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Dockerfile
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FROM rocker/geospatial:4.3.1
ENV NB_USER rstudio
ENV NB_UID 1000
ENV CONDA_DIR /srv/conda
# Set ENV for all programs...
ENV PATH ${CONDA_DIR}/bin:$PATH
# And set ENV for R! It doesn't read from the environment...
RUN echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron.site
# Add PATH to /etc/profile so it gets picked up by the terminal
RUN echo "PATH=${PATH}" >> /etc/profile
RUN echo "export PATH" >> /etc/profile
ENV HOME /home/${NB_USER}
WORKDIR ${HOME}
# Install packages needed by notebook-as-pdf
# nodejs for installing notebook / jupyterhub from source
# libarchive-dev for https://github.com/berkeley-dsep-infra/datahub/issues/1997
RUN apt-get update > /dev/null && \
apt-get install --yes \
less \
fonts-symbola \
libx11-xcb1 \
libxtst6 \
libxrandr2 \
libasound2 \
libpangocairo-1.0-0 \
libatk1.0-0 \
libatk-bridge2.0-0 \
libgtk-3-0 \
libnss3 \
libxss1 \
nodejs \
npm \
texlive-xetex \
texlive-fonts-extra \
texlive-latex-extra \
texlive-fonts-recommended \
texlive-lang-chinese \
texlive-plain-generic \
tini > /dev/null && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
COPY install-mambaforge.bash /tmp/install-mambaforge.bash
RUN /tmp/install-mambaforge.bash
USER ${NB_USER}
COPY environment.yml /tmp/environment.yml
COPY infra-requirements.txt /tmp/infra-requirements.txt
RUN mamba env update -p ${CONDA_DIR} -f /tmp/environment.yml && \
mamba clean -afy
# Install IRKernel
RUN R --quiet -e "install.packages('IRkernel', quiet = TRUE)" && \
R --quiet -e "IRkernel::installspec(prefix='${CONDA_DIR}')"
# Install extra R packages
RUN install2.r --error --skipinstalled \
## general interest
anytime \
Hmisc \
lmtest \
lubridate \
latex2exp \
MASS \
patchwork \
stargazer \
tidymodels \
wooldridge \
## machine learning
caret \
parsnip \
torch \
## 241
AER \
randomizr \
## 271
fable \
feasts \
fpp3 \
gamlr \
plm \
lme4 \
Quandl \
quantmod \
tseries \
tsibble \
vcd \
vars \
zoo
# Use simpler locking strategy
COPY file-locks /etc/rstudio/file-locks
ENTRYPOINT ["tini", "--"]