From f95db863cd0f1d0fcd3847536bd64efdfa3d89c9 Mon Sep 17 00:00:00 2001 From: Emilio Mayorga Date: Thu, 21 Nov 2024 18:50:27 -0800 Subject: [PATCH] R image: added mapplots and repmis, and made a couple of small cleanups --- r/Dockerfile | 21 ++++----------------- r/conda-linux-64.lock | 27 +++++++++++++++------------ r/environment.yml | 4 +++- 3 files changed, 22 insertions(+), 30 deletions(-) diff --git a/r/Dockerfile b/r/Dockerfile index 66bd24d..9f864f0 100644 --- a/r/Dockerfile +++ b/r/Dockerfile @@ -1,11 +1,9 @@ #syntax=docker/dockerfile:1.3 -# 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 -ENV HOME /home/jovyan +ENV HOME /home/${NB_USER} ENV CONDA_DIR /opt/conda ENV CONDA_ENV base @@ -57,18 +55,10 @@ RUN echo "${LC_ALL} UTF-8" > /etc/locale.gen && \ 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: +# # Download and install rstudio-server manually +# Get the url at https://posit.co/download/rstudio-server/: 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-1.2.5042-amd64.deb RUN curl --silent --location --fail ${RSTUDIO_URL} > /tmp/rstudio.deb && \ dpkg -i /tmp/rstudio.deb && \ rm /tmp/rstudio.deb @@ -76,7 +66,6 @@ RUN curl --silent --location --fail ${RSTUDIO_URL} > /tmp/rstudio.deb && \ USER ${USER} WORKDIR ${HOME} -USER ${USER} COPY ./conda-linux-64.lock /tmp/ @@ -95,11 +84,9 @@ RUN --mount=type=cache,id=ohw_r,target=${CONDA_DIR}/pkgs,uid=${NB_UID},gid=${NB_ 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 \ # -- Dependencies to the target packages, not already installed via the conda environment + # Install dependencies before "target" packages, either in the conda environment or here 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)" && \ diff --git a/r/conda-linux-64.lock b/r/conda-linux-64.lock index 4d43279..e19abaf 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: b064f256a2e647aa5d9387adba87783c45f7ef10612be238e19dd2c1a4fd5838 +# input_hash: e6956d4811dbd558b15d2167610a422525a87c259760b1017b4f627d6f6ee57c @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 @@ -114,7 +114,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libzip-1.11.2-h6991a6a_0.conda#a https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.9.4-hcb278e6_0.conda#318b08df404f9c9be5712aaa5a6f0bb0 https://conda.anaconda.org/conda-forge/linux-64/nano-8.2-haa1a288_0.conda#de8018f428ccd78ab5cf41bf6353e82c https://conda.anaconda.org/conda-forge/linux-64/nccl-2.23.4.1-h03a54cd_2.conda#a08604ac3f9c3dbd128bb24e089dee5f -https://conda.anaconda.org/conda-forge/linux-64/nss-3.106-hdf54f9c_0.conda#efe735c7dc47dddbb14b3433d11c6feb +https://conda.anaconda.org/conda-forge/linux-64/nss-3.107-hdf54f9c_0.conda#294b7009fe9010b35c25bb683f663bc3 https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.44-hba22ea6_2.conda#df359c09c41cd186fffb93a2d87aa6f5 https://conda.anaconda.org/conda-forge/linux-64/pixman-0.43.2-h59595ed_0.conda#71004cbf7924e19c02746ccde9fd7123 https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4 @@ -141,7 +141,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libprotobuf-4.25.3-hd5b35b9_1.co https://conda.anaconda.org/conda-forge/linux-64/libre2-11-2023.09.01-h5a48ba9_2.conda#41c69fba59d495e8cf5ffda48a607e35 https://conda.anaconda.org/conda-forge/linux-64/librttopo-1.1.0-h8917695_15.conda#20c3c14bc491f30daecaa6f73e2223ae https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h1dd3fc0_3.conda#66f03896ffbe1a110ffda05c7a856504 -https://conda.anaconda.org/conda-forge/linux-64/libxgboost-2.1.2-cuda118_h09a87be_0.conda#d59c3f95f80071f24ebce434494ead0a +https://conda.anaconda.org/conda-forge/linux-64/libxgboost-2.1.2-cuda118_h09a87be_1.conda#706196aa07632a23a1fb7d34da1ba2d1 https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.13.5-hb346dea_0.conda#c81a9f1118541aaa418ccb22190c817e https://conda.anaconda.org/conda-forge/linux-64/minizip-4.0.7-h401b404_0.conda#4474532a312b2245c5c77f1176989b46 https://conda.anaconda.org/conda-forge/linux-64/python-3.12.7-hc5c86c4_0_cpython.conda#0515111a9cdf69f83278f7c197db9807 @@ -165,7 +165,7 @@ https://conda.anaconda.org/conda-forge/noarch/certifi-2024.8.30-pyhd8ed1ab_0.con https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.0-pyhd8ed1ab_0.conda#a374efa97290b8799046df7c5ca17164 https://conda.anaconda.org/conda-forge/noarch/click-8.1.7-unix_pyh707e725_0.conda#f3ad426304898027fc619827ff428eca https://conda.anaconda.org/conda-forge/noarch/cloudpickle-3.1.0-pyhd8ed1ab_1.conda#c88ca2bb7099167912e3b26463fff079 -https://conda.anaconda.org/conda-forge/linux-64/debugpy-1.8.8-py312h2ec8cdc_0.conda#eb182854d81037c9cfd95b06aba22c06 +https://conda.anaconda.org/conda-forge/linux-64/debugpy-1.8.9-py312h2ec8cdc_0.conda#c522fd70ca7a0c2fe1a861dd13987a57 https://conda.anaconda.org/conda-forge/noarch/decorator-5.1.1-pyhd8ed1ab_0.tar.bz2#43afe5ab04e35e17ba28649471dd7364 https://conda.anaconda.org/conda-forge/noarch/defusedxml-0.7.1-pyhd8ed1ab_0.tar.bz2#961b3a227b437d82ad7054484cfa71b2 https://conda.anaconda.org/conda-forge/noarch/entrypoints-0.4-pyhd8ed1ab_0.tar.bz2#3cf04868fee0a029769bd41f4b2fbf2d @@ -187,7 +187,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-25_linux64_openbl https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.10.1-hbbe4b11_0.conda#6e801c50a40301f6978c53976917b277 https://conda.anaconda.org/conda-forge/linux-64/libgl-1.7.0-ha4b6fd6_2.conda#928b8be80851f5d8ffb016f9c81dae7a https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-25_linux64_openblas.conda#4dc03a53fc69371a6158d0ed37214cd3 -https://conda.anaconda.org/conda-forge/linux-64/libpq-16.5-h2d7952a_0.conda#3b863477ad017cfa8456a5aa0a17b950 +https://conda.anaconda.org/conda-forge/linux-64/libpq-16.6-h2d7952a_0.conda#7fa1f554b760a2d6018ecc673fb73f6c https://conda.anaconda.org/conda-forge/noarch/locket-1.0.0-pyhd8ed1ab_0.tar.bz2#91e27ef3d05cc772ce627e51cff111c4 https://conda.anaconda.org/conda-forge/linux-64/lz4-4.3.3-py312hb3f7f12_1.conda#b99d90ef4e77acdab74828f79705a919 https://conda.anaconda.org/conda-forge/linux-64/markupsafe-3.0.2-py312h178313f_0.conda#a755704ea0e2503f8c227d84829a8e81 @@ -222,7 +222,7 @@ https://conda.anaconda.org/conda-forge/linux-64/re2-2023.09.01-h7f4b329_2.conda# https://conda.anaconda.org/conda-forge/noarch/rfc3986-validator-0.1.1-pyh9f0ad1d_0.tar.bz2#912a71cc01012ee38e6b90ddd561e36f https://conda.anaconda.org/conda-forge/linux-64/rpds-py-0.21.0-py312h12e396e_0.conda#37f4ad7cb4214c799f32e5f411c6c69f https://conda.anaconda.org/conda-forge/noarch/send2trash-1.8.3-pyh0d859eb_0.conda#778594b20097b5a948c59e50ae42482a -https://conda.anaconda.org/conda-forge/noarch/setuptools-75.5.0-pyhff2d567_0.conda#ade63405adb52eeff89d506cd55908c0 +https://conda.anaconda.org/conda-forge/noarch/setuptools-75.6.0-pyhff2d567_0.conda#68d7d406366926b09a6a023e3d0f71d7 https://conda.anaconda.org/conda-forge/noarch/simpervisor-1.0.0-pyhd8ed1ab_0.conda#1f6df17b16d6295a484d59e844fef6ee https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2 https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.1-pyhd8ed1ab_0.conda#490730480d76cf9c8f8f2849719c6e2b @@ -283,7 +283,7 @@ https://conda.anaconda.org/conda-forge/noarch/partd-1.4.2-pyhd8ed1ab_0.conda#0ba https://conda.anaconda.org/conda-forge/noarch/pexpect-4.9.0-pyhd8ed1ab_0.conda#629f3203c99b32e0988910c93e77f3b6 https://conda.anaconda.org/conda-forge/linux-64/pillow-10.4.0-py312h56024de_1.conda#4bd6077376c7f9c1ce33fd8319069e5b https://conda.anaconda.org/conda-forge/linux-64/poppler-24.04.0-hb6cd0d7_0.conda#d19eed746748f1d44b575662f2bcfe95 -https://conda.anaconda.org/conda-forge/linux-64/postgresql-16.5-hb2eb5c0_0.conda#f0b1fc2c91661400dc7f516f96339e99 +https://conda.anaconda.org/conda-forge/linux-64/postgresql-16.6-hb2eb5c0_0.conda#093e98b901ac8298e77e6e3c7184b1e1 https://conda.anaconda.org/conda-forge/linux-64/proj-9.4.0-hb784bbd_2.conda#b0683c229de4c4c676450d24ff87538c https://conda.anaconda.org/conda-forge/noarch/prompt-toolkit-3.0.48-pyha770c72_0.conda#4c05134c48b6a74f33bbb9938e4a115e https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.9.0.post0-pyhff2d567_0.conda#b6dfd90a2141e573e4b6a81630b56df5 @@ -293,8 +293,8 @@ 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https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_0.conda#7e9f4612544c8edbfd6afad17f1bd045 https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-21.2.0-py312h66e93f0_5.conda#1505fc57c305c0a3174ea7aae0a0db25 https://conda.anaconda.org/conda-forge/noarch/arrow-1.3.0-pyhd8ed1ab_0.conda#b77d8c2313158e6e461ca0efb1c2c508 @@ -318,7 +318,7 @@ https://conda.anaconda.org/conda-forge/noarch/mako-1.3.6-pyhff2d567_0.conda#bcd0 https://conda.anaconda.org/conda-forge/linux-64/nlopt-2.8.0-py312h69683c5_2.conda#8582b8ef6a808ace0bfb83213ac54d54 https://conda.anaconda.org/conda-forge/linux-64/pandas-2.2.3-py312hf9745cd_1.conda#8bce4f6caaf8c5448c7ac86d87e26b4b https://conda.anaconda.org/conda-forge/linux-64/pango-1.54.0-h4c5309f_1.conda#7df02e445367703cd87a574046e3a6f0 -https://conda.anaconda.org/conda-forge/linux-64/pydantic-core-2.23.4-py312h12e396e_0.conda#0845ab52d4ea209049129a6a91bc74ba 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https://conda.anaconda.org/conda-forge/linux-64/r-magrittr-2.0.3-r43hb1dbf0f_3.conda#fc61bcf37e59037b486c8841a704e9da +https://conda.anaconda.org/conda-forge/noarch/r-mapplots-1.5.2-r43hc72bb7e_1.conda#604f73eb8dc6bf1fe7821968a0caee24 https://conda.anaconda.org/conda-forge/linux-64/r-maps-3.4.2.1-r43h2b5f3a1_0.conda#6f0792a8c58c6597b3334775ccd0bce5 https://conda.anaconda.org/conda-forge/linux-64/r-mass-7.3_60.0.1-r43hb1dbf0f_1.conda#c3c9184486ccabe19b86aba11351652e https://conda.anaconda.org/conda-forge/linux-64/r-matrixstats-1.4.1-r43h2b5f3a1_0.conda#4e7f80d3e24e7dcc88fc6f3c3ce231b1 @@ -566,7 +567,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-urlchecker-1.0.1-r43hc72bb7e_3.c https://conda.anaconda.org/conda-forge/linux-64/r-urltools-1.7.3-r43ha18555a_5.conda#7b70a8ca046c392df68deae0fe2b2336 https://conda.anaconda.org/conda-forge/linux-64/r-vctrs-0.6.5-r43h0d4f4ea_1.conda#7f4c30bb576acec2a682c40790c2d406 https://conda.anaconda.org/conda-forge/linux-64/r-websocket-1.4.1-r43h93ab643_3.conda#4f23d50519d65ae8dbf05787aa5fd908 -https://conda.anaconda.org/conda-forge/linux-64/r-xgboost-2.1.2-cuda118_r43h4cbe3ba_0.conda#dbeb47006ac4ed5737a5a1fd5ed91869 +https://conda.anaconda.org/conda-forge/linux-64/r-xgboost-2.1.2-cuda118_r43h4cbe3ba_1.conda#7ba1683254295f38290373c5d98b3d9b https://conda.anaconda.org/conda-forge/noarch/r-xopen-1.0.1-r43hc72bb7e_1.conda#f394a5d99c94c0cdded7fcd1e2117b02 https://conda.anaconda.org/conda-forge/linux-64/r-xts-0.14.1-r43h2b5f3a1_0.conda#e336d7af8b309b241e2bbbc46bfb7bf6 https://conda.anaconda.org/conda-forge/noarch/jupyter_server-2.14.2-pyhd8ed1ab_0.conda#ca23c71f70a7c7935b3d03f0f1a5801d @@ -597,6 +598,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-leaflet.providers-2.0.0-r43hc72b https://conda.anaconda.org/conda-forge/noarch/r-pillar-1.9.0-r43hc72bb7e_2.conda#49a43daa7f46eecd9d42f1073da96662 https://conda.anaconda.org/conda-forge/noarch/r-pkgbuild-1.4.5-r43hc72bb7e_0.conda#4155a239cfff00d7deea928cb35a57ce https://conda.anaconda.org/conda-forge/linux-64/r-purrr-1.0.2-r43hdb488b9_1.conda#4270c6c51a02fc0da32b9d7b453ef3f5 +https://conda.anaconda.org/conda-forge/noarch/r-r.cache-0.16.0-r43hc72bb7e_3.conda#09180fff5f2b11a8898749894719ed0c https://conda.anaconda.org/conda-forge/linux-64/r-raster-3.6_30-r43h93ab643_0.conda#bfa29868dec832c950b8f1da406244ba https://conda.anaconda.org/conda-forge/linux-64/r-sass-0.4.9-r43ha18555a_1.conda#4671c120e368b94d8651b7289d06a43f https://conda.anaconda.org/conda-forge/noarch/r-spacetime-1.3_2-r43hc72bb7e_0.conda#2ac1b8dcc50c846b7e128fe1aab566a1 @@ -628,6 +630,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-progress-1.2.3-r43hc72bb7e_1.con https://conda.anaconda.org/conda-forge/noarch/r-quantmod-0.4.26-r43hc72bb7e_1.conda#28b8367bd8320296d787ea6450713c1c https://conda.anaconda.org/conda-forge/linux-64/r-ragg-1.3.3-r43h9aa3752_0.conda#c3cd60e5eeed900f4f4c3a1e5ce6f244 https://conda.anaconda.org/conda-forge/noarch/r-rcmdcheck-1.4.0-r43h785f33e_3.conda#d49c545365e3a888f21b920b16bee319 +https://conda.anaconda.org/conda-forge/noarch/r-repmis-0.5-r43hc72bb7e_4.conda#cd91a84276e913145daa5c57e8821987 https://conda.anaconda.org/conda-forge/noarch/r-repr-1.1.7-r43h785f33e_1.conda#c5196ead473f381384bc3dda3671c346 https://conda.anaconda.org/conda-forge/linux-64/r-reshape2-1.4.4-r43h0d4f4ea_4.conda#45c563cc9243b5243331b57a4dc445f0 https://conda.anaconda.org/conda-forge/linux-64/r-rsqlite-2.3.8-r43h93ab643_0.conda#860ad80b64b7f47f7900622b9909fa42 diff --git a/r/environment.yml b/r/environment.yml index 3c3baf3..d7e0435 100644 --- a/r/environment.yml +++ b/r/environment.yml @@ -41,7 +41,6 @@ dependencies: - r-doparallel - r-dplyr - r-earth - - r-rerddap - r-fields - r-foreach - r-forecast @@ -74,6 +73,7 @@ dependencies: - r-mmand - r-mapdata - r-mapedit + - r-mapplots - r-mapproj - r-maps - r-maptools @@ -104,6 +104,8 @@ dependencies: - r-rastervis - r-readr - r-remotes + - r-repmis + - r-rerddap - r-reshape - r-rgdal >=1.5 - r-rgeos