Dockerfile

## Start with the rstudio image providing 'base R' as well as RStudio based on Debian testing
FROM rocker/geospatial
MAINTAINER Carl Boettiger cboettig@ropensci.org

## Refresh package list and upgrade
RUN apt-get update \
  && apt-get install -y --no-install-recommends \
    cdbs \
    icedtea-netx \
    libapparmor-dev \
    libgsl0-dev \
    libhiredis-dev \
    libleptonica-dev \
    libmpfr-dev \
    libpoppler-cpp-dev \
    libprotobuf-dev \
    librdf0-dev \
    libsasl2-dev \
    libtesseract-dev \
    libwebp-dev \
    libxslt1-dev \
    mdbtools \
    protobuf-compiler \
    python-pip \
    python-pdftools \
    tesseract-ocr-eng \
  && R CMD javareconf \
  && apt-get clean \
  && rm -rf /var/lib/apt/lists/ \
  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
  && wget -O /usr/local/bin/install2.r https://github.com/eddelbuettel/littler/raw/master/inst/examples/install2.r \
  && chmod +x /usr/local/bin/install2.r \
  && R CMD javareconf -e

## Install additional dependencies
RUN install2.r --error \
    -r 'http://cran.rstudio.com' \
    -r 'http://datacube.wu.ac.at' \
    -r 'http://packages.ropensci.org' \
    -r 'http://www.bioconductor.org/packages/release/bioc' \
    -r 'http://nceas.github.io/drat' \
    aws.s3 \
    dismo \
    drat \
    geiger \
    git2r \
    knitcitations \
    pander \
    phylobase \
    phytools \
    Rcampdf \
    redland \
    rJava \
    rhdf5 \
    ropkgs \
    ridigbio \
    rgeolocate \
    RJSONIO \
    sangerseqR \
    dataone \
    datapack \
    listviewer \
    getPass \
    dbplyr \
    GGally \
    Rserve \
    RSclient \
    Cairo \
    dendextend \
    IRdisplay \
    outliers \
    cranlogs \
    akima \
    mapdata \
    plot3D \
    memisc \
    rapport \
    RcppRedis \
    mongolite \
    countrycode \
    redux \
    rcdk \
    MCMCglmm \
    storr \
    purrrlyr \
    corrplot \
    protolite \
    tidytext \
    janeaustenr \
    wordcloud2 \
    webp \
    openair \
    snow \
    tmap \
    forecast \
    weathermetrics \
    rnaturalearthhires \
    rsvg \
    clipr \
    tiff \
    sys \
    Rmpfr \
    plotKML \
    readtext \
    cld3 \
    seqinr \
    jose \
  && R -e "remotes::install_github('richfitz/drat.builder')" \
  && pip install retriever \
  && install2.r --error \
    -r 'http://cran.rstudio.com' \
    -r 'http://packages.ropensci.org' \
    -r 'http://www.omegahat.net/R' \
    Rcompression \
    RHTMLForms \
    ROOXML \
    RWordXML \
    SSOAP \
#    Sxslt \
    XMLSchema \
    rrdflibs \
    rrdf \
  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds

## Install the rOpenSci R packages that are currently on CRAN. must use single quote notation
RUN R -e 'out <- ropkgs::ro_pkgs(); readr::write_lines(out$packages$name[out$packages$on_cran], "ropensci.txt")' \
  && install2.r `cat ropensci.txt`