R image: added mapplots and repmis, and made a couple of small cleanups

Author: emiliom

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
@@ -57,26 +55,17 @@ 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
 
 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)" && \

r/conda-linux-64.lock

@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: b064f256a2e647aa5d9387adba87783c45f7ef10612be238e19dd2c1a4fd5838
+# input_hash: e6956d4811dbd558b15d2167610a422525a87c259760b1017b4f627d6f6ee57c
 @EXPLICIT
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-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
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+https://conda.anaconda.org/conda-forge/linux-64/libxgboost-2.1.2-cuda118_h09a87be_1.conda#706196aa07632a23a1fb7d34da1ba2d1
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@@ -165,7 +165,7 @@ https://conda.anaconda.org/conda-forge/noarch/certifi-2024.8.30-pyhd8ed1ab_0.con
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-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
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@@ -187,7 +187,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-25_linux64_openbl
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-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
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@@ -222,7 +222,7 @@ https://conda.anaconda.org/conda-forge/linux-64/re2-2023.09.01-h7f4b329_2.conda#
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-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
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@@ -283,7 +283,7 @@ https://conda.anaconda.org/conda-forge/noarch/partd-1.4.2-pyhd8ed1ab_0.conda#0ba
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-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
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@@ -293,8 +293,8 @@ https://conda.anaconda.org/conda-forge/noarch/rfc3339-validator-0.1.4-pyhd8ed1ab
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+https://conda.anaconda.org/conda-forge/linux-64/yarl-1.18.0-py312h66e93f0_0.conda#601d2b19a54fd9346ba18c07c2516339
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@@ -318,7 +318,7 @@ https://conda.anaconda.org/conda-forge/noarch/mako-1.3.6-pyhff2d567_0.conda#bcd0
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+https://conda.anaconda.org/conda-forge/linux-64/pydantic-core-2.27.0-py312h12e396e_0.conda#9729cebbd1ad13a592359001bf4408d9
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 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

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