Working image with rclone and maap-py in rstudio working

base_images/2i2c/r-base/docker/Dockerfile

@@ -37,6 +37,10 @@ RUN apt-get clean && apt-get update && \
 
 USER ${NB_USER}
 
+# Use sharded repodata for faster resolve times 
+RUN conda install --name base 'conda-libmamba-solver>=25.11.0' -y
+RUN conda config --set plugins.use_sharded_repodata true
+
 # Install additional packages from environment.yml
 COPY ./environment.yml /tmp
 RUN conda env update -n ${CONDA_ENV} -f "/tmp/environment.yml" \
@@ -47,6 +51,14 @@ RUN conda env update -n ${CONDA_ENV} -f "/tmp/environment.yml" \
 RUN conda init
 
 USER root
+
+# Set default CRAN mirror to use pre-built binaries from Posit Package Manager
+RUN R_HOME=$(R RHOME) && \
+    echo "options(repos = c(CRAN = 'https://packagemanager.posit.co/cran/__linux__/noble/latest'))" >> "$R_HOME/etc/Rprofile.site"
+
+# Install pak for better package management
+RUN Rscript -e "install.packages('pak', repos = sprintf('https://r-lib.github.io/p/pak/devel/%s/%s/%s', .Platform\$pkgType, R.Version()\$os, R.Version()\$arch))"
+
 SHELL ["/bin/bash", "-c"]
 ADD . /
 RUN ["chmod", "+x", "/scripts/install_cran_packages_r.sh"]

base_images/2i2c/r-base/environment.yml

@@ -6,6 +6,8 @@ dependencies:
   # Python packages only - NO R packages in conda
   - gdal=3.10.2
   - nodejs=20.19.5
+  - pdal=2.8.4
+  - rclone=1.74.2
   - rtree=1.4.1 
   - unzip=6.0
   - pip=26.0

base_images/2i2c/r-base/scripts/init-user.sh

@@ -3,7 +3,7 @@
 R_SITE_ENV=$(R RHOME)/etc/Renviron.site
 
 # Variables we want to add to Renviron
-VARS=("AWS_ROLE_ARN" "AWS_WEB_IDENTITY_TOKEN_FILE" "AWS_DEFAULT_REGION" "MAAP_PGT")
+VARS=("AWS_ROLE_ARN" "AWS_WEB_IDENTITY_TOKEN_FILE" "AWS_DEFAULT_REGION")
 
 echo "--- Updating R Site Environment Variables ---"
 

base_images/2i2c/r-base/scripts/install_cran_packages_r.sh

@@ -5,51 +5,43 @@ set -e
 export DEBIAN_FRONTEND=noninteractive
 
 ## build ARGs
-NCPUS=${NCPUS:--1}
 R_LIB=${R_LIB:-/usr/local/lib/R/site-library}
 
-# Install recommended R packages first to avoid warnings
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "codetools"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "tmap"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "tidyterra"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "BIOMASS"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "nlraa"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "geojsonio"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "future"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://r-lidar.r-universe.dev" -n "$NCPUS" "lasR"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "partykit"
-# Random fields is deprecated as of 2022
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "randomForest"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "RCSF"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "RPostgreSQL"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "car"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "chron"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "egg"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "ggpubr"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "ggspatial"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "ggtext"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "gsubfn"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "microbenchmark"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "minpack.lm"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "patchwork"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "paws"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "pool"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "proto"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "protolite"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "rgee"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "rlist"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "rnaturalearth"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "rockchalk"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "RODBC"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "rstac"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "RStoolbox"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "snow"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "sqldf"
-Rscript /scripts/install2.r --error --skipmissing --skipinstalled -l "$R_LIB" -r "https://cran.r-project.org" -n "$NCPUS" "duckdb"
+# Install CRAN packages using pak (much faster with pre-built binaries)
+# pak automatically handles parallel downloads and dependency resolution
+Rscript -e "pak::pak(c(
+  'tidyterra',
+  'BIOMASS',
+  'nlraa',
+  'geojsonio',
+  'partykit',
+  'randomForest',
+  'RCSF',
+  'RPostgreSQL',
+  'car',
+  'chron',
+  'egg',
+  'ggpubr',
+  'ggtext',
+  'gsubfn',
+  'microbenchmark',
+  'minpack.lm',
+  'patchwork',
+  'paws',
+  'pool',
+  'proto',
+  'protolite',
+  'rgee',
+  'rlist',
+  'rockchalk',
+  'RODBC',
+  'RStoolbox',
+  'snow',
+  'sqldf'
+), lib = '$R_LIB', ask = FALSE)"
 
-# Install Bioconductor packages
-# BiocManager must be installed first, then use it to install Bioconductor packages
-Rscript -e "BiocManager::install('rhdf5', lib = '$R_LIB', Ncpus = $NCPUS, update = FALSE, ask = FALSE)"
+# Install lasR from r-universe (pak supports alternative repos)
+Rscript -e "pak::pak('r-lidar/lasR', lib = '$R_LIB', ask = FALSE)"
 
 # Clean up
 rm -rf /var/lib/apt/lists/*

base_images/2i2c/r/docker/Dockerfile

@@ -18,4 +18,12 @@ RUN conda init
 ARG IMAGE_REF
 ENV DOCKERIMAGE_PATH_BASE_IMAGE=${IMAGE_REF}
 ARG DEFAULT_DOCKERFILE_PATH
-ENV DOCKERIMAGE_PATH_DEFAULT=${DEFAULT_DOCKERFILE_PATH}
+ENV DOCKERIMAGE_PATH_DEFAULT=${DEFAULT_DOCKERFILE_PATH}
+
+USER root
+COPY scripts/init-user.sh /usr/local/bin/init-user.sh
+RUN chmod +x /usr/local/bin/init-user.sh
+USER ${NB_USER}
+
+# This script returns control to base image's /srv/start after, need this for rclone
+ENTRYPOINT ["/usr/local/bin/init-user.sh"]

base_images/2i2c/r/scripts/init-user.sh

@@ -1,7 +1,43 @@
 #!/bin/bash
 
-REGION="${AWS_DEFAULT_REGION:-us-west-2}"
+# First, set up R environment variables from r-base init script
+R_SITE_ENV=$(R RHOME)/etc/Renviron.site
+
+# Variables we want to add to Renviron
+VARS=("AWS_ROLE_ARN" "AWS_WEB_IDENTITY_TOKEN_FILE" "AWS_DEFAULT_REGION" "MAAP_PGT")
+
+echo "--- Updating R Site Environment Variables ---"
+
+# Loop through the variables and append them if they exist in the current shell
+for var_name in "${VARS[@]}"; do
+    # Use indirect expansion to get the value of the variable name
+    var_value="${!var_name}"
 
+    if [ -n "$var_value" ]; then
+        echo "Adding $var_name to $R_SITE_ENV"
+        # Check if the line already exists to avoid duplicates
+        if ! grep -q "^$var_name=" "$R_SITE_ENV"; then
+            echo "$var_name=$var_value" >> "$R_SITE_ENV"
+        else
+            # Update existing line if it changed
+            sed -i "s|^$var_name=.*|$var_name=$var_value|" "$R_SITE_ENV"
+        fi
+    else
+        echo "Skipping $var_name: Not set in shell environment."
+    fi
+done
+
+# File ends with a newline 
+echo "" >> "$R_SITE_ENV"
+
+# Needed to run awsv2 and aws 
+awscliv2 --install
+CONDA_BIN=$(dirname $(which python))
+ln -sf $(which awsv2) "$CONDA_BIN/aws"
+
+# Now set up rclone
+REGION="${AWS_DEFAULT_REGION:-us-west-2}"
 rclone config create maap-s3 s3 provider=AWS env_auth=true region="$REGION" no_check_bucket true
 
+# Hand control to the base image's /srv/start which handles all initialization
 exec /srv/start "$@"