Dockerfile

# mccahill/r-studio
#
# VERSION 1.4

FROM ubuntu:18.04
MAINTAINER Mark McCahill "mark.mccahill@duke.edu"

RUN apt-get  update 
RUN apt-get dist-upgrade -y 	
RUN apt-get install -y \
    gnupg2 \
    apt-utils \
    libopenblas-base \
    vim \
    less \
    net-tools \
    inetutils-ping \
    curl \
    git \
    telnet \
    nmap \
    socat \
    software-properties-common \
    wget \
    locales

# Configure default locale
RUN locale-gen en_US en_US.UTF-8 
RUN DEBIAN_FRONTEND=noninteractive dpkg-reconfigure locales

	
# get R from a CRAN archive (we want the 3.5 version of R)
RUN  echo  "deb http://cran.rstudio.com/bin/linux/ubuntu bionic-cran35/"  >>  /etc/apt/sources.list
RUN  DEBIAN_FRONTEND=noninteractive apt-key adv   --keyserver keyserver.ubuntu.com   --recv-keys  E084DAB9

RUN apt-get  update ; \
    apt-get  dist-upgrade -y 

# we need gdal > 2
RUN add-apt-repository -y ppa:ubuntugis/ubuntugis-unstable
RUN apt-get update

RUN DEBIAN_FRONTEND=noninteractive apt-get install -y \
  r-base \
  r-base-dev \
  libcurl4-gnutls-dev \
  libgit2-dev \
  libxml2-dev \
  libssl-dev \
  libudunits2-dev \
  libpoppler-cpp-dev \
  texlive \
  texlive-base \
  texlive-latex-extra \
  texlive-pstricks \
  pandoc \
  texlive-publishers \
  texlive-fonts-extra \
  texlive-latex-extra \
  texlive-humanities \
  lmodern \
  libxml2  \
  libxml2-dev  \
  libssl-dev \
  libproj-dev \
  libudunits2-0  \
  libudunits2-dev \
  software-properties-common \
  gdal-bin \
  python-gdal \
  libgdal-dev \
  gdebi-core \
  libapparmor1 \
  gdal-bin \
  python-gdal \
  libgdal-dev \
  libproj-dev \
  libudunits2-0 \
  libudunits2-dev 

# R-Studio   
# RUN DEBIAN_FRONTEND=noninteractive wget https://download2.rstudio.org/rstudio-server-1.1.383-amd64.deb
RUN DEBIAN_FRONTEND=noninteractive wget https://s3.amazonaws.com/rstudio-ide-build/server/trusty/amd64/rstudio-server-1.2.907-amd64.deb
RUN DEBIAN_FRONTEND=noninteractive gdebi --n rstudio-server-1.2.907-amd64.deb
RUN rm rstudio-server-1.2.907-amd64.deb

# update the R packages we will need for knitr
RUN DEBIAN_FRONTEND=noninteractive R --vanilla --quiet -e 'install.packages( c("xfun", "knitr", "yaml", "Rcpp", "htmltools", "caTools", "bitops", "digest", "glue", "stringr", "markdown", "highr", "formatR", "evaluate", "mime", "stringi", "magrittr"), repos="http://cran.us.r-project.org",quiet=TRUE)'

 # R packages we need for devtools - and we need devtools to be able to update the rmarkdown package
RUN DEBIAN_FRONTEND=noninteractive R --vanilla --quiet -e 'install.packages( c("processx", "ps", "callr", "crayon", "assertthat", "cli", "desc", "prettyunits", "backports", "rprojroot", "withr", "pkgbuild", "rlang", "rstudioapi", "pkgload", "rcmdcheck", "remotes", "xopen", "clipr", "clisymbols", "sessioninfo", "purrr", "usethis", "sys", "askpass", "openssl", "brew", "roxygen2", "fs", "gh", "rversions", "git2r", "devtools", "R6", "httr", "RCurl", "BH", "xml2", "curl", "jsonlite", "ini", "downloader", "memoise", "plyr", "XML", "whisker", "bitops", "nloptr"), repos="http://cran.us.r-project.org",quiet=TRUE)'

# libraries Eric Green wanted
RUN DEBIAN_FRONTEND=noninteractive R --vanilla --quiet -e 'install.packages( c("lubridate", "lazyeval", "utf8", "fansi", "zeallot", "vctrs", "pillar", "pkgconfig", "tibble", "ggplot2", "RColorBrewer", "dichromat", "colorspace", "munsell", "labeling", "viridisLite", "scales", "stargazer", "reshape2", "gtable", "proto", "minqa","RcppEigen","lme4"), repos="http://cran.us.r-project.org",quiet=TRUE)'

# more libraries Mine Cetinakya-Rundel asked for
RUN DEBIAN_FRONTEND=noninteractive R --vanilla --quiet -e 'install.packages( c("openintro", "bindr", "bindrcpp", "plogr", "tidyselect", "dplyr", "DBI"), repos="http://cran.us.r-project.org",quiet=TRUE)'
  
RUN DEBIAN_FRONTEND=noninteractive R --vanilla --quiet -e 'install.packages( c("chron", "data.table", "rematch", "cellranger", "tidyr", "googlesheets", "hms", "readr", "selectr", "rvest", "pbkrtest"), repos="http://cran.us.r-project.org",quiet=TRUE)'

# Shiny
ADD ./conf /r-studio
RUN wget https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.7.907-amd64.deb
RUN DEBIAN_FRONTEND=noninteractive gdebi -n shiny-server-1.5.7.907-amd64.deb
RUN rm shiny-server-1.5.7.907-amd64.deb
RUN R CMD BATCH /r-studio/install-Shiny.R
RUN rm /install-Shiny.Rout

RUN DEBIAN_FRONTEND=noninteractive R --vanilla --quiet -e 'install.packages( c("SparseM", "MatrixModels", "quantreg", "sp", "maptools", "haven", "ellipsis", "forcats", "readxl", "zip", "openxlsx", "rio", "abind", "carData", "car", "mosaicData", "latticeExtra", "gridExtra", "ggdendro", "mnormt", "psych", "generics", "broom", "reshape", "progress", "GGally", "ggstance", "ggformula", "mosaicCore", "ggrepel", "base64enc", "crosstalk", "htmlwidgets", "png", "raster", "viridis", "leaflet", "mosaic"), repos="http://cran.us.r-project.org",quiet=TRUE)'

# Cliburn Chan requested these:
RUN  DEBIAN_FRONTEND=noninteractive R --vanilla --quiet -e 'install.packages( c("maps", "zoo", "gcookbook", "corrplot", "grepel", "base64enc", "crosstalk", "htmlwidgets", "png", "raster", "viridis", "leaflet", "mosaic"), repos="http://cran.us.r-project.org",quiet=TRUE)'
   

# install rmarkdown
RUN R CMD BATCH /r-studio/install-rmarkdown.R
RUN rm /install-rmarkdown.Rout 

# Cliburn also wanted these
# but they have mega-dependencies, so intall them the other way
RUN R CMD BATCH /r-studio/install-dendextend.R
RUN rm /install-dendextend.Rout 
RUN R CMD BATCH /r-studio/install-igraph.R
RUN rm /install-igraph.Rout 

# install sparklyr so we can do Spark via Livy
RUN  DEBIAN_FRONTEND=noninteractive R --vanilla --quiet -e 'install.packages( c("config", "dbplyr", "rappdirs", "r2d3", "forge", "sparklyr"), repos="http://cran.us.r-project.org",quiet=TRUE)'
   

# install templates and examples from Reed and the Tufte package
RUN DEBIAN_FRONTEND=noninteractive wget \
   https://archive.linux.duke.edu/cran/src/contrib/BHH2_2016.05.31.tar.gz   
RUN DEBIAN_FRONTEND=noninteractive R CMD INSTALL \
   BHH2_2016.05.31.tar.gz   
RUN rm \
  BHH2_2016.05.31.tar.gz  
RUN R CMD BATCH /r-studio/install-reed.R
RUN rm /install-reed.Rout 


RUN DEBIAN_FRONTEND=noninteractive R --vanilla --quiet -e 'install.packages( c("rgdal", "rgeos", "uuid"), repos="http://cran.us.r-project.org",quiet=TRUE)'


RUN R CMD BATCH /r-studio/install-rappdirs.R
RUN rm /install-rappdirs.Rout 
	
# new packages for fall 2018
RUN DEBIAN_FRONTEND=noninteractive R --vanilla --quiet -e 'install.packages( c("tigris", "tidycensus", "tidyverse", "future", "doMC", "foreach", "doParallel", "furrr", "drat", "tidygraph", "here", "rticles", "styler", "lintr", "testthat", "reprex", "microbenchmark", "modelr", "globals", "listenv", "iterators", "enc", "rematch2", "rex", "stringdist", "praise", "profmem", "bench" ), repos="http://cran.us.r-project.org",quiet=TRUE)'

RUN DEBIAN_FRONTEND=noninteractive R --vanilla --quiet -e 'install.packages( c("pryr", "profvis", "RcppArmadillo", "servr", "xaringan", "rsconnect", "PKI", "RJSONIO", "packrat", "highlight", "pkgdown", "bookdown", "blogdown", "cowplot", "influenceR", "Rook", "rgexf", "visNetwork", "DiagrammeR", "farver", "tweenr", "polyclip", "ggforce", "RgoogleMaps", "rjson", "mapproj", "jpeg", "geosphere", "ggmap", "ggraph", "shinyjs", "flexdashboard"), repos="http://cran.us.r-project.org",quiet=TRUE)'

RUN DEBIAN_FRONTEND=noninteractive R --vanilla --quiet -e 'install.packages( c("nycflights13", "babynames", "janeaustenr", "NHANES", "repurrrsive", "infer", "ipred", "numDeriv", "SQUAREM", "lava", "prodlim", "kernlab", "CVST", "DRR", "dimRed", "timeDate", "sfsmisc", "magic", "lpSolve", "RcppProgress", "geometry", "DEoptimR", "robustbase", "ddalpha"), repos="http://cran.us.r-project.org",quiet=TRUE)'
	
RUN DEBIAN_FRONTEND=noninteractive R --vanilla --quiet -e 'install.packages( c("gower","RcppRoll", "pls", "recipes", "rsample", "hunspell", "SnowballC", "tokenizers", "ISOcodes", "stopwords", "tidytext", "ggridges", "bayesplot", "matrixStats", "checkmate", "loo", "StanHeaders", "inline", "rstan", "rstantools", "tidypredict"), repos="http://cran.us.r-project.org",quiet=TRUE)'
	
RUN DEBIAN_FRONTEND=noninteractive R --vanilla --quiet -e 'install.packages( c("pROC", "gtools", "gdata", "gplots", "MLmetrics", "yardstick", "xgboost", "ModelMetrics", "caret", "e1071", "dotCall64", "spam", "fields", "ROCR", "reticulate", "tfruns", "tensorflow", "zeallot", "keras", "coda", "greta" ), repos="http://cran.us.r-project.org",quiet=TRUE)'


RUN R CMD BATCH /r-studio/install-2018-packages-1.R
RUN R CMD BATCH /r-studio/install-2018-packages-2.R
RUN R CMD BATCH /r-studio/install-2018-packages-3.R
RUN R CMD BATCH /r-studio/install-2018-packages-4.R

# remove install Rout files
RUN rm \
   /install-2018-packages-1.Rout \
   /install-2018-packages-2.Rout \
   /install-2018-packages-3.Rout \
   /install-2018-packages-4.Rout 
   
	
# Supervisord
RUN DEBIAN_FRONTEND=noninteractive apt-get install -y supervisor && \
   mkdir -p /var/log/supervisor
CMD ["/usr/bin/supervisord", "-n"]

# Config files
RUN cd /r-studio && \
    cp supervisord-RStudio.conf /etc/supervisor/conf.d/supervisord-RStudio.conf
RUN rm /r-studio/*

# the default packages for everyone running R
RUN echo "" >> /etc/R/Rprofile.site && \
    echo "# add the downloader package to the default libraries" >> /etc/R/Rprofile.site && \
    echo ".First <- function(){" >> /etc/R/Rprofile.site && \
    echo "library(downloader)" >> /etc/R/Rprofile.site && \
    echo "library(knitr)" >> /etc/R/Rprofile.site && \
    echo "library(rmarkdown)" >> /etc/R/Rprofile.site && \
    echo "library(ggplot2)" >> /etc/R/Rprofile.site && \
    echo "library(googlesheets)" >> /etc/R/Rprofile.site && \
    echo "library(lubridate)" >> /etc/R/Rprofile.site && \
    echo "library(stringr)" >> /etc/R/Rprofile.site && \
    echo "library(rvest)" >> /etc/R/Rprofile.site && \
    echo "library(openintro)" >> /etc/R/Rprofile.site && \
    echo "library(broom)" >> /etc/R/Rprofile.site && \
    echo "library(GGally)" >> /etc/R/Rprofile.site && \
    echo "}" >> /etc/R/Rprofile.site  && \
    echo "" >> /etc/R/Rprofile.site
	

# add a non-root user so we can log into R studio as that user; make sure that user is in the group "users"
RUN adduser --disabled-password --gecos "" --ingroup users guest 

# add a script that supervisord uses to set the user's password based on an optional
# environmental variable ($VNCPASS) passed in when the containers is instantiated
ADD initialize.sh /


#########
#
# if you need additional tools/libraries, add them here.
# also, note that we use supervisord to launch both the password
# initialize script and the RStudio server. If you want to run other processes
# add these to the supervisord.conf file
#
#########

# expose the RStudio IDE port
EXPOSE 8787 

# expose the port for the shiny server
#EXPOSE 3838

CMD ["/usr/bin/supervisord"]