom-dev \
	libudunits2-dev \
	postgis \
	libssl-dev \
	libssh2-1-dev

## Update and install rstan
RUN apt-get update && apt-get install -y --no-install-recommends \
  	r-cran-matrix \
  	r-cran-rstudioapi \
	r-cran-stanheaders \
	r-cran-rstantools \
  	r-cran-rstan \
  	r-cran-rstanarm \
  	r-cran-loo \
  	r-cran-lme4 \
  	r-cran-nlme \
  	r-cran-codetools \
  	r-cran-rcpp \
 	r-cran-data.table \
	r-cran-latticeextra \
	r-cran-tidyverse \
	r-cran-bayesplot \
	r-cran-glmnet \
	r-cran-tinytex \
	r-cran-bayesplot \
	r-cran-knitr \
	r-cran-rmarkdown \
	r-cran-rjags \
	r-cran-igraph \
	r-cran-car \
	r-cran-inline \
	r-cran-kernsmooth \
	r-cran-mvtnorm \
	r-cran-shiny \
	r-cran-htmlwidgets \
	r-cran-jsonlite \
	r-cran-rcppeigen \
	r-cran-bh \
	r-cran-zoo \
	r-cran-brms \
	r-cran-chainladder \
	r-cran-desolve \
  	r-cran-cowplot \
  	r-cran-formatr \
  	r-cran-refmanager \
  	r-cran-bibtex \
  	r-cran-modelr \
	r-cran-kableextra \
  	r-cran-loo
  
ENV PATH=$PATH:/opt/TinyTeX/bin/x86_64-linux/

RUN wget "https://travis-bin.yihui.name/texlive-local.deb" \
  && dpkg -i texlive-local.deb \
  && rm texlive-local.deb \
  && apt-get update \
  && apt-get install -y --no-install-recommends \
    ## for rJava
    default-jdk \
    ## Nice Google fonts
    fonts-roboto \
    ## used by some base R plots
    ghostscript \
    ## used to build rJava and other packages
    libbz2-dev \
    libicu-dev \
    liblzma-dev \
    ## system dependency of hunspell (devtools)
    libhunspell-dev \
    ## system dependency of hadley/pkgdown
    libmagick++-dev \
    ## rdf, for redland / linked data
    librdf0-dev \
    ## for V8-based javascript wrappers
    libv8-dev \
    ## R CMD Check wants qpdf to check pdf sizes, or throws a Warning
    qpdf \
    ## For building PDF manuals
    texinfo \
    ## for git via ssh key
    ssh \
    ## parallelization
    libzmq3-dev \
    libopenmpi-dev \
  && apt-get clean \
  && rm -rf /var/lib/apt/lists/ \
  ## Use tinytex for LaTeX installation
  && install2.r --error tinytex \
  ## Admin-based install of TinyTeX:
  && wget -qO- \
    "https://github.com/yihui/tinytex/raw/master/tools/install-unx.sh" | \
    sh -s - --admin --no-path \
  && mv ~/.TinyTeX /opt/TinyTeX \
  && /opt/TinyTeX/bin/*/tlmgr path add \
  && tlmgr install metafont mfware inconsolata tex ae parskip listings \
  && tlmgr path add \
  && Rscript -e "tinytex::r_texmf()" \
  && chown -R root:staff /opt/TinyTeX \
  && chown -R root:staff /usr/local/lib/R/site-library \
  && chmod -R g+w /opt/TinyTeX \
  && chmod -R g+wx /opt/TinyTeX/bin 
  
RUN mkdir -p /installation/ && \
    wget https://github.com/jgm/pandoc/releases/download/2.7.2/pandoc-2.7.2-1-amd64.deb \
    --no-check-certificate \
    -O /installation/pandoc.deb

RUN install2.r --error --deps TRUE \
    bookdown raw citr tidybayes
    
RUN dpkg -i /installation/pandoc.deb && rm -rf /installation/