From cc5b3407c079fca46f1a26ffd13690da647764f2 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 18 Feb 2026 13:40:41 -0500
Subject: [PATCH 1/4] ci(docker): try pinning mamba pkg versions based on
 rs413s docker

---
 .github/workflows/docker.yml |   2 +-
 Dockerfile                   | 673 +++++++----------------------------
 Dockerfile.rs413s            | 548 ++++++++++++++++++++++++++++
 3 files changed, 674 insertions(+), 549 deletions(-)
 create mode 100644 Dockerfile.rs413s

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 9e96b07..a6822bc 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -56,4 +56,4 @@ jobs:
             BUILD_DATE=${{ steps.vars.outputs.DATE }}
             BUILD_TAG=${{ steps.vars.outputs.VERSION_TAG }}
             REPONAME=${{ env.IMAGE_NAME }}
-            R_VERSION=4.3.2
+            R_VERSION=4.1.3
diff --git a/Dockerfile b/Dockerfile
index e957f2a..d9d3c82 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,548 +1,125 @@
-FROM rocker/rstudio:4.1.3
-
-RUN apt-get update && apt-get install -y --no-install-recommends \
-      bash gcc g++ gfortran make cmake pkg-config \
-      git vim-tiny \
-      libcurl4-openssl-dev libssl-dev libxml2-dev \
-      libpng-tools \
-      libpng-dev libjpeg-dev libtiff5-dev zlib1g-dev \
-      libfreetype6-dev libharfbuzz-dev libfribidi-dev \
-      libbz2-dev liblzma-dev \
-      libgsl-dev libhdf5-dev \
-      tcl tk tcl-dev tk-dev \
-      libglpk-dev libglpk40 \
-      libgit2-dev \
-      python3 python3-venv \
-      python3-dev python3-pip \
-      libfontconfig1-dev \
-      autoconf automake libtool \
-      libgeos-dev libproj-dev \
-      libcairo2-dev libxt-dev \
-      automake \
-    && rm -rf /var/lib/apt/lists/*
-
-
-#      libpng libtiff-4 libjpeg libwebp libwebpmux 
-
-# (Optional) prevent R networking during local install steps
-# xxx rpf get rid of
-# RUN echo 'options(repos = c())' >> /usr/local/lib/R/etc/Rprofile.site
-
-#RUN pip3 install --no-cache-dir igraph leidenalg numpy
-# weird pip instal bug introduced 
-RUN pip3 install --no-cache-dir igraph "leidenalg==0.10.0" numpy
-
-WORKDIR /home/rstudio
-
-# Remove any spatstat* that might be preinstalled in the rocker image
-RUN R -q -e " \
-  for (lib in .libPaths()) { \
-    ip <- rownames(installed.packages(lib.loc = lib)); \
-    pk <- grep('^spatstat', ip, value = TRUE); \
-    if (length(pk)) { \
-      message('Removing from ', lib, ': ', paste(pk, collapse=', ')); \
-      remove.packages(pk, lib = lib); \
-    } \
-  }"
-
-# Install packages with specific versions from CRAN and Bioconductor
-RUN R --vanilla --slave << 'EOF'
-options(repos = c(CRAN = 'https://cran.r-project.org'))
-
-if (!require('BiocManager', quietly = TRUE)) {
-  install.packages('BiocManager', quiet = TRUE)
-}
-if (!require('remotes', quietly = TRUE)) {
-  install.packages('remotes', quiet = TRUE)
-}
-
-# Install specific CRAN package versions
-cran_versions <- list(
-  bitops = '1.0-8',
-  RCurl = '1.98-1.14',
-  GlobalOptions = '0.1.2',
-  bit = '4.0.4',
-  assertthat = '0.2.1',
-  bit64 = '4.0.5',
-  shape = '1.4.6',
-  colorspace = '2.0-3',
-  circlize = '0.4.15',
-  rlang = '1.1.4',
-  cli = '3.6.3',
-  glue = '1.7.0',
-  lifecycle = '1.0.4',
-  vctrs = '0.6.5',
-  blob = '1.2.3',
-  clue = '0.3-61',
-  cluster = '2.1.2',
-  codetools = '0.2-18',
-  crayon = '1.5.3',
-  data.table = '1.15.4',
-  DBI = '1.2.3',
-  dendsort = '0.3.4',
-  digest = '0.6.37',
-  ellipsis = '0.3.2',
-  evaluate = '0.24.0',
-  fansi = '1.0.6',
-  farver = '2.1.1',
-  fastmap = '1.2.0',
-  cachem = '1.1.0',
-  fastmatch = '1.1-3',
-  iterators = '1.0.14',
-  foreach = '1.5.2',
-  formatR = '1.14',
-  generics = '0.1.3',
-  rjson = '0.2.21',
-  GetoptLong = '1.0.5',
-  gtable = '0.3.5',
-  labeling = '0.4.2',
-  munsell = '0.5.0',
-  R6 = '2.5.1',
-  gridExtra = '2.3',
-  RColorBrewer = '1.1-3',
-  utf8 = '1.2.4',
-  pillar = '1.9.0',
-  pkgconfig = '2.0.3',
-  viridisLite = '0.4.1',
-  scales = '1.2.1',
-  withr = '3.0.1',
-  gtools = '3.9.5',
-  gridGraphics = '0.5-1',
-  hms = '1.1.2',
-  irlba = '2.3.5.1',
-  jsonlite = '1.8.8',
-  png = '0.1-7',
-  KernSmooth = '2.23-20',
-  lambda.r = '1.2.4',
-  lattice = '0.20-45',
-  lazyeval = '0.2.2',
-  locfit = '1.5-9.9',
-  Matrix = '1.5-1',
-  matrixStats = '0.62.0',
-  memoise = '2.0.1',
-  mgcv = '1.8-39',
-  nlme = '3.1-155',
-  rsvd = '1.0.5',
-  Rcpp = '1.0.13',
-  uuid = '1.1-0',
-  xfun = '0.47',
-  xtable = '1.8-4',
-  yaml = '2.3.10',
-  beeswarm = '0.4.0',
-  filelock = '1.0.3',
-  bslib = '0.4.2',
-  Cairo = '1.6-0',
-  desc = '1.4.2',
-  pkgload = '1.3.0',
-  brio = '1.1.3',
-  zip = '2.3.3',
-  openxlsx = '4.2.5.2',
-  praise = '1.0.0',
-  diffobj = '0.3.5',
-  waldo = '0.5.1',
-  testthat = '3.1.6',
-  nloptr = '2.0.3',
-  minqa = '1.2.5',
-  lme4 = '1.1-33',
-  MatrixModels = '0.5-1',
-  SparseM = '1.81',
-  quantreg = '5.95',
-  numDeriv = '2016.8-1.1',
-  pbkrtest = '0.5.2',
-  maptools = '1.1-7',
-  carData = '3.0-5',
-  rio = '0.5.29',
-  car = '3.0-0',
-  pROC = '1.18.2',
-  proxy = '0.4-27',
-  e1071 = '1.7-13',
-  ModelMetrics = '1.2.2.2',
-  clock = '0.7.0',
-  shinyjs = '2.1.0',
-  colourpicker = '1.2.0',
-  combinat = '0.0-8',
-  corrplot = '0.92',
-  cpp11 = '0.4.7',
-  diagram = '1.6.5',
-  DT = '0.28',
-  Rttf2pt1 = '1.3.12',
-  extrafontdb = '1.0',
-  extrafont = '0.18',
-  vipor = '0.4.7',
-  ggbeeswarm = '0.7.2',
-  ggrastr = '1.0.2',
-  fastICA = '1.2-3',
-  gdata = '2.18.0.1',
-  ggExtra = '0.10.1',
-  ggsci = '3.0.0',
-  ggsignif = '0.6.3',
-  gower = '1.0.1',
-  gridBase = '0.4-7',
-  hardhat = '1.3.0',
-  RhpcBLASctl = '0.23-42',
-  hdf5r = '1.3.5',
-  hexbin = '1.28.3',
-  survival = '3.2-13',
-  MASS = '7.3-55',
-  SQUAREM = '2021.1',
-  lava = '1.7.2.1',
-  lobstr = '1.1.2',
-  lsei = '1.3-0',
-  markdown = '1.13',
-  lpSolve = '5.6.16',
-  mclust = '6.0.0',
-  npsurv = '0.5-0',
-  pheatmap = '1.0.12',
-  polynom = '1.4-1',
-  proj4 = '1.0-12',
-  pryr = '0.1.5',
-  ps = '1.8.1',
-  RcppParallel = '5.1.6',
-  rstatix = '0.7.0',
-  timeDate = '4022.108',
-  maps = '3.4.1',
-  ggpubr = '0.4.0',
-  prodlim = '2023.03.31',
-  ipred = '0.9-14',
-  recipes = '1.0.6',
-  caret = '6.0-94',
-  quantmod = '0.4.20',
-  profvis = '0.3.7',
-  sessioninfo = '1.2.3',
-  downlit = '0.4.2',
-  whisker = '0.4.1',
-  pkgdown = '2.0.7',
-  pkgbuild = '1.4.8',
-  brew = '1.0-8',
-  roxygen2 = '7.2.3',
-  urlchecker = '1.0.1',
-  rversions = '2.1.2',
-  xopen = '1.0.0',
-  rcmdcheck = '1.4.0',
-  credentials = '1.3.2',
-  gert = '1.9.2',
-  gitcreds = '0.1.2',
-  httr2 = '0.2.3',
-  ini = '0.3.1',
-  gh = '1.4.0',
-  usethis = '3.1.0',
-  devtools = '2.4.5',
-  ggalt = '0.4.0',
-  EnhancedVolcano = '1.12.0'
-)
-
-for (pkg in names(cran_versions)) {
-  tryCatch({
-    remotes::install_version(pkg, version = cran_versions[[pkg]], repos = 'https://cran.r-project.org', quiet = TRUE)
-  }, error = function(e) {
-    message('Note: install_version failed for ', pkg, ', trying install.packages')
-    install.packages(pkg, quiet = TRUE)
-  })
-}
-
-# Install Bioconductor packages with specific versions
-bioc_versions <- list(
-  BiocGenerics = '0.40.0',
-  Biobase = '2.54.0',
-  S4Vectors = '0.32.4',
-  IRanges = '2.28.0',
-  XVector = '0.34.0',
-  GenomeInfoDbData = '1.2.7',
-  GenomeInfoDb = '1.30.1',
-  beachmat = '2.10.0',
-  edgeR = '3.36.0',
-  GenomicRanges = '1.46.1',
-  Biostrings = '2.62.0',
-  DelayedArray = '0.20.0',
-  sparseMatrixStats = '1.6.0',
-  DelayedMatrixStats = '1.16.0',
-  ScaledMatrix = '1.2.0',
-  zlibbioc = '1.40.0',
-  KEGGREST = '1.34.0',
-  AnnotationDbi = '1.56.2',
-  BiocParallel = '1.28.3',
-  BiocSingular = '1.10.0',
-  ComplexHeatmap = '2.10.0',
-  fgsea = '1.20.0',
-  BiocNeighbors = '1.12.0',
-  BiocFileCache = '2.2.1',
-  bluster = '1.4.0',
-  scuttle = '1.4.0',
-  scater = '1.22.0',
-  scran = '1.22.1',
-  SingleR = '1.8.1',
-  MAST = '1.20.0',
-  scDblFinder = '1.8.0',
-  SummarizedExperiment = '1.24.0',
-  SingleCellExperiment = '1.16.0',
-  HDF5Array = '1.22.1',
-  rhdf5 = '2.38.1',
-  rhdf5filters = '1.6.0',
-  GSVA = '1.42.0',
-  ExperimentHub = '2.2.1',
-  AnnotationHub = '3.2.2',
-  celldex = '1.4.0',
-  annotate = '1.72.0',
-  graph = '1.72.0',
-  GSEABase = '1.56.0',
-  interactiveDisplayBase = '1.32.0',
-  TrajectoryUtils = '1.2.0',
-  TSCAN = '1.32.0',
-  conquer = '1.3.3',
-  metapod = '1.2.0',
-  statmod = '1.5.0'
-)
-
-for (pkg in names(bioc_versions)) {
-  tryCatch({
-    remotes::install_version(pkg, version = bioc_versions[[pkg]], repos = BiocManager::repositories(), quiet = TRUE)
-  }, error = function(e) {
-    message('Note: install_version failed for ', pkg, ', trying BiocManager')
-    BiocManager::install(pkg, ask = FALSE, quiet = TRUE)
-  })
-}
-EOF
-
-
-# Additional packages that need special installation
-
-# Install SCWorkflow from GitHub
-COPY . /opt/SCWorkflow
-RUN R --vanilla --slave -e "remotes::install_local('/opt/SCWorkflow', dependencies = TRUE, quiet = TRUE, upgrade='never')"
-
-# Install spatstat family packages with specific versions
-RUN cat > /tmp/install_spatstat.R << 'EOFSPAT'
-options(repos = c(CRAN = 'https://cran.r-project.org'))
-if (!require('remotes', quietly = TRUE)) install.packages('remotes', quiet = TRUE)
-spatstat_versions <- list(
-  spatstat.utils = '3.1-0',
-  spatstat.data = '3.0-0',
-  deldir = '2.0-4',
-  polyclip = '1.10-7',
-  spatstat.univar = '2.0-3',
-  spatstat.geom = '3.0-3',
-  spatstat.random = '2.2-0',
-  abind = '1.4-5',
-  tensor = '1.5',
-  goftest = '1.2-3',
-  spatstat.sparse = '3.1-0',
-  spatstat.core = '2.4-2',
-  spatstat.linnet = '2.2-1'
-)
-for (pkg in names(spatstat_versions)) {
-  tryCatch({
-    remotes::install_version(pkg, version = spatstat_versions[[pkg]], repos = 'https://cran.r-project.org', quiet = TRUE)
-  }, error = function(e) {
-    message('Note: install_version for ', pkg, ' failed, trying install.packages')
-    install.packages(pkg, quiet = TRUE)
-  })
-}
-EOFSPAT
-
-RUN R --vanilla --slave --file=/tmp/install_spatstat.R
-
-# Install remaining specialized packages
-RUN cat > /tmp/install_special.R << 'EOFSPEC'
-options(repos = c(CRAN = 'https://cran.r-project.org'))
-if (!require('remotes', quietly = TRUE)) install.packages('remotes', quiet = TRUE)
-special_versions <- list(
-  RSpectra = '0.16-1',
-  dotCall64 = '1.1-1',
-  spam = '2.11-0',
-  RcppHNSW = '0.4.1',
-  leidenbase = '0.1.30',
-  fastDummies = '1.7.3',
-  sp = '1.5-0',
-  rgeos = '0.5-9',
-  SeuratObject = '4.1.1',
-  Seurat = '4.1.1',
-  XML = '3.99-0.14',
-  anndata = '0.7.5.2',
-  ash = '1.0-15',
-  viridis = '0.6.5',
-  dendextend = '1.16.0',
-  ggrepel = '0.9.5',
-  l2p = '0.0-13',
-  l2psupp = '0.0-13',
-  ica = '1.0-3',
-  Rtsne = '0.16',
-  ggridges = '0.5.3',
-  scattermore = '1.2',
-  listenv = '0.9.1',
-  globals = '0.16.3',
-  parallelly = '1.38.0',
-  future = '1.34.0',
-  future.apply = '1.11.2',
-  RcppEigen = '0.3.3.9.3',
-  RcppAnnoy = '0.0.19',
-  zoo = '1.8-12',
-  lmtest = '0.9-40',
-  fitdistrplus = '1.1-8',
-  caTools = '1.18.2',
-  gplots = '3.1.3',
-  ROCR = '1.0-11',
-  igraph = '2.0.3',
-  pbapply = '1.5-0',
-  commonmark = '1.9.0',
-  httpuv = '1.6.15',
-  sourcetools = '0.1.7-1',
-  shiny = '1.9.1',
-  miniUI = '0.1.1.1',
-  progressr = '0.14.0',
-  sitmo = '2.0.2',
-  dqrng = '0.4.1',
-  FNN = '1.1.3.2',
-  RcppProgress = '0.4.2',
-  uwot = '0.1.14',
-  cowplot = '1.1.1',
-  RcppTOML = '0.2.2',
-  rprojroot = '2.0.4',
-  here = '1.0.1',
-  reticulate = '1.40.0',
-  leiden = '0.4.3',
-  RANN = '2.6.1',
-  RcppArmadillo = '0.12.4.0.0',
-  sctransform = '0.3.4',
-  Rhdf5lib = '1.16.0',
-  xgboost = '1.7.8.1',
-  nidapFunctions = '0.7.8',
-  snow = '0.4-4',
-  BH = '1.81.0-1',
-  futile.options = '1.0.1',
-  futile.logger = '1.4.3',
-  base64enc = '0.1-3',
-  htmltools = '0.5.8.1',
-  rappdirs = '0.3.3',
-  jquerylib = '0.1.4',
-  tinytex = '0.44',
-  fs = '1.6.4',
-  sass = '0.4.6',
-  mime = '0.12',
-  magrittr = '2.0.3',
-  stringi = '1.8.4',
-  stringr = '1.5.1',
-  highr = '0.10',
-  knitr = '1.48',
-  fontawesome = '0.5.1',
-  rmarkdown = '2.28',
-  htmlwidgets = '1.6.4',
-  sys = '3.4.2',
-  askpass = '1.1',
-  openssl = '2.0.5',
-  curl = '6.4.0',
-  httr = '1.4.7',
-  timechange = '0.2.0',
-  lubridate = '1.8.0',
-  isoband = '0.2.7',
-  tibble = '3.2.1',
-  ggplot2 = '3.3.6',
-  patchwork = '1.2.0',
-  later = '1.3.2',
-  promises = '1.3.0',
-  crosstalk = '1.2.0',
-  purrr = '1.0.2',
-  tidyselect = '1.2.1',
-  dplyr = '1.1.4',
-  tidyr = '1.2.1',
-  plotly = '4.10.4',
-  plyr = '1.8.7',
-  clipr = '0.8.0',
-  prettyunits = '1.1.1',
-  progress = '1.2.2',
-  tzdb = '0.4.0',
-  vroom = '1.6.3',
-  readr = '2.1.2',
-  reshape2 = '1.4.4',
-  plogr = '0.2.0',
-  RSQLite = '2.3.9',
-  systemfonts = '1.2.3',
-  textshaping = '0.3.6',
-  ragg = '1.2.5',
-  dbplyr = '2.2.1',
-  rstudioapi = '0.14',
-  dtplyr = '1.3.1',
-  backports = '1.4.1',
-  broom = '1.0.1',
-  processx = '3.8.5',
-  callr = '3.7.3',
-  reprex = '2.0.2',
-  modelr = '0.1.9',
-  conflicted = '1.2.0',
-  rematch2 = '2.1.2',
-  gargle = '1.3.0',
-  rematch = '1.0.1',
-  cellranger = '1.1.0',
-  ids = '1.0.1',
-  googledrive = '2.0.0',
-  googlesheets4 = '1.0.1',
-  readxl = '1.4.1',
-  selectr = '0.4-2',
-  xml2 = '1.3.3',
-  rvest = '1.0.3',
-  forcats = '0.5.2',
-  haven = '2.5.1',
-  tidyverse = '1.3.2',
-  doParallel = '1.0.17',
-  MatrixGenerics = '1.6.0',
-  svglite = '2.1.0',
-  svMisc = '1.2.3',
-  xts = '0.12.2',
-  TTR = '0.24.3'
-)
-for (pkg in names(special_versions)) {
-  tryCatch({
-    remotes::install_version(pkg, version = special_versions[[pkg]], repos = 'https://cran.r-project.org', quiet = TRUE)
-  }, error = function(e) {
-    message('Note: install_version for ', pkg, ' failed, trying install.packages')
-    install.packages(pkg, quiet = TRUE)
-  })
-}
-EOFSPEC
-
-RUN R --vanilla --slave --file=/tmp/install_special.R
-
-# Install development dependencies
-RUN cat > /tmp/install_dev_dependencies.R << 'EOFDEV'
-options(repos = c(CRAN = 'https://cran.r-project.org'))
-dev_dependencies <- c('cffr', 'covr', 'goodpractice', 'here', 'lintr', 'pkgdown', 'rcmdcheck')
-
-for (pkg in dev_dependencies) {
-  tryCatch({
-    remotes::install_version(pkg, repos = 'https://cran.r-project.org', quiet = TRUE)
-  }, error = function(e) {
-    message('Note: install_version failed for ', pkg, ', trying install.packages')
-    install.packages(pkg, quiet = TRUE)
-  })
-}
-EOFDEV
-
-RUN R --vanilla --slave --file=/tmp/install_dev_dependencies.R
-
-# Verify that all dependencies from DESCRIPTION are installed
-RUN cat > /tmp/check_description_deps.R << 'EOF'
-options(repos = c(CRAN = 'https://cran.r-project.org'))
-# Read the DESCRIPTION file
-desc_file <- "/opt/SCWorkflow/DESCRIPTION"
-if (!file.exists(desc_file)) {
-  stop("DESCRIPTION file not found at ", desc_file)
-}
-# Parse dependencies from DESCRIPTION
-desc <- read.dcf(desc_file)
-deps <- unique(c(
-  strsplit(desc[1, "Imports"], ",")[[1]],
-  strsplit(desc[1, "Suggests"], ",")[[1]],
-  strsplit(desc[1, "Depends"], ",")[[1]]
-))
-deps <- trimws(deps)
-# Check if each dependency is installed
-missing <- deps[!vapply(deps, requireNamespace, quietly = TRUE, FUN.VALUE = logical(1))]
-if (length(missing) > 0) {
-  stop("The following dependencies are missing: ", paste(missing, collapse = ", "))
-} else {
-  message("All dependencies are installed.")
-}
-EOF
-
-RUN R --vanilla --slave --file=/tmp/check_description_deps.R
-
-COPY Dockerfile /
+FROM nciccbr/ccbr_ubuntu_22.04:v4
+
+# build time variables
+ARG BUILD_DATE="000000"
+ENV BUILD_DATE=${BUILD_DATE}
+ARG BUILD_TAG="000000"
+ENV BUILD_TAG=${BUILD_TAG}
+ARG REPONAME="000000"
+ENV REPONAME=${REPONAME}
+
+ARG R_VERSION=4.1.3
+ENV R_VERSION=${R_VERSION}
+
+SHELL ["/bin/bash", "-lc"]
+
+# Install conda and give write permissions to conda folder
+RUN echo 'export PATH=/opt2/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
+    wget --quiet "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" -O ~/miniforge3.sh && \
+    /bin/bash ~/miniforge3.sh -b -p /opt2/conda && \
+    rm ~/miniforge3.sh && chmod 777 -R /opt2/conda/
+ENV PATH="/opt2/conda/bin:$PATH"
+
+# Pin channels and update
+RUN conda config --add channels conda-forge \
+ && conda config --add channels bioconda \
+ && conda config --set channel_priority strict
+
+# install conda packages
+RUN mamba install -y \
+    r-base=${R_VERSION} \
+    r-anndata=0.7.5.2 \
+    r-biocmanager \
+    r-callr=3.7.3 \
+    bioconductor-celldex=1.4.0 \
+    r-colorspace=2.0-3 \
+    bioconductor-complexheatmap=2.10.0 \
+    r-cowplot=1.1.1 \
+    r-data.table=1.15.4 \
+    r-dendextend=1.16.0 \
+    r-dendsort=0.3.4 \
+    r-digest=0.6.37 \
+    r-dplyr=1.1.4 \
+    bioconductor-edger=3.36.0 \
+    r-future=1.34.0 \
+    r-future.apply=1.11.2 \
+    r-gargle=1.3.0 \
+    r-gdata=2.18.0.1 \
+    r-ggextra=0.10.1 \
+    r-ggplot2=3.3.6 \
+    r-ggpubr=0.4.0 \
+    r-ggrepel=0.9.5 \
+    r-globals=0.16.3 \
+    r-gridbase=0.4-7 \
+    r-gridextra=2.3 \
+    r-gtable=0.3.5 \
+    r-harmony \
+    bioconductor-hdf5r=1.3.5 \
+    r-htmlwidgets=1.6.4 \
+    r-httpuv=1.6.15 \
+    r-httr=1.4.7 \
+    r-jsonlite=1.8.8 \
+    r-leiden=0.4.3 \
+    bioconductor-limma \
+    r-magrittr=2.0.3 \
+    r-markdown=1.13 \
+    bioconductor-mast=1.20.0 \
+    r-pheatmap=1.0.12 \
+    r-plotly=4.10.4 \
+    r-plyr=1.8.7 \
+    r-png=0.1-7 \
+    r-progressr=0.14.0 \
+    r-purrr=1.0.2 \
+    r-quantmod=0.4.20 \
+    r-rcolorbrewer=1.1-3 \
+    r-reshape2=1.4.4 \
+    r-reticulate=1.40.0 \
+    r-rlang=1.1.4 \
+    r-scales=1.2.1 \
+    bioconductor-scdblfinder=1.8.0 \
+    r-seurat=4.1.1 \
+    bioconductor-singler=1.8.1 \
+    r-statmod=1.5.0 \
+    r-stringr=1.5.1 \
+    r-svglite=2.1.0 \
+    r-tibble=3.2.1 \
+    r-tidyr=1.2.1 \
+    r-tidyverse=1.3.2 \
+    r-viridislite=0.4.1 \
+    r-xfun=0.47 \
+    r-zip=2.3.3 \
+    r-knitr=1.48 \
+    r-rmarkdown=2.28 \
+    r-roxygen2=7.2.3 \
+    r-testthat=3.1.6 \
+    r-usethis=3.1.0 \
+    r-cffr \
+    r-covr \
+    r-goodpractice \
+    r-here=1.0.1 \
+    r-lintr \
+    r-pkgdown=2.0.7 \
+    r-rcmdcheck=1.4.0 \
+  && conda clean -afy
+
+# install R package
+COPY . /opt2/SCWorkflow
+RUN R -e "devtools::install_local('/opt2/SCWorkflow', dependencies = TRUE, upgrade = 'never', repos='http://cran.rstudio.com')"
+
+# add scworkflow exec to the path
+# RUN chmod -R +x /opt2/conda/lib/R/library/SCWorkflow/exec
+# ENV PATH="$PATH:/opt2/conda/lib/R/library/SCWorkflow/exec"
+# RUN scworkflow --help
+
+# copy example script & json to data
+COPY ./inst/extdata/example_script.sh /data2/
+COPY ./inst/extdata/json_args/ /data2/json_args/
+
+# Save Dockerfile in the docker
+COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+
+# cleanup
+WORKDIR /data2
+RUN apt-get clean && apt-get purge \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
\ No newline at end of file
diff --git a/Dockerfile.rs413s b/Dockerfile.rs413s
new file mode 100644
index 0000000..e957f2a
--- /dev/null
+++ b/Dockerfile.rs413s
@@ -0,0 +1,548 @@
+FROM rocker/rstudio:4.1.3
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+      bash gcc g++ gfortran make cmake pkg-config \
+      git vim-tiny \
+      libcurl4-openssl-dev libssl-dev libxml2-dev \
+      libpng-tools \
+      libpng-dev libjpeg-dev libtiff5-dev zlib1g-dev \
+      libfreetype6-dev libharfbuzz-dev libfribidi-dev \
+      libbz2-dev liblzma-dev \
+      libgsl-dev libhdf5-dev \
+      tcl tk tcl-dev tk-dev \
+      libglpk-dev libglpk40 \
+      libgit2-dev \
+      python3 python3-venv \
+      python3-dev python3-pip \
+      libfontconfig1-dev \
+      autoconf automake libtool \
+      libgeos-dev libproj-dev \
+      libcairo2-dev libxt-dev \
+      automake \
+    && rm -rf /var/lib/apt/lists/*
+
+
+#      libpng libtiff-4 libjpeg libwebp libwebpmux 
+
+# (Optional) prevent R networking during local install steps
+# xxx rpf get rid of
+# RUN echo 'options(repos = c())' >> /usr/local/lib/R/etc/Rprofile.site
+
+#RUN pip3 install --no-cache-dir igraph leidenalg numpy
+# weird pip instal bug introduced 
+RUN pip3 install --no-cache-dir igraph "leidenalg==0.10.0" numpy
+
+WORKDIR /home/rstudio
+
+# Remove any spatstat* that might be preinstalled in the rocker image
+RUN R -q -e " \
+  for (lib in .libPaths()) { \
+    ip <- rownames(installed.packages(lib.loc = lib)); \
+    pk <- grep('^spatstat', ip, value = TRUE); \
+    if (length(pk)) { \
+      message('Removing from ', lib, ': ', paste(pk, collapse=', ')); \
+      remove.packages(pk, lib = lib); \
+    } \
+  }"
+
+# Install packages with specific versions from CRAN and Bioconductor
+RUN R --vanilla --slave << 'EOF'
+options(repos = c(CRAN = 'https://cran.r-project.org'))
+
+if (!require('BiocManager', quietly = TRUE)) {
+  install.packages('BiocManager', quiet = TRUE)
+}
+if (!require('remotes', quietly = TRUE)) {
+  install.packages('remotes', quiet = TRUE)
+}
+
+# Install specific CRAN package versions
+cran_versions <- list(
+  bitops = '1.0-8',
+  RCurl = '1.98-1.14',
+  GlobalOptions = '0.1.2',
+  bit = '4.0.4',
+  assertthat = '0.2.1',
+  bit64 = '4.0.5',
+  shape = '1.4.6',
+  colorspace = '2.0-3',
+  circlize = '0.4.15',
+  rlang = '1.1.4',
+  cli = '3.6.3',
+  glue = '1.7.0',
+  lifecycle = '1.0.4',
+  vctrs = '0.6.5',
+  blob = '1.2.3',
+  clue = '0.3-61',
+  cluster = '2.1.2',
+  codetools = '0.2-18',
+  crayon = '1.5.3',
+  data.table = '1.15.4',
+  DBI = '1.2.3',
+  dendsort = '0.3.4',
+  digest = '0.6.37',
+  ellipsis = '0.3.2',
+  evaluate = '0.24.0',
+  fansi = '1.0.6',
+  farver = '2.1.1',
+  fastmap = '1.2.0',
+  cachem = '1.1.0',
+  fastmatch = '1.1-3',
+  iterators = '1.0.14',
+  foreach = '1.5.2',
+  formatR = '1.14',
+  generics = '0.1.3',
+  rjson = '0.2.21',
+  GetoptLong = '1.0.5',
+  gtable = '0.3.5',
+  labeling = '0.4.2',
+  munsell = '0.5.0',
+  R6 = '2.5.1',
+  gridExtra = '2.3',
+  RColorBrewer = '1.1-3',
+  utf8 = '1.2.4',
+  pillar = '1.9.0',
+  pkgconfig = '2.0.3',
+  viridisLite = '0.4.1',
+  scales = '1.2.1',
+  withr = '3.0.1',
+  gtools = '3.9.5',
+  gridGraphics = '0.5-1',
+  hms = '1.1.2',
+  irlba = '2.3.5.1',
+  jsonlite = '1.8.8',
+  png = '0.1-7',
+  KernSmooth = '2.23-20',
+  lambda.r = '1.2.4',
+  lattice = '0.20-45',
+  lazyeval = '0.2.2',
+  locfit = '1.5-9.9',
+  Matrix = '1.5-1',
+  matrixStats = '0.62.0',
+  memoise = '2.0.1',
+  mgcv = '1.8-39',
+  nlme = '3.1-155',
+  rsvd = '1.0.5',
+  Rcpp = '1.0.13',
+  uuid = '1.1-0',
+  xfun = '0.47',
+  xtable = '1.8-4',
+  yaml = '2.3.10',
+  beeswarm = '0.4.0',
+  filelock = '1.0.3',
+  bslib = '0.4.2',
+  Cairo = '1.6-0',
+  desc = '1.4.2',
+  pkgload = '1.3.0',
+  brio = '1.1.3',
+  zip = '2.3.3',
+  openxlsx = '4.2.5.2',
+  praise = '1.0.0',
+  diffobj = '0.3.5',
+  waldo = '0.5.1',
+  testthat = '3.1.6',
+  nloptr = '2.0.3',
+  minqa = '1.2.5',
+  lme4 = '1.1-33',
+  MatrixModels = '0.5-1',
+  SparseM = '1.81',
+  quantreg = '5.95',
+  numDeriv = '2016.8-1.1',
+  pbkrtest = '0.5.2',
+  maptools = '1.1-7',
+  carData = '3.0-5',
+  rio = '0.5.29',
+  car = '3.0-0',
+  pROC = '1.18.2',
+  proxy = '0.4-27',
+  e1071 = '1.7-13',
+  ModelMetrics = '1.2.2.2',
+  clock = '0.7.0',
+  shinyjs = '2.1.0',
+  colourpicker = '1.2.0',
+  combinat = '0.0-8',
+  corrplot = '0.92',
+  cpp11 = '0.4.7',
+  diagram = '1.6.5',
+  DT = '0.28',
+  Rttf2pt1 = '1.3.12',
+  extrafontdb = '1.0',
+  extrafont = '0.18',
+  vipor = '0.4.7',
+  ggbeeswarm = '0.7.2',
+  ggrastr = '1.0.2',
+  fastICA = '1.2-3',
+  gdata = '2.18.0.1',
+  ggExtra = '0.10.1',
+  ggsci = '3.0.0',
+  ggsignif = '0.6.3',
+  gower = '1.0.1',
+  gridBase = '0.4-7',
+  hardhat = '1.3.0',
+  RhpcBLASctl = '0.23-42',
+  hdf5r = '1.3.5',
+  hexbin = '1.28.3',
+  survival = '3.2-13',
+  MASS = '7.3-55',
+  SQUAREM = '2021.1',
+  lava = '1.7.2.1',
+  lobstr = '1.1.2',
+  lsei = '1.3-0',
+  markdown = '1.13',
+  lpSolve = '5.6.16',
+  mclust = '6.0.0',
+  npsurv = '0.5-0',
+  pheatmap = '1.0.12',
+  polynom = '1.4-1',
+  proj4 = '1.0-12',
+  pryr = '0.1.5',
+  ps = '1.8.1',
+  RcppParallel = '5.1.6',
+  rstatix = '0.7.0',
+  timeDate = '4022.108',
+  maps = '3.4.1',
+  ggpubr = '0.4.0',
+  prodlim = '2023.03.31',
+  ipred = '0.9-14',
+  recipes = '1.0.6',
+  caret = '6.0-94',
+  quantmod = '0.4.20',
+  profvis = '0.3.7',
+  sessioninfo = '1.2.3',
+  downlit = '0.4.2',
+  whisker = '0.4.1',
+  pkgdown = '2.0.7',
+  pkgbuild = '1.4.8',
+  brew = '1.0-8',
+  roxygen2 = '7.2.3',
+  urlchecker = '1.0.1',
+  rversions = '2.1.2',
+  xopen = '1.0.0',
+  rcmdcheck = '1.4.0',
+  credentials = '1.3.2',
+  gert = '1.9.2',
+  gitcreds = '0.1.2',
+  httr2 = '0.2.3',
+  ini = '0.3.1',
+  gh = '1.4.0',
+  usethis = '3.1.0',
+  devtools = '2.4.5',
+  ggalt = '0.4.0',
+  EnhancedVolcano = '1.12.0'
+)
+
+for (pkg in names(cran_versions)) {
+  tryCatch({
+    remotes::install_version(pkg, version = cran_versions[[pkg]], repos = 'https://cran.r-project.org', quiet = TRUE)
+  }, error = function(e) {
+    message('Note: install_version failed for ', pkg, ', trying install.packages')
+    install.packages(pkg, quiet = TRUE)
+  })
+}
+
+# Install Bioconductor packages with specific versions
+bioc_versions <- list(
+  BiocGenerics = '0.40.0',
+  Biobase = '2.54.0',
+  S4Vectors = '0.32.4',
+  IRanges = '2.28.0',
+  XVector = '0.34.0',
+  GenomeInfoDbData = '1.2.7',
+  GenomeInfoDb = '1.30.1',
+  beachmat = '2.10.0',
+  edgeR = '3.36.0',
+  GenomicRanges = '1.46.1',
+  Biostrings = '2.62.0',
+  DelayedArray = '0.20.0',
+  sparseMatrixStats = '1.6.0',
+  DelayedMatrixStats = '1.16.0',
+  ScaledMatrix = '1.2.0',
+  zlibbioc = '1.40.0',
+  KEGGREST = '1.34.0',
+  AnnotationDbi = '1.56.2',
+  BiocParallel = '1.28.3',
+  BiocSingular = '1.10.0',
+  ComplexHeatmap = '2.10.0',
+  fgsea = '1.20.0',
+  BiocNeighbors = '1.12.0',
+  BiocFileCache = '2.2.1',
+  bluster = '1.4.0',
+  scuttle = '1.4.0',
+  scater = '1.22.0',
+  scran = '1.22.1',
+  SingleR = '1.8.1',
+  MAST = '1.20.0',
+  scDblFinder = '1.8.0',
+  SummarizedExperiment = '1.24.0',
+  SingleCellExperiment = '1.16.0',
+  HDF5Array = '1.22.1',
+  rhdf5 = '2.38.1',
+  rhdf5filters = '1.6.0',
+  GSVA = '1.42.0',
+  ExperimentHub = '2.2.1',
+  AnnotationHub = '3.2.2',
+  celldex = '1.4.0',
+  annotate = '1.72.0',
+  graph = '1.72.0',
+  GSEABase = '1.56.0',
+  interactiveDisplayBase = '1.32.0',
+  TrajectoryUtils = '1.2.0',
+  TSCAN = '1.32.0',
+  conquer = '1.3.3',
+  metapod = '1.2.0',
+  statmod = '1.5.0'
+)
+
+for (pkg in names(bioc_versions)) {
+  tryCatch({
+    remotes::install_version(pkg, version = bioc_versions[[pkg]], repos = BiocManager::repositories(), quiet = TRUE)
+  }, error = function(e) {
+    message('Note: install_version failed for ', pkg, ', trying BiocManager')
+    BiocManager::install(pkg, ask = FALSE, quiet = TRUE)
+  })
+}
+EOF
+
+
+# Additional packages that need special installation
+
+# Install SCWorkflow from GitHub
+COPY . /opt/SCWorkflow
+RUN R --vanilla --slave -e "remotes::install_local('/opt/SCWorkflow', dependencies = TRUE, quiet = TRUE, upgrade='never')"
+
+# Install spatstat family packages with specific versions
+RUN cat > /tmp/install_spatstat.R << 'EOFSPAT'
+options(repos = c(CRAN = 'https://cran.r-project.org'))
+if (!require('remotes', quietly = TRUE)) install.packages('remotes', quiet = TRUE)
+spatstat_versions <- list(
+  spatstat.utils = '3.1-0',
+  spatstat.data = '3.0-0',
+  deldir = '2.0-4',
+  polyclip = '1.10-7',
+  spatstat.univar = '2.0-3',
+  spatstat.geom = '3.0-3',
+  spatstat.random = '2.2-0',
+  abind = '1.4-5',
+  tensor = '1.5',
+  goftest = '1.2-3',
+  spatstat.sparse = '3.1-0',
+  spatstat.core = '2.4-2',
+  spatstat.linnet = '2.2-1'
+)
+for (pkg in names(spatstat_versions)) {
+  tryCatch({
+    remotes::install_version(pkg, version = spatstat_versions[[pkg]], repos = 'https://cran.r-project.org', quiet = TRUE)
+  }, error = function(e) {
+    message('Note: install_version for ', pkg, ' failed, trying install.packages')
+    install.packages(pkg, quiet = TRUE)
+  })
+}
+EOFSPAT
+
+RUN R --vanilla --slave --file=/tmp/install_spatstat.R
+
+# Install remaining specialized packages
+RUN cat > /tmp/install_special.R << 'EOFSPEC'
+options(repos = c(CRAN = 'https://cran.r-project.org'))
+if (!require('remotes', quietly = TRUE)) install.packages('remotes', quiet = TRUE)
+special_versions <- list(
+  RSpectra = '0.16-1',
+  dotCall64 = '1.1-1',
+  spam = '2.11-0',
+  RcppHNSW = '0.4.1',
+  leidenbase = '0.1.30',
+  fastDummies = '1.7.3',
+  sp = '1.5-0',
+  rgeos = '0.5-9',
+  SeuratObject = '4.1.1',
+  Seurat = '4.1.1',
+  XML = '3.99-0.14',
+  anndata = '0.7.5.2',
+  ash = '1.0-15',
+  viridis = '0.6.5',
+  dendextend = '1.16.0',
+  ggrepel = '0.9.5',
+  l2p = '0.0-13',
+  l2psupp = '0.0-13',
+  ica = '1.0-3',
+  Rtsne = '0.16',
+  ggridges = '0.5.3',
+  scattermore = '1.2',
+  listenv = '0.9.1',
+  globals = '0.16.3',
+  parallelly = '1.38.0',
+  future = '1.34.0',
+  future.apply = '1.11.2',
+  RcppEigen = '0.3.3.9.3',
+  RcppAnnoy = '0.0.19',
+  zoo = '1.8-12',
+  lmtest = '0.9-40',
+  fitdistrplus = '1.1-8',
+  caTools = '1.18.2',
+  gplots = '3.1.3',
+  ROCR = '1.0-11',
+  igraph = '2.0.3',
+  pbapply = '1.5-0',
+  commonmark = '1.9.0',
+  httpuv = '1.6.15',
+  sourcetools = '0.1.7-1',
+  shiny = '1.9.1',
+  miniUI = '0.1.1.1',
+  progressr = '0.14.0',
+  sitmo = '2.0.2',
+  dqrng = '0.4.1',
+  FNN = '1.1.3.2',
+  RcppProgress = '0.4.2',
+  uwot = '0.1.14',
+  cowplot = '1.1.1',
+  RcppTOML = '0.2.2',
+  rprojroot = '2.0.4',
+  here = '1.0.1',
+  reticulate = '1.40.0',
+  leiden = '0.4.3',
+  RANN = '2.6.1',
+  RcppArmadillo = '0.12.4.0.0',
+  sctransform = '0.3.4',
+  Rhdf5lib = '1.16.0',
+  xgboost = '1.7.8.1',
+  nidapFunctions = '0.7.8',
+  snow = '0.4-4',
+  BH = '1.81.0-1',
+  futile.options = '1.0.1',
+  futile.logger = '1.4.3',
+  base64enc = '0.1-3',
+  htmltools = '0.5.8.1',
+  rappdirs = '0.3.3',
+  jquerylib = '0.1.4',
+  tinytex = '0.44',
+  fs = '1.6.4',
+  sass = '0.4.6',
+  mime = '0.12',
+  magrittr = '2.0.3',
+  stringi = '1.8.4',
+  stringr = '1.5.1',
+  highr = '0.10',
+  knitr = '1.48',
+  fontawesome = '0.5.1',
+  rmarkdown = '2.28',
+  htmlwidgets = '1.6.4',
+  sys = '3.4.2',
+  askpass = '1.1',
+  openssl = '2.0.5',
+  curl = '6.4.0',
+  httr = '1.4.7',
+  timechange = '0.2.0',
+  lubridate = '1.8.0',
+  isoband = '0.2.7',
+  tibble = '3.2.1',
+  ggplot2 = '3.3.6',
+  patchwork = '1.2.0',
+  later = '1.3.2',
+  promises = '1.3.0',
+  crosstalk = '1.2.0',
+  purrr = '1.0.2',
+  tidyselect = '1.2.1',
+  dplyr = '1.1.4',
+  tidyr = '1.2.1',
+  plotly = '4.10.4',
+  plyr = '1.8.7',
+  clipr = '0.8.0',
+  prettyunits = '1.1.1',
+  progress = '1.2.2',
+  tzdb = '0.4.0',
+  vroom = '1.6.3',
+  readr = '2.1.2',
+  reshape2 = '1.4.4',
+  plogr = '0.2.0',
+  RSQLite = '2.3.9',
+  systemfonts = '1.2.3',
+  textshaping = '0.3.6',
+  ragg = '1.2.5',
+  dbplyr = '2.2.1',
+  rstudioapi = '0.14',
+  dtplyr = '1.3.1',
+  backports = '1.4.1',
+  broom = '1.0.1',
+  processx = '3.8.5',
+  callr = '3.7.3',
+  reprex = '2.0.2',
+  modelr = '0.1.9',
+  conflicted = '1.2.0',
+  rematch2 = '2.1.2',
+  gargle = '1.3.0',
+  rematch = '1.0.1',
+  cellranger = '1.1.0',
+  ids = '1.0.1',
+  googledrive = '2.0.0',
+  googlesheets4 = '1.0.1',
+  readxl = '1.4.1',
+  selectr = '0.4-2',
+  xml2 = '1.3.3',
+  rvest = '1.0.3',
+  forcats = '0.5.2',
+  haven = '2.5.1',
+  tidyverse = '1.3.2',
+  doParallel = '1.0.17',
+  MatrixGenerics = '1.6.0',
+  svglite = '2.1.0',
+  svMisc = '1.2.3',
+  xts = '0.12.2',
+  TTR = '0.24.3'
+)
+for (pkg in names(special_versions)) {
+  tryCatch({
+    remotes::install_version(pkg, version = special_versions[[pkg]], repos = 'https://cran.r-project.org', quiet = TRUE)
+  }, error = function(e) {
+    message('Note: install_version for ', pkg, ' failed, trying install.packages')
+    install.packages(pkg, quiet = TRUE)
+  })
+}
+EOFSPEC
+
+RUN R --vanilla --slave --file=/tmp/install_special.R
+
+# Install development dependencies
+RUN cat > /tmp/install_dev_dependencies.R << 'EOFDEV'
+options(repos = c(CRAN = 'https://cran.r-project.org'))
+dev_dependencies <- c('cffr', 'covr', 'goodpractice', 'here', 'lintr', 'pkgdown', 'rcmdcheck')
+
+for (pkg in dev_dependencies) {
+  tryCatch({
+    remotes::install_version(pkg, repos = 'https://cran.r-project.org', quiet = TRUE)
+  }, error = function(e) {
+    message('Note: install_version failed for ', pkg, ', trying install.packages')
+    install.packages(pkg, quiet = TRUE)
+  })
+}
+EOFDEV
+
+RUN R --vanilla --slave --file=/tmp/install_dev_dependencies.R
+
+# Verify that all dependencies from DESCRIPTION are installed
+RUN cat > /tmp/check_description_deps.R << 'EOF'
+options(repos = c(CRAN = 'https://cran.r-project.org'))
+# Read the DESCRIPTION file
+desc_file <- "/opt/SCWorkflow/DESCRIPTION"
+if (!file.exists(desc_file)) {
+  stop("DESCRIPTION file not found at ", desc_file)
+}
+# Parse dependencies from DESCRIPTION
+desc <- read.dcf(desc_file)
+deps <- unique(c(
+  strsplit(desc[1, "Imports"], ",")[[1]],
+  strsplit(desc[1, "Suggests"], ",")[[1]],
+  strsplit(desc[1, "Depends"], ",")[[1]]
+))
+deps <- trimws(deps)
+# Check if each dependency is installed
+missing <- deps[!vapply(deps, requireNamespace, quietly = TRUE, FUN.VALUE = logical(1))]
+if (length(missing) > 0) {
+  stop("The following dependencies are missing: ", paste(missing, collapse = ", "))
+} else {
+  message("All dependencies are installed.")
+}
+EOF
+
+RUN R --vanilla --slave --file=/tmp/check_description_deps.R
+
+COPY Dockerfile /

From 83520d9d1a0b7789c3dd17638fe957a30b0bb1a5 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 18 Feb 2026 13:44:02 -0500
Subject: [PATCH 2/4] ci(docker): remove unused scripts

---
 Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index d9d3c82..61cbe12 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -112,8 +112,8 @@ RUN R -e "devtools::install_local('/opt2/SCWorkflow', dependencies = TRUE, upgra
 # RUN scworkflow --help
 
 # copy example script & json to data
-COPY ./inst/extdata/example_script.sh /data2/
-COPY ./inst/extdata/json_args/ /data2/json_args/
+# COPY ./inst/extdata/example_script.sh /data2/
+# COPY ./inst/extdata/json_args/ /data2/json_args/
 
 # Save Dockerfile in the docker
 COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}

From f142bb5ae3d2013c659b450f573ab81ee9dcb9e8 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 18 Feb 2026 13:52:23 -0500
Subject: [PATCH 3/4] ci(docker): check all pkgs installed

---
 Dockerfile | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/Dockerfile b/Dockerfile
index 61cbe12..8031b61 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -119,6 +119,43 @@ RUN R -e "devtools::install_local('/opt2/SCWorkflow', dependencies = TRUE, upgra
 COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
 RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
 
+# Verify all dependencies from DESCRIPTION are installed
+RUN cat > /tmp/check_description_deps.R << 'EOF'
+# Parse DESCRIPTION file and check if all dependencies are installed
+desc_file <- "/opt2/SCWorkflow/DESCRIPTION"
+if (!file.exists(desc_file)) {
+  stop("DESCRIPTION file not found at ", desc_file)
+}
+# Read and parse DESCRIPTION
+desc <- read.dcf(desc_file)
+# Extract dependencies
+extract_packages <- function(str) {
+  if (is.na(str) || str == "") return(character(0))
+  # Split by comma and clean up whitespace and version specs
+  pkgs <- strsplit(str, ",")[[1]]
+  pkgs <- trimws(pkgs)
+  pkgs <- gsub("\\s*\\(.*\\)$", "", pkgs)  # Remove version specs
+  pkgs <- pkgs[pkgs != ""]
+  pkgs
+}
+deps <- unique(c(
+  extract_packages(desc[1, "Depends"]),
+  extract_packages(desc[1, "Imports"]),
+  extract_packages(desc[1, "Suggests"]),
+  extract_packages(desc[1, "Config/Needs/dev"])
+))
+# Remove base R
+deps <- deps[!grepl("^R$", deps)]
+# Check if each dependency is installed
+missing <- deps[!vapply(deps, requireNamespace, quietly = TRUE, FUN.VALUE = logical(1))]
+if (length(missing) > 0) {
+  stop("The following dependencies are missing: ", paste(missing, collapse = ", "))
+} else {
+  message("All dependencies are installed.")
+}
+EOF
+RUN R --vanilla --slave --file=/tmp/check_description_deps.R
+
 # cleanup
 WORKDIR /data2
 RUN apt-get clean && apt-get purge \

From b304c8b4670b1ddb5d087b1e02508ea2fe4980d4 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 18 Feb 2026 15:01:26 -0500
Subject: [PATCH 4/4] ci(docker): try pinning only the seurat version

---
 Dockerfile | 130 +++++++++++++++++++++++++++--------------------------
 1 file changed, 66 insertions(+), 64 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 8031b61..9a4b171 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -26,80 +26,82 @@ RUN conda config --add channels conda-forge \
  && conda config --set channel_priority strict
 
 # install conda packages
+# Note: Most version pins removed to allow conda to resolve compatible versions with R 4.1.3
+# Only R version is pinned per requirement
 RUN mamba install -y \
     r-base=${R_VERSION} \
-    r-anndata=0.7.5.2 \
+    r-anndata \
     r-biocmanager \
-    r-callr=3.7.3 \
-    bioconductor-celldex=1.4.0 \
-    r-colorspace=2.0-3 \
-    bioconductor-complexheatmap=2.10.0 \
-    r-cowplot=1.1.1 \
-    r-data.table=1.15.4 \
-    r-dendextend=1.16.0 \
-    r-dendsort=0.3.4 \
-    r-digest=0.6.37 \
-    r-dplyr=1.1.4 \
-    bioconductor-edger=3.36.0 \
-    r-future=1.34.0 \
-    r-future.apply=1.11.2 \
-    r-gargle=1.3.0 \
-    r-gdata=2.18.0.1 \
-    r-ggextra=0.10.1 \
-    r-ggplot2=3.3.6 \
-    r-ggpubr=0.4.0 \
-    r-ggrepel=0.9.5 \
-    r-globals=0.16.3 \
-    r-gridbase=0.4-7 \
-    r-gridextra=2.3 \
-    r-gtable=0.3.5 \
+    r-callr \
+    bioconductor-celldex \
+    r-colorspace \
+    bioconductor-complexheatmap \
+    r-cowplot \
+    r-data.table \
+    r-dendextend \
+    r-dendsort \
+    r-digest \
+    r-dplyr \
+    bioconductor-edger \
+    r-future \
+    r-future.apply \
+    r-gargle \
+    r-gdata \
+    r-ggextra \
+    r-ggplot2 \
+    r-ggpubr \
+    r-ggrepel \
+    r-globals \
+    r-gridbase \
+    r-gridextra \
+    r-gtable \
     r-harmony \
-    bioconductor-hdf5r=1.3.5 \
-    r-htmlwidgets=1.6.4 \
-    r-httpuv=1.6.15 \
-    r-httr=1.4.7 \
-    r-jsonlite=1.8.8 \
-    r-leiden=0.4.3 \
+    r-hdf5r \
+    r-htmlwidgets \
+    r-httpuv \
+    r-httr \
+    r-jsonlite \
+    r-leiden \
     bioconductor-limma \
-    r-magrittr=2.0.3 \
-    r-markdown=1.13 \
-    bioconductor-mast=1.20.0 \
-    r-pheatmap=1.0.12 \
-    r-plotly=4.10.4 \
-    r-plyr=1.8.7 \
-    r-png=0.1-7 \
-    r-progressr=0.14.0 \
-    r-purrr=1.0.2 \
-    r-quantmod=0.4.20 \
-    r-rcolorbrewer=1.1-3 \
-    r-reshape2=1.4.4 \
-    r-reticulate=1.40.0 \
-    r-rlang=1.1.4 \
-    r-scales=1.2.1 \
-    bioconductor-scdblfinder=1.8.0 \
+    r-magrittr \
+    r-markdown \
+    bioconductor-mast \
+    r-pheatmap \
+    r-plotly \
+    r-plyr \
+    r-png \
+    r-progressr \
+    r-purrr \
+    r-quantmod \
+    r-rcolorbrewer \
+    r-reshape2 \
+    r-reticulate \
+    r-rlang \
+    r-scales \
+    bioconductor-scdblfinder \
     r-seurat=4.1.1 \
-    bioconductor-singler=1.8.1 \
-    r-statmod=1.5.0 \
-    r-stringr=1.5.1 \
-    r-svglite=2.1.0 \
-    r-tibble=3.2.1 \
-    r-tidyr=1.2.1 \
-    r-tidyverse=1.3.2 \
-    r-viridislite=0.4.1 \
-    r-xfun=0.47 \
-    r-zip=2.3.3 \
-    r-knitr=1.48 \
-    r-rmarkdown=2.28 \
-    r-roxygen2=7.2.3 \
-    r-testthat=3.1.6 \
-    r-usethis=3.1.0 \
+    bioconductor-singler \
+    r-statmod \
+    r-stringr \
+    r-svglite \
+    r-tibble \
+    r-tidyr \
+    r-tidyverse \
+    r-viridislite \
+    r-xfun \
+    r-zip \
+    r-knitr \
+    r-rmarkdown \
+    r-roxygen2 \
+    r-testthat \
+    r-usethis \
     r-cffr \
     r-covr \
     r-goodpractice \
-    r-here=1.0.1 \
+    r-here \
     r-lintr \
-    r-pkgdown=2.0.7 \
-    r-rcmdcheck=1.4.0 \
+    r-pkgdown \
+    r-rcmdcheck \
   && conda clean -afy
 
 # install R package