Attempt to convert the R image to Rocker

Attempting to convert the R image to Rocker, but it's kinda large.
oceanhackweek · Nov 19, 2024 · 7750a45 · 7750a45
1 parent 41445c1
commit 7750a45
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Showing 6 changed files with 131 additions and 935 deletions.
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -1,12 +1,14 @@
 services:
   py:
     build: ./py-base
+    platform: linux/amd64
     command: jupyter lab --port=8080 --ip=0.0.0.0
     ports:
       - "8080:8080"
 
   r:
     build: ./r
+    platform: linux/amd64
     command: jupyter lab --port=8080 --ip=0.0.0.0
     ports:
       - "8080:8080"
diff --git a/r/CONDARC b/r/CONDARC
diff --git a/r/Dockerfile b/r/Dockerfile
@@ -1,96 +1,131 @@
-#syntax=docker/dockerfile:1.3
-FROM continuumio/miniconda3:4.12.0@sha256:58b1c7df8d69655ffec017ede784a075e3c2e9feff0fc50ef65300fc75aa45ae
-
-ENV NB_USER jovyan
-ENV NB_UID 1000
-ENV HOME /home/jovyan
-
-ENV CONDA_DIR /opt/conda
-ENV CONDA_ENV base
-ENV R_LIBS_USER /opt/r
-
-# Explicitly add littler to PATH
-# See https://github.com/conda-forge/r-littler-feedstock/issues/6
-ENV PATH ${CONDA_DIR}/lib/R/library/littler/bin:${CONDA_DIR}/bin:$PATH
-
-# Output logging faster
-ENV PYTHONUNBUFFERED 1
-# Don't write bytecode
-ENV PYTHONDONTWRITEBYTECODE 1
-
-USER root
-RUN adduser --disabled-password --gecos "Default Jupyter user" ${NB_USER} \
-    && echo ". ${CONDA_DIR}/etc/profile.d/conda.sh ; conda activate ${CONDA_ENV}" > /etc/profile.d/init_conda.sh \
-    && chown -R ${NB_USER}:${NB_USER} /srv
-
-# Install these without 'recommended' packages to keep image smaller.
-# Useful utils that folks sort of take for granted
-RUN --mount=type=cache,id=ohw_r_apt,target=/var/cache/apt \
-    apt-get update -qq --yes > /dev/null && \
-    apt-get install --yes --no-install-recommends -qq \
-    curl \
-    git \
-    less \
-    tar \
-    tzdata \
-    vim \
-    wget \
-    locales \
-    psmisc \
-    sudo \
-    libapparmor1 \
-    libpq5 \
-    lsb-release \
-    ca-certificates \
-    libclang-dev > /dev/null \
-    && update-ca-certificates \
-    && rm -rf /var/lib/apt/lists/*
-
-RUN echo "${LC_ALL} UTF-8" > /etc/locale.gen && \
-    locale-gen
-
-# # Set path where R packages are installed
-# # Download and install rstudio manually
-# # Newer one has bug that doesn't work with jupyter-rsession-proxy
-ENV RSTUDIO_URL https://download2.rstudio.org/server/bionic/amd64/rstudio-server-2022.07.1-554-amd64.deb
-# ENV RSTUDIO_URL https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.2.5042-amd64.deb
-RUN curl --silent --location --fail ${RSTUDIO_URL} > /tmp/rstudio.deb && \
-    dpkg -i /tmp/rstudio.deb && \
-    rm /tmp/rstudio.deb
-
-USER ${USER}
-
-WORKDIR ${HOME}
-USER ${USER}
-
-COPY ./conda-linux-64.lock /tmp/
-
-RUN --mount=type=cache,id=ohw_r,target=/opt/conda/pkgs,uid=${NB_UID},gid=${NB_UID} \
-    conda install --name ${CONDA_ENV} --file /tmp/conda-linux-64.lock && \
-    # micromamba install --name ${CONDA_ENV} --file environment.yml && \
-    find -name '*.a' -delete && \
-    # rm -rf /opt/conda/conda-meta && \
-    rm -rf ${CONDA_DIR}/include && \
-    find -name '__pycache__' -type d -exec rm -rf '{}' '+'
-
-ARG MAMBA_DOCKERFILE_ACTIVATE=1
-
-# Install R libs from CRAN and GitHub
-# 2024-10-10: Have there been improvements in install_cran and install_github such that 
-# dependencies, upgrade_dependencies, upgrade could now be set to TRUE or the default?
-# RUN installGithub.R BigelowLab/rasf BigelowLab/ohwobpg  # not working on GH but works locally :-/
-RUN Rscript -e "remotes::install_cran('assertthat', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_cran('forecast', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_cran('ggspatial', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_cran('plot.matrix', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_cran('isdparser', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_cran('geonames', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_cran('readHAC', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_cran('rnoaa', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_cran('greybox', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_cran('sfnetworks', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_cran('smooth', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_github('BigelowLab/ohwobpg', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
+FROM ghcr.io/rocker-org/binder:4.4.1@sha256:0206f61770c76c3744ecd898c273a5778ad3dd18d1b30e396f90f00dec42d787
+
+ENV NB_UID=1000
+
+RUN --mount=type=cache,id=ohw_r,target=/tmp/downloaded_packages,uid=${NB_UID},gid=${NB_UID} \
+    install2.r -e \
+    assertthat \
+    forecast \
+    ggspatial \
+    plot.matrix \
+    isdparser \
+    geonames \
+    readHAC \
+    # rnoaa \ not available for this version of R
+    greybox \
+    sfnetworks \
+    smooth \
+    akima \
+    ape \
+    automap \
+    biomod2 \
+    bitops \
+    caret \
+    # catools \ not available for this version of R
+    checkmate \
+    commonmark \
+    cowplot \
+    crul \
+    # dbi \
+    # devtools \
+    # dichromat \
+    dismo \
+    # doparallel \ not available for this version of R
+    # dplyr \
+    earth \
+    rerddap \
+    foreach \
+    # foreign \
+    # fracdiff \
+    gbm >=2.1.3 \
+    geometry \
+    # geosphere \
+    # ggplot2 \
+    glmnet \
+    # gridextra \ not available for this version of R
+    gsw \
+    hexbin \
+    httpcache \
+    # httr \
+    # igraph \
+    # irkernel \
+    # jsonlite \
+    # knitr \
+    # lattice \
+    # leaflet \
+    # littler \
+    # lmtest \
+    # lpsolve \ not available for this version of R
+    # lubridate \
+    mmand \
+    # mapdata \
+    mapedit \
+    # maps \
+    # maptools \ not available for this version of R
+    marmap \
+    markdown \
+    # mass \
+    mda \
+    # metr \ not available for this version of R
+    # ncdf4 \
+    # nnet \
+    # nloptr \
+    oce \
+    ocedata \
+    rosm \
+    palmerpenguins \
+    patchwork \
+    PCICt \
+    plotly \
+    # proc >=1.15.0 \ not available for this version of R
+    # ps>=1.3.4 \
+    # purrr \
+    # r.utils \ not available for this version of R
+    # randomforest \ not available for this version of R
+    # rann \ not available for this version of R
+    # raster >=1.4.3 \
+    # rastervis \ not available for this version of R
+    # readr \
+    # remotes \
+    reshape \
+    # rgdal >=1.5 \ not available for this version of R
+    # rgeos \ not available for this version of R
+    rlang \
+    # rmarkdown \
+    rnaturalearth \
+    rnaturalearthdata \
+    robis \
+    # rpart \
+    # rsqlite \
+    rstackdeque \
+    rvest \
+    # s2 \
+    # scales \
+    # sf >=0.9_5 \
+    # sp \
+    # stars \
+    # terra \
+    # tibble \
+    # tidyr \
+    # tidygraph \
+    # tidyverse \
+    tiff \
+    # tmap \
+    # tmaptools \
+    # tseries \
+    tsibble \
+    tzdb \
+    udunits2 \
+    # urca \
+    vegan \
+    viridis \
+    # vroom \
+    wdpar \
+    xaringan
+    # xml2 \
+    # xts \
+
+RUN Rscript -e "remotes::install_github('BigelowLab/ohwobpg', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
     Rscript -e "remotes::install_github('BigelowLab/rasf', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
     Rscript -e "remotes::install_github('BigelowLab/xyzt', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
     Rscript -e "remotes::install_github('BigelowLab/ghrsst', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
@@ -102,15 +137,4 @@ RUN Rscript -e "remotes::install_cran('assertthat', dependencies=FALSE, upgrade_
     Rscript -e "remotes::install_github('hvillalo/periods', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
     Rscript -e "remotes::install_github('hvillalo/satin', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
     Rscript -e "remotes::install_github('kwstat/pals', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_github('JorGarMol/VoCC', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)"
-
-COPY CONDARC ./.condarc
-COPY Rprofile.site /opt/conda/lib/R/etc/
-
-ENV PATH /usr/lib/rstudio-server/bin/:${PATH}
-
-ENV LD_LIBRARY_PATH=${CONDA_DIR}/lib
-
-# USER root
-# RUN chown -R jovyan ${CONDA_DIR}
-USER ${NB_USER}
+    Rscript -e "remotes::install_github('JorGarMol/VoCC', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)"
diff --git a/r/Rprofile.site b/r/Rprofile.site