Separate r-base image and tested #192
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| FROM ghcr.io/nmfs-opensci/container-images/py-rocket-geospatial-2:2026.01.25 | ||
| ENV LANG=en_US.UTF-8 | ||
| ENV TZ=US/Pacific | ||
| ARG DEBIAN_FRONTEND=noninteractive | ||
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| USER root | ||
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| # Install system R and development libraries | ||
| # R will be completely separate from conda | ||
| RUN apt-get clean && apt-get update && \ | ||
| apt-get install -y --no-install-recommends \ | ||
| gdal-bin=3.8.4+dfsg-3ubuntu3 \ | ||
| lbzip2=2.5-2.3 \ | ||
| libfftw3-dev=3.3.10-1ubuntu3 \ | ||
| libgdal-dev=3.8.4+dfsg-3ubuntu3 \ | ||
| libgeos-dev=3.12.1-3build1 \ | ||
| libgl1-mesa-dev=25.0.7-0ubuntu0.24.04.2 \ | ||
| libglu1-mesa-dev=9.0.2-1.1build1 \ | ||
| libhdf4-alt-dev=4.2.16-4build1 \ | ||
| libhdf5-dev=1.10.10+repack-3.1ubuntu4 \ | ||
| libjq-dev=1.7.1-3ubuntu0.24.04.1 \ | ||
| libpq-dev=16.11-0ubuntu0.24.04.1 \ | ||
| libproj-dev=9.4.0-1build2 \ | ||
| libprotobuf-dev=3.21.12-8.2ubuntu0.2 \ | ||
| libnetcdf-dev=1:4.9.2-5ubuntu4 \ | ||
| libsqlite3-dev=3.45.1-1ubuntu2.5 \ | ||
| libssl-dev=3.0.13-0ubuntu3.6 \ | ||
| libudunits2-dev=2.2.28-7build1 \ | ||
| netcdf-bin=1:4.9.2-5ubuntu4 \ | ||
| postgis=3.4.2+dfsg-1ubuntu3 \ | ||
| protobuf-compiler=3.21.12-8.2ubuntu0.2 \ | ||
| sqlite3=3.45.1-1ubuntu2.5 \ | ||
| tk-dev=8.6.14build1 \ | ||
| unixodbc-dev=2.3.12-1ubuntu0.24.04.1 && \ | ||
| apt-get clean && \ | ||
| rm -rf /var/lib/apt/lists/* | ||
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| USER ${NB_USER} | ||
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| # Install additional packages from environment.yml | ||
| COPY ./environment.yml /tmp | ||
| RUN conda env update -n ${CONDA_ENV} -f "/tmp/environment.yml" \ | ||
| && find ${CONDA_DIR}/ -follow -type f -name '*.a' -delete \ | ||
| && find ${CONDA_DIR}/ -follow -type f -name '*.js.map' -delete \ | ||
| && ${CONDA_DIR}/bin/conda clean -afy | ||
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| RUN conda init | ||
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| RUN awscliv2 --install | ||
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| USER root | ||
| SHELL ["/bin/bash", "-c"] | ||
| ADD . / | ||
| RUN ["chmod", "+x", "/scripts/install_cran_packages_r.sh"] | ||
| # Install R packages using SYSTEM R (not conda R) | ||
| # Do NOT activate conda environment here | ||
| # Clear conda's compiler paths to force use of system compiler | ||
| RUN export PATH=/usr/local/bin:/usr/bin:/bin:$PATH && \ | ||
| /scripts/install_cran_packages_r.sh | ||
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| RUN PYTHON_PATH=$(which python) && \ | ||
| R_HOME=$(R RHOME) && \ | ||
| echo "library(reticulate)" >> "$R_HOME/etc/Rprofile.site" && \ | ||
| echo "use_python(\"$PYTHON_PATH\", required = TRUE)" >> "$R_HOME/etc/Rprofile.site" && \ | ||
| echo "py_config()" >> "$R_HOME/etc/Rprofile.site" | ||
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| COPY scripts/init-user.sh /usr/local/bin/init-user.sh | ||
| RUN chmod +x /usr/local/bin/init-user.sh | ||
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| USER ${NB_USER} | ||
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| # This script returns control to base image's /srv/start after | ||
| ENTRYPOINT ["/usr/local/bin/init-user.sh"] | ||
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| Original file line number | Diff line number | Diff line change |
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| name: notebook | ||
| channels: | ||
| - conda-forge | ||
| - nodefaults | ||
| dependencies: | ||
| # Python packages only - NO R packages in conda | ||
| - gdal=3.10.2 | ||
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Contributor
There was a problem hiding this comment. Can you put a comment here indicated why we are pinning this version of gdal from conda?
Member
Author
There was a problem hiding this comment. That is because it was the last version the R image was built with and we pin our packages in our environment.ymls for reproducibility
Contributor
There was a problem hiding this comment. That seems ok if the idea is to just match the conda gdal to the same version and the system gdal (that R uses). I do anticipate keeping track of that being a hassle later. |
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| - nodejs=20.19.5 | ||
| - rtree=1.4.1 | ||
| - unzip=6.0 | ||
| - pip=26.0 | ||
| - pip: | ||
| # - git+https://github.com/MAAP-Project/stac_ipyleaflet.git@0.3.6 | ||
| - morecantile==6.1.0 | ||
| - rio-tiler==7.2.2 | ||
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This fix did not work and I need to debug if we want to keep awscliv2, can resolve in another PR along with rgee bug