From 40c28d2f4a37ee2bfcc54019b88dde15c1dc022f Mon Sep 17 00:00:00 2001
From: grallewellyn <grace.llewellyn@jpl.nasa.gov>
Date: Fri, 8 May 2026 10:14:28 -0700
Subject: [PATCH] updates to all images but r still has maap-py bug

---
 base_images/2i2c/isce3/environment.yml        |   8 +-
 base_images/2i2c/pangeo/docker/Dockerfile     |   2 -
 base_images/2i2c/pangeo/environment.yml       |   4 +-
 base_images/2i2c/pytorch/docker/Dockerfile    |   2 +-
 base_images/2i2c/pytorch/environment.yml      |   2 +-
 base_images/2i2c/r-base/docker/Dockerfile     |  60 +++---
 base_images/2i2c/r-base/environment.yml       |  16 +-
 base_images/2i2c/r-base/scripts/install2.r    | 186 ------------------
 .../r-base/scripts/install_cran_packages_r.sh |  76 ++++---
 .../r-base/scripts/print_package_versions.R   |  55 ------
 .../r-base/scripts/r_package_versions.txt     |  45 -----
 base_images/2i2c/r/docker/Dockerfile          |  13 +-
 base_images/2i2c/r/environment.yml            |   2 +-
 base_images/2i2c/r/scripts/init-user.sh       |   7 +
 .../2i2c/tensorflow2/docker/Dockerfile        |   6 +-
 base_images/2i2c/tensorflow2/environment.yml  |   2 +-
 16 files changed, 110 insertions(+), 376 deletions(-)
 delete mode 100644 base_images/2i2c/r-base/scripts/install2.r
 delete mode 100644 base_images/2i2c/r-base/scripts/print_package_versions.R
 delete mode 100644 base_images/2i2c/r-base/scripts/r_package_versions.txt
 create mode 100644 base_images/2i2c/r/scripts/init-user.sh

diff --git a/base_images/2i2c/isce3/environment.yml b/base_images/2i2c/isce3/environment.yml
index f55e56e..14ed989 100644
--- a/base_images/2i2c/isce3/environment.yml
+++ b/base_images/2i2c/isce3/environment.yml
@@ -52,14 +52,14 @@ dependencies:
   - unidecode=1.4.0
   - unzip=6.0
   - xarray=2026.4.0
-  - pip=26.0.1
+  - pip=26.1.1
   - pip:
-    - jupyter-resource-usage==1.2.0
+    - jupyter-resource-usage==1.2.1
     - jupyter-sshd-proxy==0.3.0
     - jupyterlab-bxplorer==0.2.30
     # - git+https://github.com/MAAP-Project/stac_ipyleaflet.git@0.3.6
-    - morecantile==6.1.0
-    - rio-tiler==7.2.2
+    - morecantile==7.0.3
+    - rio-tiler==9.0.6
     - maap-py==4.2.0
     - maap-algorithms-jupyter-extension==0.5.1
     - maap-jupyter-server-extension==3.0.0
diff --git a/base_images/2i2c/pangeo/docker/Dockerfile b/base_images/2i2c/pangeo/docker/Dockerfile
index d60f5eb..2b56ba9 100644
--- a/base_images/2i2c/pangeo/docker/Dockerfile
+++ b/base_images/2i2c/pangeo/docker/Dockerfile
@@ -18,8 +18,6 @@ RUN conda env update -n ${CONDA_ENV} -f "/tmp/environment.yml" \
 
 RUN conda init
 
-RUN jupyter server extension enable maap_jupyter_server_extension
-
 USER root
 COPY scripts/init-user.sh /usr/local/bin/init-user.sh
 RUN chmod +x /usr/local/bin/init-user.sh
diff --git a/base_images/2i2c/pangeo/environment.yml b/base_images/2i2c/pangeo/environment.yml
index d162cf6..a196470 100644
--- a/base_images/2i2c/pangeo/environment.yml
+++ b/base_images/2i2c/pangeo/environment.yml
@@ -6,9 +6,9 @@ dependencies:
   - icu=78.2
   - nodejs=22.22.0
   - rustac=0.9.9
-  - pip=26.0.1
+  - pip=26.1.1
   - pip:
-    - rio-tiler==8.0.5
+    - rio-tiler==9.0.6
     - maap-py==4.2.0
     - maap-algorithms-jupyter-extension==0.5.1
     - maap-jupyter-server-extension==3.0.0
diff --git a/base_images/2i2c/pytorch/docker/Dockerfile b/base_images/2i2c/pytorch/docker/Dockerfile
index 611a89b..5d08aa3 100644
--- a/base_images/2i2c/pytorch/docker/Dockerfile
+++ b/base_images/2i2c/pytorch/docker/Dockerfile
@@ -1,4 +1,4 @@
-FROM quay.io/pangeo/pytorch-notebook:2025.12.30
+FROM quay.io/pangeo/pytorch-notebook:2026.04.29
 ENV LANG=en_US.UTF-8
 ENV TZ=US/Pacific
 ARG DEBIAN_FRONTEND=noninteractive
diff --git a/base_images/2i2c/pytorch/environment.yml b/base_images/2i2c/pytorch/environment.yml
index 21ab024..65e08f6 100644
--- a/base_images/2i2c/pytorch/environment.yml
+++ b/base_images/2i2c/pytorch/environment.yml
@@ -6,7 +6,7 @@ dependencies:
   # Dependencies for VS Code IDE
   - code-server>=3.2
   - jupyter-vscode-proxy=0.7
-  - pre_commit=3.4.0
+  - pre_commit
   # Upgrade from py torch notebook image
   - earthaccess>=0.16.0
   # Pin down to avoid https://github.com/holoviz/pyviz_comms/issues/143
diff --git a/base_images/2i2c/r-base/docker/Dockerfile b/base_images/2i2c/r-base/docker/Dockerfile
index 6cd925e..dda9542 100644
--- a/base_images/2i2c/r-base/docker/Dockerfile
+++ b/base_images/2i2c/r-base/docker/Dockerfile
@@ -1,4 +1,4 @@
-FROM ghcr.io/nmfs-opensci/container-images/py-rocket-geospatial-2:2026.01.25
+FROM ghcr.io/nmfs-opensci/container-images/py-rocket-geospatial-2:2026.02.18
 ENV LANG=en_US.UTF-8
 ENV TZ=US/Pacific
 ARG DEBIAN_FRONTEND=noninteractive
@@ -9,34 +9,38 @@ USER root
 # 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 && \
+    gdal-bin \
+    lbzip2 \
+    libfftw3-dev \
+    libgdal-dev \
+    libgeos-dev \
+    libgl1-mesa-dev \
+    libglu1-mesa-dev \
+    libhdf4-alt-dev \
+    libhdf5-dev \
+    libjq-dev \
+    libpq-dev \
+    libproj-dev \
+    libprotobuf-dev \
+    libnetcdf-dev \
+    libsqlite3-dev \
+    libssl-dev \
+    libudunits2-dev \
+    netcdf-bin \
+    postgis \
+    protobuf-compiler \
+    sqlite3 \
+    tk-dev \
+    unixodbc-dev && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
 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"]
diff --git a/base_images/2i2c/r-base/environment.yml b/base_images/2i2c/r-base/environment.yml
index 8a7485e..7051269 100644
--- a/base_images/2i2c/r-base/environment.yml
+++ b/base_images/2i2c/r-base/environment.yml
@@ -4,12 +4,18 @@ channels:
   - nodefaults
 dependencies:
   # Python packages only - NO R packages in conda
-  - gdal=3.10.2
-  - nodejs=20.19.5
+  - gdal>=3.12.2
+  - nodejs>=20.20.2
+  - pdal>=2.8.4 
+  - py-xgboost=3.2.0
+  - python>=3.12.0  
+  - qgis>=3.44.7
+  - rclone=1.74.0
   - rtree=1.4.1 
+  - sqlite>=3.45
   - unzip=6.0
-  - pip=26.0
+  - pip=26.1.1
   - pip:
     # - git+https://github.com/MAAP-Project/stac_ipyleaflet.git@0.3.6
-    - morecantile==6.1.0
-    - rio-tiler==7.2.2
\ No newline at end of file
+    - morecantile==7.0.3
+    - rio-tiler==9.0.6
\ No newline at end of file
diff --git a/base_images/2i2c/r-base/scripts/install2.r b/base_images/2i2c/r-base/scripts/install2.r
deleted file mode 100644
index 4a2d6d1..0000000
--- a/base_images/2i2c/r-base/scripts/install2.r
+++ /dev/null
@@ -1,186 +0,0 @@
-#!/usr/bin/env r
-#
-# A second example to install one or more packages, now with option parsing
-#
-# Copyright (C) 2011 - 2014  Dirk Eddelbuettel
-# Copyright (C) 2014 - 2017  Carl Boettiger and Dirk Eddelbuettel
-# Copyright (C) 2018 - 2023  Carl Boettiger, Dirk Eddelbuettel, Brandon Bertelsen, and SHIMA Tatsuya
-#
-# Released under GPL (>= 2)
-# This file was extracted from this repository https://github.com/rocker-org/rocker-versioned2
-# The license of this repository (rocker-versioned2) can be view here: 
-# https://github.com/rocker-org/rocker-versioned2/blob/master/LICENSE
-
-#    Warranty description we are required to convey: 
-#    This program is free software; you can redistribute it and/or modify
-#    it under the terms of the GNU General Public License as published by
-#    the Free Software Foundation; either version 2 of the License, or
-#    (at your option) any later version.
-
-#    This program is distributed in the hope that it will be useful,
-#    but WITHOUT ANY WARRANTY; without even the implied warranty of
-#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#    GNU General Public License for more details.
-
-#    You should have received a copy of the GNU General Public License along
-#    with this program; if not, write to the Free Software Foundation, Inc.,
-#    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-
-#    Any questions, please contact: grace.llewellyn@jpl.nasa.gov 
-
-
-## load docopt package from CRAN
-# Grace Llewellyn added the repos parameter to fix a bug
-# Use first library location in .libPaths() for consistent installation
-libloc <- .libPaths()[1]
-install.packages('docopt', repos = "http://cran.us.r-project.org", lib = libloc)
-library(docopt)
-
-## configuration for docopt
-doc <- paste0("Usage: install2.r [-l LIBLOC] [-h] [-x] [-s] [-d DEPS] [-n NCPUS] [-r REPOS...] [-m METHOD] [-t TYPE] [--error] [--skipmissing] [--] [PACKAGES ...]
-
--l --libloc LIBLOC  location in which to install [default: ", libloc, "]
--d --deps DEPS      install suggested dependencies as well [default: NA]
--n --ncpus NCPUS    number of processes to use for parallel install, -1 selects all cores [default: getOption]
--r --repos REPOS    repositor(y|ies) to use, or NULL for file [default: getOption]
--e --error          throw error and halt instead of a warning [default: FALSE]
---skipmissing       use with the --error option, skip the packages missing error [default: FALSE]
--s --skipinstalled  skip installing already installed packages [default: FALSE]
--m --method METHOD  method to be used for downloading files [default: auto]
--t --type TYPE      installation type as used by `install.packages` [default: getOption]
--h --help           show this help text
--x --usage          show help and short example usage")
-opt <- docopt(doc)			# docopt parsing
-if (opt$usage) {
-    cat(doc, "\n\n")
-    cat("where PACKAGES... can be one or more CRAN package names, or local (binary or source)
-package files (where extensions .tar.gz, .tgz and .zip are recognised). Optional
-arguments understood by R CMD INSTALL can be passed interspersed in the PACKAGES, though
-this requires use of '--'.
-
-Examples:
-  install2.r -l /tmp/lib Rcpp BH                    # install into given library
-  install2.r -- --with-keep.source drat             # keep the source
-  install2.r -- --data-compress=bzip2 stringdist    # prefer bz2 compression
-  install2.r \".\"                                  # install package in current directory
-  install2.r -n 6 ggplot2                           # parallel install: (6 processes)
-
-install2.r is part of littler which brings 'r' to the command-line.
-See https://dirk.eddelbuettel.com/code/littler.html for more information.\n")
-    q("no")
-}
-if (opt$deps == "TRUE" || opt$deps == "FALSE") {
-    opt$deps <- as.logical(opt$deps)
-} else if (opt$deps == "NA") {
-    opt$deps <- NA
-}
-## docopt results are characters, so if we meant NULL we have to set NULL
-if (length(opt$repos) == 1 && "NULL" %in% opt$repos) {
-    opt$repos <- NULL
-}
-
-if ("getOption" %in% opt$repos) {
-    ## as littler can now read ~/.littler.r and/or /etc/littler.r we can preset elsewhere
-    opt$repos <- c(opt$repos[which(opt$repos != "getOption")], getOption("repos"))
-}
-
-if (opt$ncpus == "getOption") {
-    opt$ncpus <- getOption("Ncpus", 1L)
-} else if (opt$ncpus == "-1") {
-    ## parallel comes with R 2.14+
-    opt$ncpus <- max(1L, parallel::detectCores())
-}
-
-## type should reflects bspm where available
-if (opt$type == "getOption") {
-    opt$type <- getOption("pkgType")
-    #if (requireNamespace("bspm", quietly=TRUE) && Sys.info()[["sysname"]] == "Linux") opt$type <- "binary-source"
-
-}
-
-## ensure installation is stripped
-Sys.setenv("_R_SHLIB_STRIP_"="true")
-install_packages2 <- function(pkgs, ..., error = FALSE, skipmissing = FALSE, skipinstalled = FALSE) {
-    e <- NULL
-    capture <- function(e) {
-        if (error) {
-            catch <-
-                grepl("(download|installation) of package .* failed", e$message) ||
-                (grepl("(dependenc|package).*(is|are) not available", e$message) && !skipmissing) ||
-                grepl("installation of package.*had non-zero exit status", e$message) ||
-                grepl("installation of .+ package(|s) failed", e$message)
-            if (catch) {
-                e <<- e
-            }
-        }
-    }
-    if (skipinstalled) {
-        pkgs <- setdiff(pkgs, installed.packages()[,1])
-    }
-    if (length(pkgs) > 0) {
-        withCallingHandlers(install.packages(pkgs, ...), warning = capture)
-        if (!is.null(e)) {
-            stop(e$message, call. = FALSE)
-        }
-    }
-}
-
-## helper function to for existing files with matching extension
-isMatchingFile <- function(f) (file.exists(f) && grepl("(\\.tar\\.gz|\\.tgz|\\.zip)$", f)) || (f == ".")
-
-## helper function which switches to local (ie NULL) repo if matching file is presented
-installArg <- function(f, lib, rep, dep, iopts, error, skipmissing, skipinstalled, ncpus, method, type) {
-    install_packages2(pkgs=f,
-                      lib=lib,
-                      repos=if (isMatchingFile(f)) NULL else rep,
-                      dependencies=dep,
-                      INSTALL_opts=iopts,
-                      Ncpus = ncpus,
-                      method = method,
-                      type = type,
-                      error = error,
-                      skipmissing = skipmissing,
-                      skipinstalled = skipinstalled)
-}
-
-## strip out arguments to be passed to R CMD INSTALL
-isArg <- grepl('^--',opt$PACKAGES)
-installOpts <- opt$PACKAGES[isArg]
-opt$PACKAGES <- opt$PACKAGES[!isArg]
-
-if (length(opt$PACKAGES)==0 && file.exists("DESCRIPTION") && file.exists("NAMESPACE")) {
-    ## we are in a source directory, so build it
-    message("* installing *source* package found in current working directory ...")
-    opt$PACKAGES <- "."
-}
-
-## helper function to for existing files with matching extension
-isMatchingFile <-
-    function(f) (file.exists(f) &&
-                 grepl("(\\.tar\\.gz|\\.tgz|\\.zip)$", f)) || (f == ".")
-
-## check arguments for local files -- if none, then we can pass vector on
-isLocal <- sapply(opt$PACKAGES, isMatchingFile)
-
-## for any local sources loop explicitly as before, otherwise for remote
-## packages pass vector to install_packages2 which does the rest (and
-## possibly in parallel using up to ncpus)
-if (any(isLocal)) {
-    sapply(opt$PACKAGES, installArg, opt$libloc, opt$repos, opt$deps,
-           installOpts, opt$error, opt$skipmissing, opt$skipinstalled, opt$ncpus, opt$method, opt$type)
-} else {
-    install_packages2(pkgs = opt$PACKAGES,
-                      lib = opt$libloc,
-                      repos = opt$repos,
-                      dependencies = opt$deps,
-                      INSTALL_opts = installOpts,
-                      Ncpus = opt$ncpus,
-                      method = opt$method,
-                      type = opt$type,
-                      error = opt$error,
-                      skipmissing = opt$skipmissing,
-                      skipinstalled = opt$skipinstalled)
-}
-
-## clean up any temp file containing CRAN directory information
-sapply(list.files(path=tempdir(), pattern="^(repos|libloc).*\\.rds$", full.names=TRUE), unlink)
\ No newline at end of file
diff --git a/base_images/2i2c/r-base/scripts/install_cran_packages_r.sh b/base_images/2i2c/r-base/scripts/install_cran_packages_r.sh
index 160ef4b..01c7d59 100644
--- a/base_images/2i2c/r-base/scripts/install_cran_packages_r.sh
+++ b/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/*
diff --git a/base_images/2i2c/r-base/scripts/print_package_versions.R b/base_images/2i2c/r-base/scripts/print_package_versions.R
deleted file mode 100644
index 2d1bb43..0000000
--- a/base_images/2i2c/r-base/scripts/print_package_versions.R
+++ /dev/null
@@ -1,55 +0,0 @@
-#!/usr/bin/env Rscript
-
-# Script to print all R packages defined in install_cran_packages_r.sh
-# along with their current versions
-
-cat("R Package Versions\n")
-cat("==================\n\n")
-
-# Read the install script
-script_path <- "/scripts/install_cran_packages_r.sh"
-if (!file.exists(script_path)) {
-  # If running locally, try the relative path
-  script_path <- "install_cran_packages_r.sh"
-}
-
-# Read the script content
-script_lines <- readLines(script_path)
-
-# Extract package names from Rscript install2.r lines
-packages <- c()
-
-for (line in script_lines) {
-  # Match lines with install2.r and extract package name (last quoted argument)
-  if (grepl("install2\\.r.*\"[^\"]+\"\\s*$", line)) {
-    # Extract the last quoted string
-    match <- regmatches(line, regexpr("\"([^\"]+)\"\\s*$", line))
-    if (length(match) > 0) {
-      package_name <- gsub("\"", "", match)
-      packages <- c(packages, package_name)
-    }
-  }
-
-  # Also match Bioconductor packages from BiocManager::install
-  if (grepl("BiocManager::install\\('([^']+)'", line)) {
-    match <- regmatches(line, regexpr("'([^']+)'", line))
-    if (length(match) > 0) {
-      package_name <- gsub("'", "", match)
-      packages <- c(packages, package_name)
-    }
-  }
-}
-
-# Get versions for each package
-cat(sprintf("Found %d packages\n\n", length(packages)))
-
-for (pkg in packages) {
-  tryCatch({
-    version <- as.character(packageVersion(pkg))
-    cat(sprintf("%-20s %s\n", pkg, version))
-  }, error = function(e) {
-    cat(sprintf("%-20s NOT INSTALLED\n", pkg))
-  })
-}
-
-cat("\n")
diff --git a/base_images/2i2c/r-base/scripts/r_package_versions.txt b/base_images/2i2c/r-base/scripts/r_package_versions.txt
deleted file mode 100644
index 35f5464..0000000
--- a/base_images/2i2c/r-base/scripts/r_package_versions.txt
+++ /dev/null
@@ -1,45 +0,0 @@
-Since it is difficult to pin the version for R packages because once the current package we have pinned goes
-into the archives because a new package was released, the link like https://cran.r-project.org/src/contrib/codetools_0.2-20.tar.gz
-will break because archive needs to be added to the url for that version 
-To avoid constantly having to update these links, I propose we just record the package versions for our R packages
-in this text file in case we need to reference them later 
-The R script called print_package_versions.R will generate a list of all R package versions for the R packages we are installing in install_cran_packages_r.sh
-
-Release 5.0: 
-codetools            0.2.20
-tidyterra            0.7.2
-BIOMASS              2.2.4.1
-nlraa                1.9.10
-essentials           0.1.0
-geojsonio            0.11.3
-future               1.68.0
-lasR                 0.17.3
-partykit             1.2.24
-randomForest         4.7.1.2
-RCSF                 1.0.2
-RPostgreSQL          0.7.8
-car                  3.1.3
-chron                2.3.62
-egg                  0.4.5
-ggpubr               0.6.2
-ggspatial            1.1.10
-ggtext               0.1.2
-gsubfn               0.7
-microbenchmark       1.5.0
-minpack.lm           1.2.4
-patchwork            1.3.2
-paws                 0.9.0
-pool                 1.0.4
-proto                1.0.0
-protolite            2.3.1
-rgee                 1.1.8
-rlist                0.4.6.2
-rnaturalearth        1.0.1
-rockchalk            1.8.157
-RODBC                1.3.26
-rstac                1.0.1
-RStoolbox            1.0.2.1
-snow                 0.4.4
-sqldf                0.4.11
-duckdb               1.2.1
-rhdf5                2.50.2
\ No newline at end of file
diff --git a/base_images/2i2c/r/docker/Dockerfile b/base_images/2i2c/r/docker/Dockerfile
index ace3c7a..1f354fd 100644
--- a/base_images/2i2c/r/docker/Dockerfile
+++ b/base_images/2i2c/r/docker/Dockerfile
@@ -1,5 +1,4 @@
-ARG BASE_IMAGE
-FROM ${BASE_IMAGE}
+FROM mas.dit.maap-project.org/root/maap-workspaces/2i2c/r-base:pak
 ENV LANG=en_US.UTF-8
 ENV TZ=US/Pacific
 ARG DEBIAN_FRONTEND=noninteractive
@@ -18,4 +17,12 @@ RUN conda init
 ARG IMAGE_REF
 ENV DOCKERIMAGE_PATH_BASE_IMAGE=${IMAGE_REF}
 ARG DEFAULT_DOCKERFILE_PATH
-ENV DOCKERIMAGE_PATH_DEFAULT=${DEFAULT_DOCKERFILE_PATH}
\ No newline at end of file
+ENV DOCKERIMAGE_PATH_DEFAULT=${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 ${NB_USER}
+
+# This script returns control to base image's /srv/start after 
+ENTRYPOINT ["/usr/local/bin/init-user.sh"]
\ No newline at end of file
diff --git a/base_images/2i2c/r/environment.yml b/base_images/2i2c/r/environment.yml
index 463c083..08b7729 100644
--- a/base_images/2i2c/r/environment.yml
+++ b/base_images/2i2c/r/environment.yml
@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - pip=26.0
+  - pip=26.1.1
   - pip:
     - maap-py==4.2.0
     - maap-algorithms-jupyter-extension==0.5.1
diff --git a/base_images/2i2c/r/scripts/init-user.sh b/base_images/2i2c/r/scripts/init-user.sh
new file mode 100644
index 0000000..c8c5bc4
--- /dev/null
+++ b/base_images/2i2c/r/scripts/init-user.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+REGION="${AWS_DEFAULT_REGION:-us-west-2}"
+
+rclone config create maap-s3 s3 provider=AWS env_auth=true region="$REGION" no_check_bucket true
+
+exec /srv/start "$@"
\ No newline at end of file
diff --git a/base_images/2i2c/tensorflow2/docker/Dockerfile b/base_images/2i2c/tensorflow2/docker/Dockerfile
index 4fd574d..7ba9def 100644
--- a/base_images/2i2c/tensorflow2/docker/Dockerfile
+++ b/base_images/2i2c/tensorflow2/docker/Dockerfile
@@ -1,4 +1,4 @@
-FROM quay.io/pangeo/ml-notebook:2025.12.30
+FROM quay.io/pangeo/ml-notebook:2026.04.29
 ENV LANG=en_US.UTF-8
 ENV TZ=US/Pacific
 ARG DEBIAN_FRONTEND=noninteractive
@@ -10,6 +10,4 @@ RUN conda env update -n ${CONDA_ENV} -f "/tmp/environment.yml" \
     && find ${CONDA_DIR}/ -follow -type f -name '*.js.map' -delete \
     && ${CONDA_DIR}/bin/conda clean -afy
 
-RUN conda init
-
-RUN jupyter server extension enable maap_jupyter_server_extension
\ No newline at end of file
+RUN conda init
\ No newline at end of file
diff --git a/base_images/2i2c/tensorflow2/environment.yml b/base_images/2i2c/tensorflow2/environment.yml
index afac672..da2b82d 100644
--- a/base_images/2i2c/tensorflow2/environment.yml
+++ b/base_images/2i2c/tensorflow2/environment.yml
@@ -6,7 +6,7 @@ dependencies:
   # Dependencies for VS Code IDE
   - code-server>=3.2
   - jupyter-vscode-proxy=0.7
-  - pre_commit=3.4.0
+  - pre_commit
   # Upgrade from ml notebook image
   - earthaccess>=0.16.0
   # Pin down to avoid https://github.com/holoviz/pyviz_comms/issues/143