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FROM r-base:latest

LABEL maintener="Jean-François Rey <jean-francois.rey@inra.fr>"
LABEL description="r-base image for BioSP by adding packages dependencies"

RUN echo "deb http://http.debian.net/debian sid main contrib non-free" > /etc/apt/sources.list.d/debian-unstable.list

# install dependances
RUN apt-get update \
	&& apt-get install -y --no-install-recommends \
  sudo \
  ntp \
  libxml2 libxml2-dev \
  gdal-bin libgdal-dev\
  libfftw3-bin libfftw3-dev \
  texlive texinfo \
  texlive-fonts-extra \
  libqpdf26 qpdf \
  libudunits2-dev libudunits2-0 \
  libgsl-dev \
  libgeos-dev \
  libgeos++-dev \
  && apt-get clean \
	&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
	&& rm -rf /var/lib/apt/lists/*

# set France time zone
ENV CONTAINER_TIMEZONE Europe/Paris
ENV TZ Europe/Paris

RUN sudo echo "Europe/Paris" > /etc/timezone
RUN echo "fr_FR.UTF-8 UTF-8" >> /etc/locale.gen \
  && locale-gen fr_FR.UTF8 \
  && /usr/sbin/update-locale LANG=fr_FR.UTF-8

ENV LC_ALL fr_FR.UTF-8
ENV LANG fr_FR.UTF-8

# install R packages
#RUN Rscript -e "options(warn=2) ; install.packages(c('rgeos'), repos='https://cran.biotools.fr', dependencies=TRUE)"
#with littler
RUN install.r -r https://cran.biotools.fr -d TRUE -e \
  deSolve \
  methods \
  grDevices \
  graphics \
  sp \
  stats \
  rgeos \
  fields \
  MASS \
  Matrix \
  rgeos \
  deldir \
  pracma \
  raster \
  fftwtools \
  mvtnorm \
  rgdal \
  knitr \
  maptools \
  sf \
  splancs \
  RCALI \
  rmarkdown \
  testthat \
  roxygen2 \
  Rcpp \
  RcppArmadillo \
  fasterize \
  shiny \
  htmltools \
  shinydashboard \
  ggplot2 \
  dplyr \
  dbplyr \
  DT \
  magrittr \
  devtools \
  shinyjs \
  stringi \
  stringr \
  jsonlite \
  data.table \
  htmlwidgets \
  RSQLite \
  BiocManager \
  foreach \
  doParallel \
  mvtnorm \
  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds

RUN Rscript -e 'BiocManager::install(c("Biostrings"))'
# force update to last version
RUN Rscript -e "update.packages(ask=FALSE)"

#ENTRYPOINT ["/bin/sh", "-c"]
WORKDIR /home/docker
CMD ["R"]