anchor.diff:  FROM ubuntu:18.04
   MAINTAINER Mark McCahill "mark.mccahill@duke.edu"
   
  -RUN apt-get  update ; \
  -    apt-get  install gnupg2 -y
  +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
  
positive.code: # environmental variable ($VNCPASS) passed in when the containers is instantiated
  ADD initialize.sh /
  
  # set the locale so RStudio doesn't complain about UTF-8
  RUN apt-get install  -y locales 
  RUN locale-gen en_US en_US.UTF-8
  RUN DEBIAN_FRONTEND=noninteractive dpkg-reconfigure locales
  
  
  #########
  #
  
negative.code: 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
  
  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
  #RUN wget https://download3.rstudio.org/ubuntu-12.04/x86_64/shiny-server-1.5.3.838-amd64.deb
  