diff --git a/.github/workflows/build-image.yml b/.github/workflows/build-image.yml index adf8f53..371cfdb 100644 --- a/.github/workflows/build-image.yml +++ b/.github/workflows/build-image.yml @@ -66,6 +66,10 @@ jobs: image_ref: ${{ steps.env_var.outputs.image_ref }} steps: + - name: Delete huge unnecessary tools folder + run: rm -rf /opt/hostedtoolcache + # https://github.com/orgs/community/discussions/25678#discussioncomment-5242449 + - name: Checkout Repository uses: actions/checkout@v2 diff --git a/r/Dockerfile b/r/Dockerfile index b532766..66bd24d 100644 --- a/r/Dockerfile +++ b/r/Dockerfile @@ -1,5 +1,7 @@ #syntax=docker/dockerfile:1.3 -FROM continuumio/miniconda3:4.12.0@sha256:58b1c7df8d69655ffec017ede784a075e3c2e9feff0fc50ef65300fc75aa45ae +# FROM continuumio/miniconda3:4.12.0@sha256:58b1c7df8d69655ffec017ede784a075e3c2e9feff0fc50ef65300fc75aa45ae +# 11/14/24: Use a miniconda image that's a bit older than the rstudio-server package; just in case +FROM continuumio/miniconda3:24.7.1-0@sha256:f37f8c7db26ae7ec0098df530e96c9cde139026b9faf3914800d1522c47a49b1 ENV NB_USER jovyan ENV NB_UID 1000 @@ -11,6 +13,7 @@ ENV R_LIBS_USER /opt/r # Explicitly add littler to PATH # See https://github.com/conda-forge/r-littler-feedstock/issues/6 +# 11/14/2024: The littler path appears to be solved already ENV PATH ${CONDA_DIR}/lib/R/library/littler/bin:${CONDA_DIR}/bin:$PATH # Output logging faster @@ -38,8 +41,12 @@ RUN --mount=type=cache,id=ohw_r_apt,target=/var/cache/apt \ locales \ psmisc \ sudo \ + # 11/14/24: should this lib version be udpated? libapparmor1 \ + libfmt-dev \ + # 11/14/24: should this lib version be udpated? libpq5 \ + libssl-dev \ lsb-release \ ca-certificates \ libclang-dev > /dev/null \ @@ -51,8 +58,16 @@ RUN echo "${LC_ALL} UTF-8" > /etc/locale.gen && \ # # Set path where R packages are installed # # Download and install rstudio manually +# 11/13/2024: (using $ cat /etc/os-release) 2i2c hub currently runs on Ubuntu jammy (22), not bionic (18). +# Drilling down to jammy at https://posit.co/download/rstudio-server/, it looks like the latest rstudio-server deb is: +ENV RSTUDIO_URL https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2024.09.1-394-amd64.deb + +# 11/19/2024: Tried Ubuntu focal (20). It didn't make a difference +# ENV RSTUDIO_URL https://download2.rstudio.org/server/focal/amd64/rstudio-server-2024.09.1-394-amd64.deb + +# # (11/13/2024: The comment below is at from 2022 or earlier) # # 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-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 && \ @@ -65,9 +80,13 @@ USER ${USER} COPY ./conda-linux-64.lock /tmp/ -RUN --mount=type=cache,id=ohw_r,target=/opt/conda/pkgs,uid=${NB_UID},gid=${NB_UID} \ +RUN --mount=type=cache,id=ohw_r,target=${CONDA_DIR}/pkgs,uid=${NB_UID},gid=${NB_UID} \ + # https://github.com/jupyterhub/jupyterhub-deploy-docker/issues/91#issuecomment-525563836 + # To avoid libmamba and libarchive channel conflicts, make sure conda-forge is the only channel + # https://github.com/conda/conda-libmamba-solver/issues/283#issuecomment-1949560105 + conda config --add channels conda-forge && \ + conda update --all && \ 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 && \ @@ -79,9 +98,10 @@ ARG MAMBA_DOCKERFILE_ACTIVATE=1 # 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)" && \ +RUN \ + # -- Dependencies to the target packages, not already installed via the conda environment + Rscript -e "remotes::install_cran('PBSmapping', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \ + # -- Target packages 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)" && \ @@ -101,11 +121,10 @@ RUN Rscript -e "remotes::install_cran('assertthat', dependencies=FALSE, upgrade_ Rscript -e "remotes::install_github('hvillalo/echogram', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \ 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/ +COPY Rprofile.site ${CONDA_DIR}/lib/R/etc/ ENV PATH /usr/lib/rstudio-server/bin/:${PATH} @@ -113,4 +132,6 @@ ENV LD_LIBRARY_PATH=${CONDA_DIR}/lib # USER root # RUN chown -R jovyan ${CONDA_DIR} +# https://github.com/oceanhackweek/jupyter-image/pull/97#issuecomment-2488105625 +RUN chown -R ${NB_USER} ${HOME}/.cache USER ${NB_USER} diff --git a/r/conda-linux-64.lock b/r/conda-linux-64.lock index e87b360..4d43279 100644 --- a/r/conda-linux-64.lock +++ b/r/conda-linux-64.lock @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: 14e740f705caa869b76806a168d973e8e241f499b4059e032c825c0589eb1b04 +# input_hash: b064f256a2e647aa5d9387adba87783c45f7ef10612be238e19dd2c1a4fd5838 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38 @@ -11,32 +11,35 @@ https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7 -https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-he073ed8_17.conda#285931bd28b3b8f176d46dd9fd627a09 +https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-he073ed8_18.conda#ad8527bf134a90e1c9ed35fa0b64318c https://conda.anaconda.org/conda-forge/linux-64/pandoc-3.5-ha770c72_0.conda#2889e6b9c666c3a564ab90cedc5832fd https://conda.anaconda.org/conda-forge/noarch/poppler-data-0.4.12-hd8ed1ab_0.conda#d8d7293c5b37f39b2ac32940621c6592 -https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.9-5_cp39.conda#40363a30db350596b5f225d0d5a33328 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-5_cp312.conda#0424ae29b104430108f5218a66db7260 https://conda.anaconda.org/conda-forge/noarch/tzdata-2024b-hc8b5060_0.conda#8ac3367aafb1cc0a068483c580af8015 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29 -https://conda.anaconda.org/conda-forge/linux-64/gh-2.59.0-h76a2195_0.conda#f4a5ec48b85f2b1ca358849c73e6f825 -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_1.conda#83e1364586ceb8d0739fbc85b5c95837 +https://conda.anaconda.org/conda-forge/linux-64/gh-2.62.0-h76a2195_0.conda#57e2188ecd61e12d1aa842ee9b033d1e +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_2.conda#048b02e3962f066da18efe3a21b77672 https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-14.2.0-h41c2201_101.conda#fb126e22f5350c15fec6ddbd062f4871 +https://conda.anaconda.org/conda-forge/linux-64/libglvnd-1.7.0-ha4b6fd6_2.conda#434ca7e50e40f4918ab701e3facd59a0 https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h77fa898_1.conda#cc3573974587f12dda90d96e3e55a702 https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-14.2.0-h41c2201_101.conda#60b9a16fd147f7184b5a964aa08f3b0f -https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_17.conda#f58cb23983633068700a756f0b5f165a +https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.17-h4a8ded7_18.conda#0ea96f90a10838f58412aa84fdd9df09 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.43-h4bf12b8_1.conda#5f354010f194e85dc681dec92405ef9e +https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.43-h4bf12b8_2.conda#cf0c5521ac2a20dfa6c662a4009eeef6 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab +https://conda.anaconda.org/conda-forge/linux-64/libegl-1.7.0-ha4b6fd6_2.conda#c151d5eb730e9b7480e6d48c0fc44048 https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h77fa898_1.conda#3cb76c3f10d3bc7f1105b2fc9db984df https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.9.28-hb9d3cd8_0.conda#1b53af320b24547ce0fb8196d2604542 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.2-heb4867d_0.conda#2b780c0338fc0ffa678ac82c54af51fd -https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.3-h5888daf_0.conda#59f4c43bb1b5ef1c71946ff2cbf59524 +https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.3-heb4867d_0.conda#09a6c610d002e54e18353c06ef61a253 +https://conda.anaconda.org/conda-forge/linux-64/libbrotlicommon-1.1.0-hb9d3cd8_2.conda#41b599ed2b02abcfdd84302bff174b23 +https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.4-h5888daf_0.conda#db833e03127376d461e1e13e76f09b6c https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.2.0-h69a702a_1.conda#e39480b9ca41323497b05492a63bc35b https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-14.2.0-hd5240d6_1.conda#9822b874ea29af082e5d36098d25427d https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.2.0-hc0a3c3a_1.conda#234a5554c53625688d51062645337328 -https://conda.anaconda.org/conda-forge/linux-64/libuv-1.49.1-hb9d3cd8_0.conda#52849ca4b3be33ac3f01c77da737e068 +https://conda.anaconda.org/conda-forge/linux-64/libuv-1.49.2-hb9d3cd8_0.conda#070e3c9ddab77e38799d5c30b109c633 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 https://conda.anaconda.org/conda-forge/linux-64/make-4.4.1-hb9d3cd8_2.conda#33405d2a66b1411db9f7242c8b97c9e7 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.3.2-hb9d3cd8_0.conda#4d638782050ab6faa27275bed57e9b4e +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.0-hb9d3cd8_0.conda#23cc74f77eb99315c0360ec3533147a9 https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-hb9d3cd8_1002.conda#b3c17d95b5a10c6e64a21fa17573e70e https://conda.anaconda.org/conda-forge/linux-64/tzcode-2024b-hb9d3cd8_0.conda#db124840386e1f842f93372897d1b857 https://conda.anaconda.org/conda-forge/linux-64/xorg-libice-1.1.1-hb9d3cd8_1.conda#19608a9656912805b2b9a2f6bd257b04 @@ -48,31 +51,38 @@ https://conda.anaconda.org/conda-forge/linux-64/aws-c-compression-0.2.19-h756ea9 https://conda.anaconda.org/conda-forge/linux-64/aws-c-sdkutils-0.1.19-h756ea98_3.conda#bfe6623096906d2502c78ccdbfc3bc7a https://conda.anaconda.org/conda-forge/linux-64/aws-checksums-0.1.20-h756ea98_0.conda#ff7dbb319545f4bd1e5e0f8555cf9e7f https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 -https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.3-h5888daf_0.conda#6595440079bed734b113de44ffd3cd0a +https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.4-h5888daf_0.conda#1d6afef758879ef5ee78127eb4cd2c4a https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.10-h36c2ea0_0.tar.bz2#ac7bc6a654f8f41b352b38f4051135f8 +https://conda.anaconda.org/conda-forge/linux-64/gflags-2.2.2-h5888daf_1005.conda#d411fc29e338efb48c5fd4576d71d881 https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.2-hd590300_0.conda#3bf7b9fd5a7136126e0234db4b87c8b6 https://conda.anaconda.org/conda-forge/linux-64/json-c-0.17-h1220068_1.conda#f8f0f0c4338bad5c34a4e9e11460481d https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 +https://conda.anaconda.org/conda-forge/linux-64/libbrotlidec-1.1.0-hb9d3cd8_2.conda#9566f0bd264fbd463002e759b8a82401 +https://conda.anaconda.org/conda-forge/linux-64/libbrotlienc-1.1.0-hb9d3cd8_2.conda#06f70867945ea6a84d35836af780f1de https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda#8e88f9389f1165d7c0936fe40d9a9a79 https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055 +https://conda.anaconda.org/conda-forge/linux-64/libevent-2.1.12-hf998b51_1.conda#a1cfcc585f0c42bf8d5546bb1dfb668d https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 https://conda.anaconda.org/conda-forge/linux-64/libgfortran-14.2.0-h69a702a_1.conda#f1fd30127802683586f768875127a987 https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-hd590300_2.conda#d66573916ffcf376178462f1b61c941e https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.0.0-hd590300_1.conda#ea25936bb4080d843790b586850f82b8 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7 +https://conda.anaconda.org/conda-forge/linux-64/libpciaccess-0.18-hd590300_0.conda#48f4330bfcd959c3cfb704d424903c82 https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.44-hadc24fc_0.conda#f4cc49d7aa68316213e4b12be35308d1 https://conda.anaconda.org/conda-forge/linux-64/libsanitizer-14.2.0-h2a3dede_1.conda#160623b9425f5c04941586da43bd1a9c https://conda.anaconda.org/conda-forge/linux-64/libsodium-1.0.20-h4ab18f5_0.conda#a587892d3c13b6621a6091be690dbca2 -https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.46.1-hadc24fc_0.conda#36f79405ab16bf271edb55b213836dac +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.47.0-hadc24fc_1.conda#b6f02b52a174e612e89548f4663ce56a https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.2.0-h4852527_1.conda#8371ac6457591af2cf6159439c1fd051 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jsonschema-with-format-nongpl to address a deployment error @@ -22,12 +23,14 @@ dependencies: - r-abind - r-akima - r-ape + - r-assertthat - r-automap - r-biomod2 - r-bitops - r-caret - r-catools - r-checkmate + - r-circstats - r-commonmark - r-cowplot - r-crul @@ -39,13 +42,16 @@ dependencies: - r-dplyr - r-earth - r-rerddap + - r-fields - r-foreach + - r-forecast - r-foreign - r-fracdiff - r-gbm >=2.1.3 - r-geometry - r-geosphere - r-ggplot2 + - r-ggspatial - r-glmnet - r-gridextra - r-gsw @@ -68,11 +74,13 @@ dependencies: - r-mmand - r-mapdata - r-mapedit + - r-mapproj - r-maps - r-maptools - r-marmap - r-markdown - r-mass + - r-matrixstats - r-mda - r-metr - r-ncdf4 @@ -80,12 +88,13 @@ dependencies: - r-nloptr - r-oce - r-ocedata - - r-rosm - r-palmerpenguins + - r-pals - r-patchwork - r-PCICt - r-plotly - r-proc >=1.15.0 + - r-pracma - r-ps>=1.3.4 - r-purrr - r-r.utils @@ -98,11 +107,13 @@ dependencies: - r-reshape - r-rgdal >=1.5 - r-rgeos + - r-rjson - r-rlang - r-rmarkdown - r-rnaturalearth - r-rnaturalearthdata - r-robis + - r-rosm - r-rpart - r-rsqlite - r-rstackdeque @@ -111,8 +122,11 @@ dependencies: - r-scales - r-sf >=0.9_5 - r-sp + - r-splancs - r-stars + - r-statmod - r-terra + - r-texreg - r-tibble - r-tidyr - r-tidygraph