From 9feb7083b3e8171a96de8ee7dfb893b5b9b7b636 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 17 Feb 2026 15:30:10 -0500
Subject: [PATCH 01/18] ci: add gha workflows from MOSuite

---
 .github/CONTRIBUTING.md                    | 288 +++++++++++++++++++++
 .github/ISSUE_TEMPLATE/bug_report.yml      |  45 ++++
 .github/ISSUE_TEMPLATE/config.yml          |   4 +
 .github/ISSUE_TEMPLATE/feature_request.yml |  11 +
 .github/PULL_REQUEST_TEMPLATE.md           |  24 ++
 .github/workflows/R-CMD-check.yaml         |  85 ++++++
 .github/workflows/test-coverage.yaml       |  58 +++++
 .github/workflows/user-projects.yml        |  23 ++
 8 files changed, 538 insertions(+)
 create mode 100644 .github/CONTRIBUTING.md
 create mode 100644 .github/ISSUE_TEMPLATE/bug_report.yml
 create mode 100644 .github/ISSUE_TEMPLATE/config.yml
 create mode 100644 .github/ISSUE_TEMPLATE/feature_request.yml
 create mode 100644 .github/PULL_REQUEST_TEMPLATE.md
 create mode 100644 .github/workflows/R-CMD-check.yaml
 create mode 100644 .github/workflows/test-coverage.yaml
 create mode 100644 .github/workflows/user-projects.yml

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
new file mode 100644
index 0000000..875ae87
--- /dev/null
+++ b/.github/CONTRIBUTING.md
@@ -0,0 +1,288 @@
+# Contributing to SCWorkflow
+
+## Proposing changes with issues
+
+If you want to make a change, it's a good idea to first
+[open an issue](https://code-review.tidyverse.org/issues/)
+and make sure someone from the team agrees that it’s needed.
+
+If you've decided to work on an issue,
+[assign yourself to the issue](https://docs.github.com/en/issues/tracking-your-work-with-issues/assigning-issues-and-pull-requests-to-other-github-users#assigning-an-individual-issue-or-pull-request)
+so others will know you're working on it.
+
+## Pull request process
+
+We use [GitHub Flow](https://docs.github.com/en/get-started/using-github/github-flow)
+as our collaboration process.
+Follow the steps below for detailed instructions on contributing changes to
+SCWorkflow.
+
+![GitHub Flow diagram](https://raw.githubusercontent.com/CCBR/CCBR_NextflowTemplate/main/.github/img/GitHub-Flow_bg-white.png)
+
+
+### Clone the repo
+
+If you are a member of [CCBR](https://github.com/CCBR),
+you can clone this repository to your computer or development environment.
+Otherwise, you will first need to
+[fork](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo)
+the repo and clone your fork. You only need to do this step once.
+
+```sh
+git clone https://github.com/CCBR/SCWorkflow
+```
+
+> Cloning into 'SCWorkflow'... <br>
+> remote: Enumerating objects: 1136, done. <br>
+> remote: Counting objects: 100% (463/463), done. <br>
+> remote: Compressing objects: 100% (357/357), done. <br>
+> remote: Total 1136 (delta 149), reused 332 (delta 103), pack-reused 673 <br>
+> Receiving objects: 100% (1136/1136), 11.01 MiB | 9.76 MiB/s, done. <br>
+> Resolving deltas: 100% (530/530), done. <br>
+
+```sh
+cd SCWorkflow
+```
+
+### If this is your first time cloning the repo, install dependencies
+
+- In an R console, install the R development dependencies with
+  `devtools::install_dev_deps()`, and then make sure the package passes R CMD
+  check by running `devtools::check()`. If R CMD check doesn't pass cleanly,
+  it's a good idea to ask for help before continuing.
+
+- Install [`pre-commit`](https://pre-commit.com/#install) if you don't already
+  have it. Then from the repo's root directory, run
+
+  ```sh
+  pre-commit install
+  ```
+
+  This will install the repo's pre-commit hooks.
+  You'll only need to do this step the first time you clone the repo.
+
+### Create a branch
+
+  Create a Git branch for your pull request (PR). Give the branch a descriptive
+  name for the changes you will make, such as `iss-10` if it is for a specific
+  issue.
+
+  ```sh
+  # create a new branch and switch to it
+  git branch iss-10
+  git switch iss-10
+  ```
+
+  > Switched to a new branch 'iss-10'
+
+### Make your changes
+
+Edit the code, write unit tests, and update the documentation as needed.
+
+#### style
+
+New code should follow the [tidyverse style guide](https://style.tidyverse.org).
+You can use the [styler](https://CRAN.R-project.org/package=styler) package to
+apply these styles, but please don't restyle code that has nothing to do with
+your PR.
+
+A brief overview of conventions according to the tidyverse style guide:
+
+- most object names (variables and functions) should be in [snake_case](https://style.tidyverse.org/syntax.html#sec-objectnames)
+- function names should use [verbs](https://style.tidyverse.org/functions.html#naming) where possible
+- use `<-` for assignment
+- use [pipes](https://style.tidyverse.org/pipes.html) to chain operations on a single object
+
+Please see the [tidyverse style guide](https://style.tidyverse.org) for more details.
+
+#### test
+
+Most changes to the code will also need unit tests to demonstrate that the
+changes work as intended.
+Use [`testthat`](https://testthat.r-lib.org/) to create your unit tests and test
+the code.
+Test files are organized as described in
+<https://style.tidyverse.org/tests.html>.
+Take a look at the existing code in this package for examples.
+
+#### document
+
+If you have written a new function or changed the API of an existing function,
+you will need to update the function's documentation using
+[roxygen2](https://cran.r-project.org/package=roxygen2) with
+[Markdown syntax](https://roxygen2.r-lib.org/articles/rd-formatting.html).
+See instructions on writing roxygen2 comments here:
+<https://r-pkgs.org/man.html>.
+If the function is used in a vignette, you may also need to update the vignette.
+
+#### check
+
+After making your changes, run `devtools::check()` from an R console to make
+sure the package still passes R CMD check.
+
+### Commit and push your changes
+
+If you're not sure how often you should commit or what your commits should
+consist of, we recommend following the "atomic commits" principle where each
+commit contains one new feature, fix, or task.
+Learn more about atomic commits here:
+<https://www.freshconsulting.com/insights/blog/atomic-commits/>
+
+First, add the files that you changed to the staging area:
+
+```sh
+git add path/to/changed/files/
+```
+
+Then make the commit.
+Your commit message should follow the
+[Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0/)
+specification.
+Briefly, each commit should start with one of the approved types such as
+`feat`, `fix`, `docs`, etc. followed by a description of the commit.
+Take a look at the [Conventional Commits specification](https://www.conventionalcommits.org/en/v1.0.0/#summary)
+for more detailed information about how to write commit messages.
+
+
+```sh
+git commit -m 'feat: create function for awesome feature'
+```
+
+pre-commit will enforce that your commit message and the code changes are
+styled correctly and will attempt to make corrections if needed.
+
+> Check for added large files..............................................Passed <br>
+> Fix End of Files.........................................................Passed <br>
+> Trim Trailing Whitespace.................................................Failed <br>
+> - hook id: trailing-whitespace <br>
+> - exit code: 1 <br>
+> - files were modified by this hook <br>
+> <br>
+> Fixing path/to/changed/files/file.txt <br>
+> <br>
+> codespell................................................................Passed <br>
+> style-files..........................................(no files to check)Skipped <br>
+> readme-rmd-rendered..................................(no files to check)Skipped <br>
+> use-tidy-description.................................(no files to check)Skipped <br>
+
+In the example above, one of the hooks modified a file in the proposed commit,
+so the pre-commit check failed. You can run `git diff` to see the changes that
+pre-commit made and `git status` to see which files were modified. To proceed
+with the commit, re-add the modified file(s) and re-run the commit command:
+
+```sh
+git add path/to/changed/files/file.txt
+git commit -m 'feat: create function for awesome feature'
+```
+
+This time, all the hooks either passed or were skipped
+(e.g. hooks that only run on R code will not run if no R files were
+committed).
+When the pre-commit check is successful, the usual commit success message
+will appear after the pre-commit messages showing that the commit was created.
+
+> Check for added large files..............................................Passed <br>
+> Fix End of Files.........................................................Passed <br>
+> Trim Trailing Whitespace.................................................Passed <br>
+> codespell................................................................Passed <br>
+> style-files..........................................(no files to check)Skipped <br>
+> readme-rmd-rendered..................................(no files to check)Skipped <br>
+> use-tidy-description.................................(no files to check)Skipped <br>
+> Conventional Commit......................................................Passed <br>
+> [iss-10 9ff256e] feat: create function for awesome feature <br>
+> 1 file changed, 22 insertions(+), 3 deletions(-) <br>
+
+Finally, push your changes to GitHub:
+
+```sh
+git push
+```
+
+If this is the first time you are pushing this branch, you may have to
+explicitly set the upstream branch:
+
+```sh
+git push --set-upstream origin iss-10
+```
+
+> Enumerating objects: 7, done. <br>
+> Counting objects: 100% (7/7), done. <br>
+> Delta compression using up to 10 threads <br>
+> Compressing objects: 100% (4/4), done. <br>
+> Writing objects: 100% (4/4), 648 bytes | 648.00 KiB/s, done. <br>
+> Total 4 (delta 3), reused 0 (delta 0), pack-reused 0 <br>
+> remote: Resolving deltas: 100% (3/3), completed with 3 local objects. <br>
+> remote: <br>
+> remote: Create a pull request for 'iss-10' on GitHub by visiting: <br>
+> remote: https://github.com/CCBR/SCWorkflow/pull/new/iss-10 <br>
+> remote: <br>
+> To https://github.com/CCBR/SCWorkflow <br>
+> <br>
+>   [new branch] iss-10 -> iss-10 <br>
+>   branch 'iss-10' set up to track 'origin/iss-10'. <br>
+
+We recommend pushing your commits often so they will be backed up on GitHub.
+You can view the files in your branch on GitHub at
+`https://github.com/CCBR/SCWorkflow/tree/<your-branch-name>`
+(replace `<your-branch-name>` with the actual name of your branch).
+
+### Create the PR
+
+Once your branch is ready, create a PR on GitHub:
+<https://github.com/CCBR/SCWorkflow/pull/new/>
+
+Select the branch you just pushed:
+
+![Create a new PR from your branch](https://raw.githubusercontent.com/CCBR/CCBR_NextflowTemplate/main/.github/img/new-PR.png)
+
+Edit the PR title and description.
+The title should briefly describe the change.
+Follow the comments in the template to fill out the body of the PR, and
+you can delete the comments (everything between `<!--` and `-->`) as you go.
+When you're ready, click 'Create pull request' to open it.
+
+![Open the PR after editing the title and description](https://raw.githubusercontent.com/CCBR/CCBR_NextflowTemplate/main/.github/img/create-PR.png)
+
+Optionally, you can mark the PR as a draft if you're not yet ready for it to
+be reviewed, then change it later when you're ready.
+
+### Wait for a maintainer to review your PR
+
+We will do our best to follow the tidyverse code review principles:
+<https://code-review.tidyverse.org/>.
+The reviewer may suggest that you make changes before accepting your PR in
+order to improve the code quality or style.
+If that's the case, continue to make changes in your branch and push them to
+GitHub, and they will appear in the PR.
+
+Once the PR is approved, the maintainer will merge it and the issue(s) the PR
+links will close automatically.
+Congratulations and thank you for your contribution!
+
+### After your PR has been merged
+
+After your PR has been merged, update your local clone of the repo by
+switching to the main branch and pulling the latest changes:
+
+```sh
+git checkout main
+git pull
+```
+
+It's a good idea to run `git pull` before creating a new branch so it will
+start from the most recent commits in main.
+
+## Helpful links for more information
+
+- This contributing guide was adapted from the [tidyverse contributing guide](https://github.com/tidyverse/tidyverse/blob/main/.github/CONTRIBUTING.md)
+- [GitHub Flow](https://docs.github.com/en/get-started/using-github/github-flow)
+- [tidyverse style guide](https://style.tidyverse.org)
+- [tidyverse code review principles](https://code-review.tidyverse.org)
+- [reproducible examples](https://www.tidyverse.org/help/#reprex)
+- [R packages book](https://r-pkgs.org/)
+- packages:
+  - [usethis](https://usethis.r-lib.org/)
+  - [devtools](https://devtools.r-lib.org/)
+  - [testthat](https://testthat.r-lib.org/)
+  - [styler](https://styler.r-lib.org/)
+  - [roxygen2](https://roxygen2.r-lib.org)
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
new file mode 100644
index 0000000..95c98d1
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -0,0 +1,45 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Before you submit this issue, please check the documentation: <https://ccbr.github.io/SCWorkflow/>
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of the bug
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: reprex
+    attributes:
+      label: Code and output
+      description: Please include a minimal reproducible example (AKA a reprex). If you've never heard of a [reprex](http://reprex.tidyverse.org/) before, start by reading <https://www.tidyverse.org/help/#reprex>.
+      render: console
+      placeholder: |
+        library(SCWorkflow)
+        ... insert_your_code_here() ...
+
+        Paste some output where something broke
+
+  - type: textarea
+    id: files
+    attributes:
+      label: Relevant files
+      description: |
+        Please drag and drop any relevant files here if applicable. Create a `.zip` archive if the extension is not allowed.
+
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: |
+        * Version of R
+        * Version of CCBR/SCWorkflow
+        * OS _(eg. Ubuntu Linux, macOS)_
+        * Hardware _(eg. HPC, Desktop)_
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
new file mode 100644
index 0000000..84f8757
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/config.yml
@@ -0,0 +1,4 @@
+contact_links:
+  - name: Discussions
+    url: https://github.com/CCBR/SCWorkflow/discussions
+    about: Please ask and answer questions here.
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
new file mode 100644
index 0000000..73a08f5
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -0,0 +1,11 @@
+name: Feature request
+description: Suggest an idea for the package
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
new file mode 100644
index 0000000..bc679fa
--- /dev/null
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -0,0 +1,24 @@
+## Changes
+
+<!--
+Provide a brief summary of what is included in this Pull Request (PR).
+-->
+
+## Issues
+
+<!--
+Reference any issues related to this PR.
+If this PR fixes any issues,
+[use a keyword](https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue#linking-a-pull-request-to-an-issue-using-a-keyword)
+when referring to the issue so it will be closed automatically when the PR is merged.
+-->
+
+## PR Checklist
+
+(~Strikethrough~ any points that are not applicable.)
+
+- [ ] This comment contains a description of changes with justifications, with any relevant issues linked.
+- [ ] Write unit tests for any new features, bug fixes, or other code changes.
+- [ ] Update the docs if there are any API changes (roxygen2 comments, vignettes, readme, etc.).
+- [ ] Update `NEWS.md` with a short description of any user-facing changes and reference the PR number. Follow the style described in <https://style.tidyverse.org/news.html>
+- [ ] Run `devtools::check()` locally and fix all notes, warnings, and errors.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
new file mode 100644
index 0000000..9bae4b4
--- /dev/null
+++ b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,85 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  workflow_dispatch:
+
+name: R-CMD-check
+
+permissions:
+  contents: read
+  pull-requests: read
+
+jobs:
+  R-CMD-check:
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: ubuntu-latest, r: 'release' }
+          - { os: ubuntu-latest, r: 'oldrel-1' }
+          - { os: macos-latest, r: 'release' }
+
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: CCBR/actions/install-r-pak@main
+        with:
+          versions-file: .github/package-versions.txt
+          extra-packages: local::.
+          needs: dev
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: CCBR/actions/install-r-pak@main
+        with:
+          r-version: 4.4
+          versions-file: .github/package-versions.txt
+          needs: dev
+
+      - name: Good Practice checks
+        shell: Rscript {0}
+        run: |
+          g <- goodpractice::gp()
+          g
+          n_failed <- length(goodpractice::failed_checks(g))
+          if (n_failed > 0) {
+            warning(paste(n_failed, "failed checks"))
+          }
+
+      - name: Lint
+        shell: Rscript {0}
+        run: lintr::lint_package()
+        env:
+          LINTR_ERROR_ON_LINT: false
+
+  check: # make sure all check jobs pass. https://github.com/orgs/community/discussions/4324#discussioncomment-3477871
+    runs-on: ubuntu-latest
+    needs: [R-CMD-check, lint]
+    if: always()
+    steps:
+      - name: Successful build
+        if: ${{ !(contains(needs.*.result, 'failure')) }}
+        run: exit 0
+      - name: Failing build
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
new file mode 100644
index 0000000..0d48214
--- /dev/null
+++ b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,58 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: CCBR/actions/install-r-pak@main
+        with:
+          r-version: 4.4
+          versions-file: .github/package-versions.txt
+          needs: dev
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/.github/workflows/user-projects.yml b/.github/workflows/user-projects.yml
new file mode 100644
index 0000000..c189ef6
--- /dev/null
+++ b/.github/workflows/user-projects.yml
@@ -0,0 +1,23 @@
+name: user-projects
+
+on:
+  issues:
+    types:
+      - assigned
+  pull_request:
+    types:
+      - assigned
+
+permissions:
+  issues: write
+  pull-requests: write
+
+jobs:
+  add-to-project:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: CCBR/actions/user-projects@main
+        with:
+          app-id: ${{ vars.CCBR_BOT_APP_ID }}
+          app-private-key: ${{ secrets.CCBR_BOT_PRIVATE_KEY }}
+          token-owner: "CCBR"

From d28169515d44562c7f8fde4a5245da9e4bce649b Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 17 Feb 2026 15:34:06 -0500
Subject: [PATCH 02/18] ci: run on dev branches

---
 .github/workflows/R-CMD-check.yaml   | 4 ++--
 .github/workflows/test-coverage.yaml | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 9bae4b4..5c4f3f3 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, dev, DEV]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev, DEV]
   workflow_dispatch:
 
 name: R-CMD-check
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 0d48214..fc851f7 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, dev, DEV]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev, DEV]
 
 name: test-coverage
 

From e4d28ef6ca47229af9f431564d6e787ad79036db Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 17 Feb 2026 15:51:03 -0500
Subject: [PATCH 03/18] ci: force R version 4.1.3

---
 .github/workflows/R-CMD-check.yaml   | 8 ++++----
 .github/workflows/pkgdown.yaml       | 2 +-
 .github/workflows/test-coverage.yaml | 2 +-
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 5c4f3f3..9a97fff 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -20,9 +20,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: 'release' }
-          - { os: ubuntu-latest, r: 'oldrel-1' }
-          - { os: macos-latest, r: 'release' }
+          - { os: ubuntu-latest, r: '4.1.3' }
+          #- { os: ubuntu-latest, r: 'oldrel-1' }
+          #- { os: macos-latest, r: 'release' }
 
     runs-on: ${{ matrix.config.os }}
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@@ -52,7 +52,7 @@ jobs:
 
       - uses: CCBR/actions/install-r-pak@main
         with:
-          r-version: 4.4
+          r-version: 4.1.3
           versions-file: .github/package-versions.txt
           needs: dev
 
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index f9745ba..3f53415 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -31,7 +31,7 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-          r-version: 4.3
+          r-version: 4.1.3
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index fc851f7..4ac1c43 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -21,7 +21,7 @@ jobs:
 
       - uses: CCBR/actions/install-r-pak@main
         with:
-          r-version: 4.4
+          r-version: 4.1.3
           versions-file: .github/package-versions.txt
           needs: dev
 

From 55e2dfebff689e03fe192a5f51562ae0455abfae Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 17 Feb 2026 15:53:09 -0500
Subject: [PATCH 04/18] chore: delete pryr from deps

---
 DESCRIPTION | 1 -
 1 file changed, 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index cdf6c35..9c6d5ad 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -46,7 +46,6 @@ Imports:
     methods (>= 4.1.3),
     plotly (>= 4.10.0), 
     progressr (>= 0.10.1),
-    pryr (>= 0.1.5),
     purrr (>= 0.3.4),
     quantmod (>= 0.4.20),
     reshape2 (>= 1.4.4),

From e6080c32aa5ce65af5a834e9785b04a2105086ae Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 17 Feb 2026 15:58:06 -0500
Subject: [PATCH 05/18] chore: add dev deps

---
 DESCRIPTION | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index 9c6d5ad..1da46e9 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -85,4 +85,11 @@ Imports:
     tidyr,
     htmlwidgets,
     scDblFinder
+Suggests:
+    knitr,
+    testthat (>= 3.0.0),
+    rmarkdown,
+    roxygen2,
+    usethis
 Config/testthat/edition: 3
+Config/Needs/dev: cffr, covr, goodpractice, here, lintr, pkgdown, rcmdcheck

From f4add3daa5db71a3eb8804a4bb8296acf668b9ce Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 17 Feb 2026 16:03:10 -0500
Subject: [PATCH 06/18] ci(pkgdown): use custom installation

---
 .github/workflows/pkgdown.yaml | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 3f53415..0459bb7 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, GalaxyCLI]
+    branches: [main, master]
   pull_request:
     branches: [main, master]
   release:
@@ -26,17 +26,12 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - uses: r-lib/actions/setup-r@v2
+      - uses: CCBR/actions/install-r-pak@main
         with:
-          use-public-rspm: true
           r-version: 4.1.3
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::pkgdown, local::.
-          needs: website
+          versions-file: .github/package-versions.txt
+          extra-packages: local::.
+          needs: dev
 
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)

From 2f2e45b369179e6a57ef7a41dd3d0af89e88e66a Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 17 Feb 2026 16:03:19 -0500
Subject: [PATCH 07/18] chore: pin seurat & matrix

---
 .github/package-versions.txt | 2 ++
 .gitignore                   | 1 -
 2 files changed, 2 insertions(+), 1 deletion(-)
 create mode 100644 .github/package-versions.txt

diff --git a/.github/package-versions.txt b/.github/package-versions.txt
new file mode 100644
index 0000000..df0dde1
--- /dev/null
+++ b/.github/package-versions.txt
@@ -0,0 +1,2 @@
+any::Seurat@4.1.1
+any::Matrix@1.5-1
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index 55ed9b9..17be9e8 100755
--- a/.gitignore
+++ b/.gitignore
@@ -5,4 +5,3 @@ Rcheck.txt
 *.pdf
 tests/testthat/otherData/
 .Rproj.user
-*.txt

From 71e36e7177c54ce3c5d173eaa0b96829cdd63b64 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 17 Feb 2026 16:05:08 -0500
Subject: [PATCH 08/18] chore: Matrix version with period instead of hyphen

---
 .github/package-versions.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/package-versions.txt b/.github/package-versions.txt
index df0dde1..81c250e 100644
--- a/.github/package-versions.txt
+++ b/.github/package-versions.txt
@@ -1,2 +1,2 @@
 any::Seurat@4.1.1
-any::Matrix@1.5-1
\ No newline at end of file
+any::Matrix@1.5.1
\ No newline at end of file

From c9286fbefcf44169235014cc0a4dacb78ea1e876 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 17 Feb 2026 16:07:52 -0500
Subject: [PATCH 09/18] chore: fix pkg version format

---
 .github/package-versions.txt | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/package-versions.txt b/.github/package-versions.txt
index 81c250e..2facfd9 100644
--- a/.github/package-versions.txt
+++ b/.github/package-versions.txt
@@ -1,2 +1 @@
-any::Seurat@4.1.1
-any::Matrix@1.5.1
\ No newline at end of file
+any::Seurat@4.1.1, any::Matrix@1.5.1
\ No newline at end of file

From 62b22beef36bec2aa77bdeea97ac587ea1516e2f Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 17 Feb 2026 16:11:17 -0500
Subject: [PATCH 10/18] chore: remove duplicate suggests field

---
 DESCRIPTION | 2 --
 1 file changed, 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 1da46e9..7a014cb 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -19,8 +19,6 @@ License: MIT
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-Suggests: 
-    testthat (>= 3.0.0)
 Depends:
     R (>= 4.0)
 Imports:

From 766bc55c1ed7714c4b7320728c4f131b16fc4540 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 17 Feb 2026 16:13:18 -0500
Subject: [PATCH 11/18] chore: usethis::use_tidy_description()

---
 DESCRIPTION | 106 ++++++++++++++++++++++++++++------------------------
 1 file changed, 58 insertions(+), 48 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 7a014cb..3bbcff8 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,93 +1,103 @@
 Package: SCWorkflow
 Title: SCWorkflow from NIDAP
 Version: 1.0.2
-Authors@R:  c(person("Maggie", "Cam", email = "maggie.cam@nih.gov", role = "aut", comment = c(ORCID = "0000-0001-8190-9766")), 
-    person("Thomas", "Meyer", email = "thomas.meyer@nih.gov", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7185-5597")), 
-    person("Jing", "Bian", email = "bianjh@nih.gov", role = "aut", comment = c(ORCID = "0000-0001-7109-716X")), 
-    person("Alexandra", "Michalowski", email = "michaloa@mail.nih.gov", role = "aut", comment = c(ORCID = "0000-0001-9259-6101")),
-    person("Alexei", "Lobanov", email = "alexei.lobanov@nih.gov", role = "aut", comment = c(ORCID = "0000-0002-9883-4374")),
-    person("Philip", "Homan", email = "philip.homan@nih.gov", role = "aut", comment = c(ORCID = "0000-0002-3389-4931")),
-    person("Rui", "He", email = "rui.he@nih.gov", role = "aut"))
-Description: A set of functions for analyzing single-cell RNA-seq data using the
-    Seurat workflow. The user provides H5 files containing the results of the
-    upstream processing through CellRanger, and the package functions allow for
-    the QC, filtering, normalization, annotation, differential gene expression,
-    and further visualizations and analysis based on user input. This package can
-    be run both in a docker container and in user-friendly web-based interactive
-    notebooks (NIDAP, Palantir Foundry).
+Authors@R: c(
+    person("Maggie", "Cam", , "maggie.cam@nih.gov", role = "aut",
+           comment = c(ORCID = "0000-0001-8190-9766")),
+    person("Thomas", "Meyer", , "thomas.meyer@nih.gov", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0002-7185-5597")),
+    person("Jing", "Bian", , "bianjh@nih.gov", role = "aut",
+           comment = c(ORCID = "0000-0001-7109-716X")),
+    person("Alexandra", "Michalowski", , "michaloa@mail.nih.gov", role = "aut",
+           comment = c(ORCID = "0000-0001-9259-6101")),
+    person("Alexei", "Lobanov", , "alexei.lobanov@nih.gov", role = "aut",
+           comment = c(ORCID = "0000-0002-9883-4374")),
+    person("Philip", "Homan", , "philip.homan@nih.gov", role = "aut",
+           comment = c(ORCID = "0000-0002-3389-4931")),
+    person("Rui", "He", , "rui.he@nih.gov", role = "aut")
+  )
+Description: A set of functions for analyzing single-cell RNA-seq data
+    using the Seurat workflow. The user provides H5 files containing the
+    results of the upstream processing through CellRanger, and the package
+    functions allow for the QC, filtering, normalization, annotation,
+    differential gene expression, and further visualizations and analysis
+    based on user input. This package can be run both in a docker
+    container and in user-friendly web-based interactive notebooks (NIDAP,
+    Palantir Foundry).
 License: MIT
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
 Depends:
     R (>= 4.0)
 Imports:
     anndata (>= 0.7.5.2),
+    BiocManager,
     callr (>= 3.7.1),
+    celldex,
+    colorspace,
+    ComplexHeatmap (>= 2.10.0),
     cowplot (>= 1.1.1),
     data.table (>= 1.14.2),
+    dendextend,
+    dendsort,
+    digest (>= 0.6.29),
     dplyr (>= 1.0.9),
     edgeR (>= 3.36.0),
-    future.apply (>= 1.9.0),
     future (>= 1.27.0),
+    future.apply (>= 1.9.0),
     gargle (>= 1.2.0),
+    gdata,
+    ggExtra,
     ggplot2 (>= 3.3.6),
     ggpubr (>= 0.4.0),
+    ggrepel,
     globals (>= 0.16.1),
+    gridBase (>= 0.4-7),
+    gridExtra (>= 2.3),
+    gtable (>= 0.3.1),
     harmony (>= 0.1.1),
     hdf5r (>= 1.3.5),
+    htmlwidgets,
     httpuv (>= 1.6.5),
+    httr,
+    jsonlite,
     leiden (>= 0.4.2),
     limma (>= 3.50.3),
     magrittr (>= 2.0.3),
     markdown (>= 1.1),
+    MAST (>= 1.20.0),
     methods (>= 4.1.3),
-    plotly (>= 4.10.0), 
+    pheatmap,
+    plotly (>= 4.10.0),
+    plyr,
+    png,
     progressr (>= 0.10.1),
     purrr (>= 0.3.4),
     quantmod (>= 0.4.20),
+    RColorBrewer (>= 1.1-3),
     reshape2 (>= 1.4.4),
     reticulate (>= 1.25),
     rlang (>= 1.0.6),
+    scales,
+    scDblFinder,
+    Seurat (>= 4.1.1),
+    SingleR (>= 1.8.1),
     statmod (>= 1.4.37),
     stringr (>= 1.4.1),
     svglite (>= 2.1.0),
     tibble (>= 3.1.8),
+    tidyr,
     tidyverse (>= 1.3.2),
     viridisLite (>= 0.4.0),
     xfun (>= 0.32),
-    zip (>= 2.2.0),
-    ComplexHeatmap (>= 2.10.0),
-    MAST (>= 1.20.0),
-    SingleR (>= 1.8.1),
-    BiocManager,
-    gridBase (>= 0.4-7),
-    gridExtra (>= 2.3),
-    RColorBrewer (>= 1.1-3),
-    Seurat (>= 4.1.1),
-    gtable (>= 0.3.1),
-    digest (>= 0.6.29),
-    png,
-    ggExtra,
-    httr,
-    jsonlite,
-    plyr,
-    colorspace,
-    dendextend,
-    dendsort,
-    pheatmap,
-    scales,
-    celldex,
-    gdata,
-    ggrepel,
-    tidyr,
-    htmlwidgets,
-    scDblFinder
+    zip (>= 2.2.0)
 Suggests:
     knitr,
-    testthat (>= 3.0.0),
     rmarkdown,
     roxygen2,
+    testthat (>= 3.0.0),
     usethis
+Config/Needs/dev: cffr, covr, goodpractice, here, lintr, pkgdown,
+    rcmdcheck
 Config/testthat/edition: 3
-Config/Needs/dev: cffr, covr, goodpractice, here, lintr, pkgdown, rcmdcheck
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3

From cb473909aa55ffb9f324b5cfac0ac74711eab1f1 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 17 Feb 2026 16:13:33 -0500
Subject: [PATCH 12/18] chore(docker): set R version 4.1.3

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index b91c92f..0d61765 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -8,7 +8,7 @@ ENV BUILD_TAG=${BUILD_TAG}
 ARG REPONAME="000000"
 ENV REPONAME=${REPONAME}
 
-ARG R_VERSION=4.3.2
+ARG R_VERSION=4.1.3
 ENV R_VERSION=${R_VERSION}
 
 SHELL ["/bin/bash", "-lc"]

From 3fa6404527a8959226461f617d0599788ab4b23f Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 17 Feb 2026 16:34:08 -0500
Subject: [PATCH 13/18] ci(docker): add dockerfile from Rich

Co-authored-by: Rich Finney <finneyr@users.noreply.github.com>
---
 Dockerfile | 709 ++++++++++++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 645 insertions(+), 64 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 0d61765..51230bc 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,64 +1,645 @@
-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 -c conda-forge \
-    r-base=${R_VERSION} \
-    r-devtools \
-    r-ggplot2 \
-    r-ggrepel r-viridis r-upsetr r-patchwork r-plotly \
-    r-matrix r-mgcv r-survival \
-    bioconductor-genomicranges \
-    bioconductor-summarizedexperiment \
-    bioconductor-delayedarray \
-    bioconductor-s4arrays \
-    bioconductor-annotationdbi \
-    bioconductor-annotate \
-    bioconductor-keggrest \
-  && conda clean -afy
-
-# install R package
-COPY . /opt2/SCWorkflow
-RUN R -e "devtools::install_local('/opt2/SCWorkflow', dependencies = TRUE, repos='http://cran.rstudio.com')"
-
-# add scworkflow exec to the path
-# RUN chmod -R +x /opt2/conda/lib/R/library/SCWorkflow/exec
-# ENV PATH="$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/*
+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
+# Copy your local tarballs (ensure PACKAGESS is in the build context)
+
+COPY PACKAGESS/ /opt/pkgs/
+
+# 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); \
+    } \
+  }"
+
+
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/bitops_1.0-8.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/RCurl_1.98-1.14.tar.gz
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/GlobalOptions_0.1.2.tar.gz \
+ /opt/pkgs/bit_4.0.4.tar.gz \
+ /opt/pkgs/BiocGenerics_0.40.0.tar.gz 
+
+#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/RCurl_1.98.1.16.tar.gz
+#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/RCurl_1.98.1.12.tar.gz
+
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/assertthat_0.2.1.tar.gz \
+ /opt/pkgs/Biobase_2.54.0.tar.gz \
+ /opt/pkgs/bit64_4.0.5.tar.gz \
+ /opt/pkgs/shape_1.4.6.tar.gz
+
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/remotes_2.5.0.tar.gz
+RUN R -e "remotes::install_github('NIDAP-Community/SCWorkflow', ref = 'GalaxyCLI')"
+
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/colorspace_2.0-3.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/circlize_0.4.15.tar.gz
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/rlang_1.1.4.tar.gz \
+ /opt/pkgs/cli_3.6.3.tar.gz \
+ /opt/pkgs/glue_1.7.0.tar.gz 
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/lifecycle_1.0.4.tar.gz \
+ /opt/pkgs/vctrs_0.6.5.tar.gz \
+ /opt/pkgs/blob_1.2.3.tar.gz \
+ /opt/pkgs/clue_0.3-61.tar.gz \
+ /opt/pkgs/cluster_2.1.2.tar.gz \
+ /opt/pkgs/codetools_0.2-18.tar.gz \
+ /opt/pkgs/crayon_1.5.3.tar.gz \
+ /opt/pkgs/data.table_1.15.4.tar.gz \
+ /opt/pkgs/DBI_1.2.3.tar.gz
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/dendsort_0.3.4.tar.gz \
+ /opt/pkgs/digest_0.6.37.tar.gz \
+ /opt/pkgs/ellipsis_0.3.2.tar.gz \
+ /opt/pkgs/evaluate_0.24.0.tar.gz \
+ /opt/pkgs/fansi_1.0.6.tar.gz \
+ /opt/pkgs/farver_2.1.1.tar.gz \
+ /opt/pkgs/fastmap_1.2.0.tar.gz \
+ /opt/pkgs/cachem_1.1.0.tar.gz \
+ /opt/pkgs/fastmatch_1.1-3.tar.gz \
+ /opt/pkgs/iterators_1.0.14.tar.gz \
+ /opt/pkgs/foreach_1.5.2.tar.gz \
+ /opt/pkgs/formatR_1.14.tar.gz
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/generics_0.1.3.tar.gz \
+ /opt/pkgs/rjson_0.2.21.tar.gz \
+ /opt/pkgs/GetoptLong_1.0.5.tar.gz \
+ /opt/pkgs/gtable_0.3.5.tar.gz \
+ /opt/pkgs/labeling_0.4.2.tar.gz \
+ /opt/pkgs/munsell_0.5.0.tar.gz \
+ /opt/pkgs/R6_2.5.1.tar.gz \
+ /opt/pkgs/gridExtra_2.3.tar.gz \
+ /opt/pkgs/RColorBrewer_1.1-3.tar.gz \
+ /opt/pkgs/utf8_1.2.4.tar.gz \
+ /opt/pkgs/pillar_1.9.0.tar.gz 
+
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/pkgconfig_2.0.3.tar.gz \
+ /opt/pkgs/viridisLite_0.4.1.tar.gz \
+ /opt/pkgs/scales_1.2.1.tar.gz \
+ /opt/pkgs/withr_3.0.1.tar.gz \
+ /opt/pkgs/gtools_3.9.5.tar.gz \
+ /opt/pkgs/gridGraphics_0.5-1.tar.gz \
+ /opt/pkgs/hms_1.1.2.tar.gz \
+ /opt/pkgs/S4Vectors_0.32.4.tar.gz \
+ /opt/pkgs/IRanges_2.28.0.tar.gz \
+ /opt/pkgs/irlba_2.3.5.1.tar.gz \
+ /opt/pkgs/jsonlite_1.8.8.tar.gz 
+
+# /opt/pkgs/jsonlite_1.8.8.tar.gz
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/png_0.1-7.tar.gz \
+ /opt/pkgs/KernSmooth_2.23-20.tar.gz  \
+ /opt/pkgs/lambda.r_1.2.4.tar.gz \
+ /opt/pkgs/lattice_0.20-45.tar.gz  \
+ /opt/pkgs/lazyeval_0.2.2.tar.gz \
+ /opt/pkgs/limma_3.50.3.tar.gz \
+ /opt/pkgs/locfit_1.5-9.9.tar.gz \
+ /opt/pkgs/Matrix_1.5-1.tar.gz \
+ /opt/pkgs/matrixStats_0.62.0.tar.gz \
+ /opt/pkgs/MatrixGenerics_1.6.0.tar.gz \
+ /opt/pkgs/memoise_2.0.1.tar.gz \
+ /opt/pkgs/mgcv_1.8-39.tar.gz
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/nlme_3.1-155.tar.gz \
+ /opt/pkgs/rsvd_1.0.5.tar.gz \
+ /opt/pkgs/DelayedArray_0.20.0.tar.gz \
+ /opt/pkgs/Rcpp_1.0.13.tar.gz \
+ /opt/pkgs/sparseMatrixStats_1.6.0.tar.gz \
+ /opt/pkgs/DelayedMatrixStats_1.16.0.tar.gz \
+ /opt/pkgs/ScaledMatrix_1.2.0.tar.gz \
+ /opt/pkgs/uuid_1.1-0.tar.gz \
+ /opt/pkgs/xfun_0.47.tar.gz \
+ /opt/pkgs/xtable_1.8-4.tar.gz \
+ /opt/pkgs/zlibbioc_1.40.0.tar.gz \
+ /opt/pkgs/XVector_0.34.0.tar.gz
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/yaml_2.3.10.tar.gz \
+ /opt/pkgs/GenomeInfoDbData_1.2.7.tar.gz \
+ /opt/pkgs/GenomeInfoDb_1.30.1.tar.gz \
+ /opt/pkgs/beachmat_2.10.0.tar.gz \
+ /opt/pkgs/doParallel_1.0.17.tar.gz \
+ /opt/pkgs/edgeR_3.36.0.tar.gz \
+ /opt/pkgs/futile.options_1.0.1.tar.gz \
+ /opt/pkgs/futile.logger_1.4.3.tar.gz \
+ /opt/pkgs/GenomicRanges_1.46.1.tar.gz \
+ /opt/pkgs/base64enc_0.1-3.tar.gz \
+ /opt/pkgs/htmltools_0.5.8.1.tar.gz \
+ /opt/pkgs/rappdirs_0.3.3.tar.gz
+
+#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/tinytex_0.45.tar.gz
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/jquerylib_0.1.4.tar.gz \
+ /opt/pkgs/tinytex_0.44.tar.gz \
+ /opt/pkgs/fs_1.6.4.tar.gz \
+ /opt/pkgs/sass_0.4.6.tar.gz \
+ /opt/pkgs/mime_0.12.tar.gz \
+ /opt/pkgs/bslib_0.4.2.tar.gz \
+ /opt/pkgs/magrittr_2.0.3.tar.gz \
+ /opt/pkgs/stringi_1.8.4.tar.gz \
+ /opt/pkgs/stringr_1.5.1.tar.gz \
+ /opt/pkgs/highr_0.10.tar.gz \
+ /opt/pkgs/knitr_1.48.tar.gz \
+ /opt/pkgs/fontawesome_0.5.1.tar.gz
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/rmarkdown_2.28.tar.gz \
+ /opt/pkgs/htmlwidgets_1.6.4.tar.gz \
+ /opt/pkgs/sys_3.4.1.tar.gz \
+ /opt/pkgs/askpass_1.1.tar.gz \
+ /opt/pkgs/openssl_2.0.5.tar.gz \
+ /opt/pkgs/curl_6.4.0.tar.gz \
+ /opt/pkgs/httr_1.4.7.tar.gz \
+ /opt/pkgs/Biostrings_2.62.0.tar.gz \
+ /opt/pkgs/cpp11_0.4.7.tar.gz \
+ /opt/pkgs/timechange_0.2.0.tar.gz
+
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/lubridate_1.8.0.tar.gz \
+ /opt/pkgs/isoband_0.2.7.tar.gz \
+ /opt/pkgs/tibble_3.2.1.tar.gz \
+ /opt/pkgs/ggplot2_3.3.6.tar.gz \
+ /opt/pkgs/patchwork_1.2.0.tar.gz \
+ /opt/pkgs/later_1.3.2.tar.gz \
+ /opt/pkgs/promises_1.3.0.tar.gz \
+ /opt/pkgs/crosstalk_1.2.0.tar.gz \
+ /opt/pkgs/purrr_1.0.2.tar.gz \
+ /opt/pkgs/tidyselect_1.2.1.tar.gz \
+ /opt/pkgs/dplyr_1.1.4.tar.gz \
+ /opt/pkgs/tidyr_1.2.1.tar.gz
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/plotly_4.10.4.tar.gz \
+ /opt/pkgs/plyr_1.8.7.tar.gz \
+ /opt/pkgs/clipr_0.8.0.tar.gz \
+ /opt/pkgs/prettyunits_1.1.1.tar.gz \
+ /opt/pkgs/progress_1.2.2.tar.gz \
+ /opt/pkgs/tzdb_0.4.0.tar.gz \
+ /opt/pkgs/vroom_1.6.3.tar.gz \
+ /opt/pkgs/readr_2.1.2.tar.gz \
+ /opt/pkgs/reshape2_1.4.4.tar.gz \
+ /opt/pkgs/plogr_0.2.0.tar.gz \
+ /opt/pkgs/RSQLite_2.3.9.tar.gz \
+ /opt/pkgs/systemfonts_1.2.3.tar.gz
+
+
+# /opt/pkgs/vroom_1.6.1.tar.gz \
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/textshaping_0.3.6.tar.gz \
+ /opt/pkgs/ragg_1.2.5.tar.gz \
+ /opt/pkgs/dbplyr_2.2.1.tar.gz \
+ /opt/pkgs/rstudioapi_0.14.tar.gz \
+ /opt/pkgs/dtplyr_1.3.1.tar.gz \
+ /opt/pkgs/backports_1.4.1.tar.gz \
+ /opt/pkgs/broom_1.0.1.tar.gz \
+ /opt/pkgs/ps_1.8.1.tar.gz \
+ /opt/pkgs/processx_3.8.5.tar.gz \
+ /opt/pkgs/callr_3.7.3.tar.gz \
+ /opt/pkgs/reprex_2.0.2.tar.gz \
+ /opt/pkgs/modelr_0.1.9.tar.gz
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/conflicted_1.2.0.tar.gz \
+ /opt/pkgs/rematch2_2.1.2.tar.gz \
+ /opt/pkgs/gargle_1.3.0.tar.gz \
+ /opt/pkgs/rematch_1.0.1.tar.gz \
+ /opt/pkgs/cellranger_1.1.0.tar.gz \
+ /opt/pkgs/ids_1.0.1.tar.gz \
+ /opt/pkgs/googledrive_2.0.0.tar.gz \
+ /opt/pkgs/googlesheets4_1.0.1.tar.gz \
+ /opt/pkgs/readxl_1.4.1.tar.gz \
+ /opt/pkgs/selectr_0.4-2.tar.gz \
+ /opt/pkgs/xml2_1.3.3.tar.gz \
+ /opt/pkgs/rvest_1.0.3.tar.gz \
+ /opt/pkgs/forcats_0.5.2.tar.gz \
+ /opt/pkgs/haven_2.5.1.tar.gz \
+ /opt/pkgs/tidyverse_1.3.2.tar.gz 
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/KEGGREST_1.34.0.tar.gz \
+ /opt/pkgs/AnnotationDbi_1.56.2.tar.gz \
+ /opt/pkgs/snow_0.4-4.tar.gz \
+ /opt/pkgs/BH_1.81.0-1.tar.gz \
+ /opt/pkgs/BiocParallel_1.28.3.tar.gz \
+ /opt/pkgs/BiocSingular_1.10.0.tar.gz \
+ /opt/pkgs/ComplexHeatmap_2.10.0.tar.gz \
+ /opt/pkgs/viridis_0.6.5.tar.gz
+
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/dendextend_1.16.0.tar.gz \
+ /opt/pkgs/fgsea_1.20.0.tar.gz \
+ /opt/pkgs/ggrepel_0.9.5.tar.gz \
+ /opt/pkgs/l2p_0.0-13.tar.gz  \
+ /opt/pkgs/l2psupp_0.0-13.tar.gz  \
+ /opt/pkgs/ica_1.0-3.tar.gz \
+ /opt/pkgs/Rtsne_0.16.tar.gz \
+ /opt/pkgs/ggridges_0.5.3.tar.gz \
+ /opt/pkgs/scattermore_1.2.tar.gz \
+ /opt/pkgs/listenv_0.9.1.tar.gz \
+ /opt/pkgs/globals_0.16.3.tar.gz \
+ /opt/pkgs/parallelly_1.38.0.tar.gz 
+
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/future_1.34.0.tar.gz \
+ /opt/pkgs/future.apply_1.11.2.tar.gz \
+ /opt/pkgs/RcppEigen_0.3.3.9.3.tar.gz \
+ /opt/pkgs/RcppAnnoy_0.0.19.tar.gz \
+ /opt/pkgs/zoo_1.8-12.tar.gz \
+ /opt/pkgs/lmtest_0.9-40.tar.gz \
+ /opt/pkgs/fitdistrplus_1.1-8.tar.gz 
+
+ # /opt/pkgs/gplots_3.1.3.tar.gz \
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/caTools_1.18.2.tar.gz \
+ /opt/pkgs/gplots_3.1.3.tar.gz \
+ /opt/pkgs/ROCR_1.0-11.tar.gz \
+ /opt/pkgs/igraph_2.0.3.tar.gz \
+ /opt/pkgs/pbapply_1.5-0.tar.gz \
+ /opt/pkgs/commonmark_1.9.0.tar.gz \
+ /opt/pkgs/httpuv_1.6.15.tar.gz \
+ /opt/pkgs/sourcetools_0.1.7-1.tar.gz \
+ /opt/pkgs/shiny_1.9.1.tar.gz \
+ /opt/pkgs/miniUI_0.1.1.1.tar.gz
+
+#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/igraph_2.0.3.tar.gz
+
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/progressr_0.14.0.tar.gz \
+ /opt/pkgs/sitmo_2.0.2.tar.gz \
+ /opt/pkgs/dqrng_0.4.1.tar.gz \
+ /opt/pkgs/FNN_1.1.3.2.tar.gz \
+ /opt/pkgs/RcppProgress_0.4.2.tar.gz \
+ /opt/pkgs/uwot_0.1.14.tar.gz \
+ /opt/pkgs/cowplot_1.1.1.tar.gz 
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/RcppTOML_0.2.2.tar.gz \
+ /opt/pkgs/rprojroot_2.0.4.tar.gz \
+ /opt/pkgs/here_1.0.1.tar.gz \
+ /opt/pkgs/reticulate_1.40.0.tar.gz \
+ /opt/pkgs/leiden_0.4.3.tar.gz \
+ /opt/pkgs/RANN_2.6.1.tar.gz \
+ /opt/pkgs/RcppArmadillo_0.12.4.0.0.tar.gz \
+ /opt/pkgs/sctransform_0.3.4.tar.gz
+
+# see https://github.com/satijalab/seurat/issues/8948
+#devtools::install_version("spatstat.core", version = "2.4-0", repos='http://cran.us.r-project.org')
+#devtools::install_version("spatstat.data", version = "2.1-2", repos='http://cran.us.r-project.org')
+#devtools::install_version("spatstat.geom", version = "2.3-2", repos='http://cran.us.r-project.org')
+#devtools::install_version("spatstat.random", version = "2.1-0", repos='http://cran.us.r-project.org')
+
+# old - phils spec ...
+# /opt/pkgs/spatstat.core_2.4-4.tar.gz \
+# /opt/pkgs/spatstat.data_3.1-2.tar.gz \
+# /opt/pkgs/spatstat.geom_3.3-2.tar.gz \
+# /opt/pkgs/spatstat.random_3.3-1.tar.gz \
+# /opt/pkgs/spatstat.explore_3.1-0.tar.gz \
+# /opt/pkgs/spatstat.univar_3.0-0.tar.gz \
+
+#      /opt/pkgs/spatstat.geom_3.2-1.tar.gz \
+#      /opt/pkgs/spatstat.data_3.1-2.tar.gz \
+#      /opt/pkgs/spatstat.data_2.1-2.tar.gz \
+#      /opt/pkgs/spatstat.random_3.1-5.tar.gz \
+#      /opt/pkgs/spatstat.geom_2.3-2.tar.gz \
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+      /opt/pkgs/spatstat.utils_3.1-0.tar.gz \
+      /opt/pkgs/spatstat.data_3.0-0.tar.gz \
+      /opt/pkgs/deldir_2.0-4.tar.gz \
+      /opt/pkgs/polyclip_1.10-7.tar.gz \
+      /opt/pkgs/spatstat.univar_2.0-3.tar.gz \
+      /opt/pkgs/spatstat.geom_3.0-3.tar.gz \
+      /opt/pkgs/spatstat.random_2.2-0.tar.gz \
+      /opt/pkgs/abind_1.4-5.tar.gz \
+      /opt/pkgs/tensor_1.5.tar.gz \
+      /opt/pkgs/goftest_1.2-3.tar.gz \
+      /opt/pkgs/spatstat.sparse_3.1-0.tar.gz 
+
+#      /opt/pkgs/spatstat.explore_3.0-3.tar.gz \
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+      /opt/pkgs/spatstat.core_2.4-2.tar.gz \
+      /opt/pkgs/spatstat.linnet_2.2-1.tar.gz 
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/RSpectra_0.16-1.tar.gz \
+ /opt/pkgs/dotCall64_1.1-1.tar.gz \
+ /opt/pkgs/spam_2.11-0.tar.gz  \
+ /opt/pkgs/RcppHNSW_0.4.1.tar.gz \
+ /opt/pkgs/leidenbase_0.1.30.tar.gz 
+
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/fastDummies_1.7.3.tar.gz \
+ /opt/pkgs/sp_1.5-0.tar.gz \
+ /opt/pkgs/rgeos_0.5-9.tar.gz \
+ /opt/pkgs/SeuratObject_4.1.1.tar.gz \
+ /opt/pkgs/Seurat_4.1.1.tar.gz \
+ /opt/pkgs/XML_3.99-0.14.tar.gz \
+ /opt/pkgs/anndata_0.7.5.2.tar.gz \
+ /opt/pkgs/annotate_1.72.0.tar.gz \
+ /opt/pkgs/ash_1.0-15.tar.gz 
+
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/beeswarm_0.4.0.tar.gz \
+ /opt/pkgs/filelock_1.0.3.tar.gz \
+ /opt/pkgs/BiocFileCache_2.2.1.tar.gz \
+ /opt/pkgs/BiocManager_1.30.26.tar.gz \
+ /opt/pkgs/BiocNeighbors_1.12.0.tar.gz \
+ /opt/pkgs/BiocVersion_3.14.0.tar.gz \
+ /opt/pkgs/bluster_1.4.0.tar.gz \
+ /opt/pkgs/bslib_0.5.0.tar.gz \
+ /opt/pkgs/cachem_1.1.0.tar.gz \
+ /opt/pkgs/Cairo_1.6-0.tar.gz \
+ /opt/pkgs/desc_1.4.2.tar.gz \
+ /opt/pkgs/pkgload_1.3.0.tar.gz \
+ /opt/pkgs/brio_1.1.3.tar.gz
+
+#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/BiocManager_1.30.26.tar.gz
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/zip_2.3.3.tar.gz \
+ /opt/pkgs/openxlsx_4.2.5.2.tar.gz \
+ /opt/pkgs/praise_1.0.0.tar.gz \
+ /opt/pkgs/diffobj_0.3.5.tar.gz \
+ /opt/pkgs/waldo_0.5.1.tar.gz \
+ /opt/pkgs/testthat_3.1.6.tar.gz \
+ /opt/pkgs/nloptr_2.0.3.tar.gz \
+ /opt/pkgs/minqa_1.2.5.tar.gz \
+ /opt/pkgs/lme4_1.1-33.tar.gz \
+ /opt/pkgs/MatrixModels_0.5-1.tar.gz \
+ /opt/pkgs/SparseM_1.81.tar.gz \
+ /opt/pkgs/quantreg_5.95.tar.gz \
+ /opt/pkgs/numDeriv_2016.8-1.1.tar.gz \
+ /opt/pkgs/pbkrtest_0.5.2.tar.gz \
+ /opt/pkgs/maptools_1.1-7.tar.gz \
+ /opt/pkgs/carData_3.0-5.tar.gz \
+ /opt/pkgs/rio_0.5.29.tar.gz \
+ /opt/pkgs/car_3.0-0.tar.gz 
+
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/pROC_1.18.2.tar.gz \
+ /opt/pkgs/proxy_0.4-27.tar.gz \
+ /opt/pkgs/e1071_1.7-13.tar.gz \
+ /opt/pkgs/ModelMetrics_1.2.2.2.tar.gz \
+ /opt/pkgs/SummarizedExperiment_1.24.0.tar.gz \
+ /opt/pkgs/SingleCellExperiment_1.16.0.tar.gz 
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/clock_0.7.0.tar.gz \
+ /opt/pkgs/shinyjs_2.1.0.tar.gz \
+ /opt/pkgs/colourpicker_1.2.0.tar.gz \
+ /opt/pkgs/combinat_0.0-8.tar.gz \
+ /opt/pkgs/conquer_1.3.3.tar.gz \
+ /opt/pkgs/corrplot_0.92.tar.gz \
+ /opt/pkgs/cpp11_0.4.7.tar.gz \
+ /opt/pkgs/diagram_1.6.5.tar.gz \
+ /opt/pkgs/DT_0.28.tar.gz \
+ /opt/pkgs/Rttf2pt1_1.3.12.tar.gz \
+ /opt/pkgs/extrafontdb_1.0.tar.gz \
+ /opt/pkgs/extrafont_0.18.tar.gz \
+ /opt/pkgs/vipor_0.4.7.tar.gz \
+ /opt/pkgs/ggbeeswarm_0.7.2.tar.gz \
+ /opt/pkgs/ggrastr_1.0.2.tar.gz \
+ /opt/pkgs/fastICA_1.2-3.tar.gz \
+ /opt/pkgs/gdata_2.18.0.1.tar.gz \
+ /opt/pkgs/ggExtra_0.10.1.tar.gz
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/ggsci_3.0.0.tar.gz \
+ /opt/pkgs/ggsignif_0.6.3.tar.gz \
+ /opt/pkgs/gower_1.0.1.tar.gz \
+ /opt/pkgs/graph_1.72.0.tar.gz \
+ /opt/pkgs/gridBase_0.4-7.tar.gz \
+ /opt/pkgs/GSEABase_1.56.0.tar.gz \
+ /opt/pkgs/hardhat_1.3.0.tar.gz \
+ /opt/pkgs/RhpcBLASctl_0.23-42.tar.gz \
+ /opt/pkgs/hdf5r_1.3.5.tar.gz \
+ /opt/pkgs/hexbin_1.28.3.tar.gz \
+ /opt/pkgs/interactiveDisplayBase_1.32.0.tar.gz \
+ /opt/pkgs/survival_3.2-13.tar.gz \
+ /opt/pkgs/MASS_7.3.55-tar.gz \
+ /opt/pkgs/SQUAREM_2021.1.tar.gz \
+ /opt/pkgs/lava_1.7.2.1.tar.gz \
+ /opt/pkgs/lobstr_1.1.2.tar.gz \
+ /opt/pkgs/lsei_1.3-0.tar.gz \
+ /opt/pkgs/markdown_1.13.tar.gz \
+ /opt/pkgs/MAST_1.20.0.tar.gz 
+
+# /opt/pkgs/zip_2.3.3.tar.gz \
+
+RUN set -eux; \
+    R CMD INSTALL -l /usr/local/lib/R/site-library \
+ /opt/pkgs/lpSolve_5.6.16.tar.gz \
+ /opt/pkgs/mclust_6.0.0.tar.gz \
+ /opt/pkgs/metapod_1.2.0.tar.gz \
+ /opt/pkgs/npsurv_0.5-0.tar.gz \
+ /opt/pkgs/pheatmap_1.0.12.tar.gz \
+ /opt/pkgs/polynom_1.4-1.tar.gz \
+ /opt/pkgs/proj4_1.0-12.tar.gz \
+ /opt/pkgs/pryr_0.1.5.tar.gz \
+ /opt/pkgs/ps_1.8.1.tar.gz \
+ /opt/pkgs/RcppParallel_5.1.6.tar.gz \
+ /opt/pkgs/Rhdf5lib_1.16.0.tar.gz \
+ /opt/pkgs/rstatix_0.7.0.tar.gz \
+ /opt/pkgs/scuttle_1.4.0.tar.gz
+
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/scater_1.22.0.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/statmod_1.5.0.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/scran_1.22.1.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/SingleR_1.8.1.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/svglite_2.1.0.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/svMisc_1.2.3.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/sys_3.4.2.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/timeDate_4022.108.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/TrajectoryUtils_1.2.0.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/TSCAN_1.32.0.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/xts_0.12.2.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/TTR_0.24.3.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/xml2_1.3.3.tar.gz
+
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/maps_3.4.1.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/ggpubr_0.4.0.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/harmony_0.1.1.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/prodlim_2023.03.31.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/ipred_0.9-14.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/recipes_1.0.6.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/caret_6.0-94.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/quantmod_0.4.20.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/rhdf5filters_1.6.0.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/rhdf5_2.38.1.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/HDF5Array_1.22.1.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/GSVA_1.42.0.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/AnnotationHub_3.2.2.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/ExperimentHub_2.2.1.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/celldex_1.4.0.tar.gz
+
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/xgboost_1.7.8.1.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/scDblFinder_1.8.0.tar.gz
+# new
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/profvis_0.3.7.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/sessioninfo_1.2.3.tar.gz
+
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/downlit_0.4.2.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/whisker_0.4.1.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/pkgdown_2.0.7.tar.gz
+
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/pkgbuild_1.4.8.tar.gz
+
+
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/brew_1.0-8.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/roxygen2_7.2.3.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/urlchecker_1.0.1.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/rversions_2.1.2.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/xopen_1.0.0.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/rcmdcheck_1.4.0.tar.gz
+
+
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/credentials_1.3.2.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/gert_1.9.2.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/gitcreds_0.1.2.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/httr2_0.2.3.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/ini_0.3.1.tar.gz
+
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/gh_1.4.0.tar.gz
+
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/usethis_3.1.0.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/devtools_2.4.5.tar.gz
+
+#deprecated
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/ggalt_0.4.0.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/EnhancedVolcano_1.12.0.tar.gz
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/nidapFunctions_0.7.8.tar.gz
+
+# RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/SparseArray_1.2.0.tar.gz
+
+# _______ end 
+
+# hold off for now 
+#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/SCWorkflow_NA.tar.gz
+
+# hard  - difficult dependencies
+#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/litedown_0.1.tar.gz
+#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/litedown_0.7.tar.gz
+#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/SparseArray_1.8.0.tar.gz
+# genomation ?  what for? it's just data for genomation
+#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/genomationData_1.24.0.tar.gz
+
+# not quite version ... use older version 
+#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/xgboost_1.7.8.1.tar.gz
+
+# RUN R -e "install.packages('https://github.com/NIDAP-Community/nidapFunctions/raw/main/nidapFunctions_0.7.8.tar.gz', repos=NULL)"
+
+# problems:
+# RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/vector_0.0.2.tar.gz   NO 
+# RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/arrow_4.0.1.tar.gz   NO 
+# RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/FoundryObjects_0.86.0.tar.gz   NO 
+# RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/FoundrySparkR_0.2.0.tar.gz   NO 
+# RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/SparkR_3.4.1.tar.gz   NO 
+
+#dupes:
+# /opt/pkgs/viridis_0.6.5.tar.gz \
+# RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/plotly_4.10.4.tar.gz
+# RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/dplyr_1.1.4.tar.gz
+#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/GenomeInfoDbData_1.2.7.tar.gz
+
+#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/SCWorkflow_NA.tar.gz
+
+RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/remotes_2.5.0.tar.gz
+#        RUN R -e "remotes::install_github('NIDAP-Community/SCWorkflow/tree/GalaxyCLI')"
+# worked RUN R -e "remotes::install_github('https://github.com/NIDAP-Community/SCWorkflow/tree/GalaxyCLI')"
+
+RUN R -e "remotes::install_github('NIDAP-Community/SCWorkflow', ref = 'GalaxyCLI')"
+
+COPY Dockerfile /
+
+RUN rm -rf /opt/pkgs
+
+

From 66f9f47cc939ceb4069f2e558ebc700748504afa Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 17 Feb 2026 16:42:54 -0500
Subject: [PATCH 14/18] chore(docker): switch to use remotes::install_version
 instead of biowulf pkgs

---
 Dockerfile | 1041 ++++++++++++++++++++++------------------------------
 1 file changed, 448 insertions(+), 593 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 51230bc..f08ed89 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -33,9 +33,6 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
 RUN pip3 install --no-cache-dir igraph "leidenalg==0.10.0" numpy
 
 WORKDIR /home/rstudio
-# Copy your local tarballs (ensure PACKAGESS is in the build context)
-
-COPY PACKAGESS/ /opt/pkgs/
 
 # Remove any spatstat* that might be preinstalled in the rocker image
 RUN R -q -e " \
@@ -48,598 +45,456 @@ RUN R -q -e " \
     } \
   }"
 
+# Install packages with specific versions from CRAN and Bioconductor
+RUN R --vanilla --slave -e " \
+  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) \
+    }) \
+  }; \
+  \
+  message('All packages installed successfully')"
+
+
+# Additional packages that need special installation
+
+# Install SCWorkflow from GitHub
+RUN R --vanilla --slave -e "remotes::install_github('NIDAP-Community/SCWorkflow', ref = 'GalaxyCLI', quiet = TRUE)"
+
+# Install spatstat family packages with specific versions
+RUN R --vanilla --slave -e " \
+  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) \
+    }) \
+  }"
 
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/bitops_1.0-8.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/RCurl_1.98-1.14.tar.gz
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/GlobalOptions_0.1.2.tar.gz \
- /opt/pkgs/bit_4.0.4.tar.gz \
- /opt/pkgs/BiocGenerics_0.40.0.tar.gz 
-
-#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/RCurl_1.98.1.16.tar.gz
-#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/RCurl_1.98.1.12.tar.gz
-
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/assertthat_0.2.1.tar.gz \
- /opt/pkgs/Biobase_2.54.0.tar.gz \
- /opt/pkgs/bit64_4.0.5.tar.gz \
- /opt/pkgs/shape_1.4.6.tar.gz
-
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/remotes_2.5.0.tar.gz
-RUN R -e "remotes::install_github('NIDAP-Community/SCWorkflow', ref = 'GalaxyCLI')"
-
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/colorspace_2.0-3.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/circlize_0.4.15.tar.gz
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/rlang_1.1.4.tar.gz \
- /opt/pkgs/cli_3.6.3.tar.gz \
- /opt/pkgs/glue_1.7.0.tar.gz 
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/lifecycle_1.0.4.tar.gz \
- /opt/pkgs/vctrs_0.6.5.tar.gz \
- /opt/pkgs/blob_1.2.3.tar.gz \
- /opt/pkgs/clue_0.3-61.tar.gz \
- /opt/pkgs/cluster_2.1.2.tar.gz \
- /opt/pkgs/codetools_0.2-18.tar.gz \
- /opt/pkgs/crayon_1.5.3.tar.gz \
- /opt/pkgs/data.table_1.15.4.tar.gz \
- /opt/pkgs/DBI_1.2.3.tar.gz
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/dendsort_0.3.4.tar.gz \
- /opt/pkgs/digest_0.6.37.tar.gz \
- /opt/pkgs/ellipsis_0.3.2.tar.gz \
- /opt/pkgs/evaluate_0.24.0.tar.gz \
- /opt/pkgs/fansi_1.0.6.tar.gz \
- /opt/pkgs/farver_2.1.1.tar.gz \
- /opt/pkgs/fastmap_1.2.0.tar.gz \
- /opt/pkgs/cachem_1.1.0.tar.gz \
- /opt/pkgs/fastmatch_1.1-3.tar.gz \
- /opt/pkgs/iterators_1.0.14.tar.gz \
- /opt/pkgs/foreach_1.5.2.tar.gz \
- /opt/pkgs/formatR_1.14.tar.gz
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/generics_0.1.3.tar.gz \
- /opt/pkgs/rjson_0.2.21.tar.gz \
- /opt/pkgs/GetoptLong_1.0.5.tar.gz \
- /opt/pkgs/gtable_0.3.5.tar.gz \
- /opt/pkgs/labeling_0.4.2.tar.gz \
- /opt/pkgs/munsell_0.5.0.tar.gz \
- /opt/pkgs/R6_2.5.1.tar.gz \
- /opt/pkgs/gridExtra_2.3.tar.gz \
- /opt/pkgs/RColorBrewer_1.1-3.tar.gz \
- /opt/pkgs/utf8_1.2.4.tar.gz \
- /opt/pkgs/pillar_1.9.0.tar.gz 
-
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/pkgconfig_2.0.3.tar.gz \
- /opt/pkgs/viridisLite_0.4.1.tar.gz \
- /opt/pkgs/scales_1.2.1.tar.gz \
- /opt/pkgs/withr_3.0.1.tar.gz \
- /opt/pkgs/gtools_3.9.5.tar.gz \
- /opt/pkgs/gridGraphics_0.5-1.tar.gz \
- /opt/pkgs/hms_1.1.2.tar.gz \
- /opt/pkgs/S4Vectors_0.32.4.tar.gz \
- /opt/pkgs/IRanges_2.28.0.tar.gz \
- /opt/pkgs/irlba_2.3.5.1.tar.gz \
- /opt/pkgs/jsonlite_1.8.8.tar.gz 
-
-# /opt/pkgs/jsonlite_1.8.8.tar.gz
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/png_0.1-7.tar.gz \
- /opt/pkgs/KernSmooth_2.23-20.tar.gz  \
- /opt/pkgs/lambda.r_1.2.4.tar.gz \
- /opt/pkgs/lattice_0.20-45.tar.gz  \
- /opt/pkgs/lazyeval_0.2.2.tar.gz \
- /opt/pkgs/limma_3.50.3.tar.gz \
- /opt/pkgs/locfit_1.5-9.9.tar.gz \
- /opt/pkgs/Matrix_1.5-1.tar.gz \
- /opt/pkgs/matrixStats_0.62.0.tar.gz \
- /opt/pkgs/MatrixGenerics_1.6.0.tar.gz \
- /opt/pkgs/memoise_2.0.1.tar.gz \
- /opt/pkgs/mgcv_1.8-39.tar.gz
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/nlme_3.1-155.tar.gz \
- /opt/pkgs/rsvd_1.0.5.tar.gz \
- /opt/pkgs/DelayedArray_0.20.0.tar.gz \
- /opt/pkgs/Rcpp_1.0.13.tar.gz \
- /opt/pkgs/sparseMatrixStats_1.6.0.tar.gz \
- /opt/pkgs/DelayedMatrixStats_1.16.0.tar.gz \
- /opt/pkgs/ScaledMatrix_1.2.0.tar.gz \
- /opt/pkgs/uuid_1.1-0.tar.gz \
- /opt/pkgs/xfun_0.47.tar.gz \
- /opt/pkgs/xtable_1.8-4.tar.gz \
- /opt/pkgs/zlibbioc_1.40.0.tar.gz \
- /opt/pkgs/XVector_0.34.0.tar.gz
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/yaml_2.3.10.tar.gz \
- /opt/pkgs/GenomeInfoDbData_1.2.7.tar.gz \
- /opt/pkgs/GenomeInfoDb_1.30.1.tar.gz \
- /opt/pkgs/beachmat_2.10.0.tar.gz \
- /opt/pkgs/doParallel_1.0.17.tar.gz \
- /opt/pkgs/edgeR_3.36.0.tar.gz \
- /opt/pkgs/futile.options_1.0.1.tar.gz \
- /opt/pkgs/futile.logger_1.4.3.tar.gz \
- /opt/pkgs/GenomicRanges_1.46.1.tar.gz \
- /opt/pkgs/base64enc_0.1-3.tar.gz \
- /opt/pkgs/htmltools_0.5.8.1.tar.gz \
- /opt/pkgs/rappdirs_0.3.3.tar.gz
-
-#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/tinytex_0.45.tar.gz
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/jquerylib_0.1.4.tar.gz \
- /opt/pkgs/tinytex_0.44.tar.gz \
- /opt/pkgs/fs_1.6.4.tar.gz \
- /opt/pkgs/sass_0.4.6.tar.gz \
- /opt/pkgs/mime_0.12.tar.gz \
- /opt/pkgs/bslib_0.4.2.tar.gz \
- /opt/pkgs/magrittr_2.0.3.tar.gz \
- /opt/pkgs/stringi_1.8.4.tar.gz \
- /opt/pkgs/stringr_1.5.1.tar.gz \
- /opt/pkgs/highr_0.10.tar.gz \
- /opt/pkgs/knitr_1.48.tar.gz \
- /opt/pkgs/fontawesome_0.5.1.tar.gz
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/rmarkdown_2.28.tar.gz \
- /opt/pkgs/htmlwidgets_1.6.4.tar.gz \
- /opt/pkgs/sys_3.4.1.tar.gz \
- /opt/pkgs/askpass_1.1.tar.gz \
- /opt/pkgs/openssl_2.0.5.tar.gz \
- /opt/pkgs/curl_6.4.0.tar.gz \
- /opt/pkgs/httr_1.4.7.tar.gz \
- /opt/pkgs/Biostrings_2.62.0.tar.gz \
- /opt/pkgs/cpp11_0.4.7.tar.gz \
- /opt/pkgs/timechange_0.2.0.tar.gz
-
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/lubridate_1.8.0.tar.gz \
- /opt/pkgs/isoband_0.2.7.tar.gz \
- /opt/pkgs/tibble_3.2.1.tar.gz \
- /opt/pkgs/ggplot2_3.3.6.tar.gz \
- /opt/pkgs/patchwork_1.2.0.tar.gz \
- /opt/pkgs/later_1.3.2.tar.gz \
- /opt/pkgs/promises_1.3.0.tar.gz \
- /opt/pkgs/crosstalk_1.2.0.tar.gz \
- /opt/pkgs/purrr_1.0.2.tar.gz \
- /opt/pkgs/tidyselect_1.2.1.tar.gz \
- /opt/pkgs/dplyr_1.1.4.tar.gz \
- /opt/pkgs/tidyr_1.2.1.tar.gz
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/plotly_4.10.4.tar.gz \
- /opt/pkgs/plyr_1.8.7.tar.gz \
- /opt/pkgs/clipr_0.8.0.tar.gz \
- /opt/pkgs/prettyunits_1.1.1.tar.gz \
- /opt/pkgs/progress_1.2.2.tar.gz \
- /opt/pkgs/tzdb_0.4.0.tar.gz \
- /opt/pkgs/vroom_1.6.3.tar.gz \
- /opt/pkgs/readr_2.1.2.tar.gz \
- /opt/pkgs/reshape2_1.4.4.tar.gz \
- /opt/pkgs/plogr_0.2.0.tar.gz \
- /opt/pkgs/RSQLite_2.3.9.tar.gz \
- /opt/pkgs/systemfonts_1.2.3.tar.gz
-
-
-# /opt/pkgs/vroom_1.6.1.tar.gz \
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/textshaping_0.3.6.tar.gz \
- /opt/pkgs/ragg_1.2.5.tar.gz \
- /opt/pkgs/dbplyr_2.2.1.tar.gz \
- /opt/pkgs/rstudioapi_0.14.tar.gz \
- /opt/pkgs/dtplyr_1.3.1.tar.gz \
- /opt/pkgs/backports_1.4.1.tar.gz \
- /opt/pkgs/broom_1.0.1.tar.gz \
- /opt/pkgs/ps_1.8.1.tar.gz \
- /opt/pkgs/processx_3.8.5.tar.gz \
- /opt/pkgs/callr_3.7.3.tar.gz \
- /opt/pkgs/reprex_2.0.2.tar.gz \
- /opt/pkgs/modelr_0.1.9.tar.gz
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/conflicted_1.2.0.tar.gz \
- /opt/pkgs/rematch2_2.1.2.tar.gz \
- /opt/pkgs/gargle_1.3.0.tar.gz \
- /opt/pkgs/rematch_1.0.1.tar.gz \
- /opt/pkgs/cellranger_1.1.0.tar.gz \
- /opt/pkgs/ids_1.0.1.tar.gz \
- /opt/pkgs/googledrive_2.0.0.tar.gz \
- /opt/pkgs/googlesheets4_1.0.1.tar.gz \
- /opt/pkgs/readxl_1.4.1.tar.gz \
- /opt/pkgs/selectr_0.4-2.tar.gz \
- /opt/pkgs/xml2_1.3.3.tar.gz \
- /opt/pkgs/rvest_1.0.3.tar.gz \
- /opt/pkgs/forcats_0.5.2.tar.gz \
- /opt/pkgs/haven_2.5.1.tar.gz \
- /opt/pkgs/tidyverse_1.3.2.tar.gz 
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/KEGGREST_1.34.0.tar.gz \
- /opt/pkgs/AnnotationDbi_1.56.2.tar.gz \
- /opt/pkgs/snow_0.4-4.tar.gz \
- /opt/pkgs/BH_1.81.0-1.tar.gz \
- /opt/pkgs/BiocParallel_1.28.3.tar.gz \
- /opt/pkgs/BiocSingular_1.10.0.tar.gz \
- /opt/pkgs/ComplexHeatmap_2.10.0.tar.gz \
- /opt/pkgs/viridis_0.6.5.tar.gz
-
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/dendextend_1.16.0.tar.gz \
- /opt/pkgs/fgsea_1.20.0.tar.gz \
- /opt/pkgs/ggrepel_0.9.5.tar.gz \
- /opt/pkgs/l2p_0.0-13.tar.gz  \
- /opt/pkgs/l2psupp_0.0-13.tar.gz  \
- /opt/pkgs/ica_1.0-3.tar.gz \
- /opt/pkgs/Rtsne_0.16.tar.gz \
- /opt/pkgs/ggridges_0.5.3.tar.gz \
- /opt/pkgs/scattermore_1.2.tar.gz \
- /opt/pkgs/listenv_0.9.1.tar.gz \
- /opt/pkgs/globals_0.16.3.tar.gz \
- /opt/pkgs/parallelly_1.38.0.tar.gz 
-
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/future_1.34.0.tar.gz \
- /opt/pkgs/future.apply_1.11.2.tar.gz \
- /opt/pkgs/RcppEigen_0.3.3.9.3.tar.gz \
- /opt/pkgs/RcppAnnoy_0.0.19.tar.gz \
- /opt/pkgs/zoo_1.8-12.tar.gz \
- /opt/pkgs/lmtest_0.9-40.tar.gz \
- /opt/pkgs/fitdistrplus_1.1-8.tar.gz 
-
- # /opt/pkgs/gplots_3.1.3.tar.gz \
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/caTools_1.18.2.tar.gz \
- /opt/pkgs/gplots_3.1.3.tar.gz \
- /opt/pkgs/ROCR_1.0-11.tar.gz \
- /opt/pkgs/igraph_2.0.3.tar.gz \
- /opt/pkgs/pbapply_1.5-0.tar.gz \
- /opt/pkgs/commonmark_1.9.0.tar.gz \
- /opt/pkgs/httpuv_1.6.15.tar.gz \
- /opt/pkgs/sourcetools_0.1.7-1.tar.gz \
- /opt/pkgs/shiny_1.9.1.tar.gz \
- /opt/pkgs/miniUI_0.1.1.1.tar.gz
-
-#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/igraph_2.0.3.tar.gz
-
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/progressr_0.14.0.tar.gz \
- /opt/pkgs/sitmo_2.0.2.tar.gz \
- /opt/pkgs/dqrng_0.4.1.tar.gz \
- /opt/pkgs/FNN_1.1.3.2.tar.gz \
- /opt/pkgs/RcppProgress_0.4.2.tar.gz \
- /opt/pkgs/uwot_0.1.14.tar.gz \
- /opt/pkgs/cowplot_1.1.1.tar.gz 
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/RcppTOML_0.2.2.tar.gz \
- /opt/pkgs/rprojroot_2.0.4.tar.gz \
- /opt/pkgs/here_1.0.1.tar.gz \
- /opt/pkgs/reticulate_1.40.0.tar.gz \
- /opt/pkgs/leiden_0.4.3.tar.gz \
- /opt/pkgs/RANN_2.6.1.tar.gz \
- /opt/pkgs/RcppArmadillo_0.12.4.0.0.tar.gz \
- /opt/pkgs/sctransform_0.3.4.tar.gz
-
-# see https://github.com/satijalab/seurat/issues/8948
-#devtools::install_version("spatstat.core", version = "2.4-0", repos='http://cran.us.r-project.org')
-#devtools::install_version("spatstat.data", version = "2.1-2", repos='http://cran.us.r-project.org')
-#devtools::install_version("spatstat.geom", version = "2.3-2", repos='http://cran.us.r-project.org')
-#devtools::install_version("spatstat.random", version = "2.1-0", repos='http://cran.us.r-project.org')
-
-# old - phils spec ...
-# /opt/pkgs/spatstat.core_2.4-4.tar.gz \
-# /opt/pkgs/spatstat.data_3.1-2.tar.gz \
-# /opt/pkgs/spatstat.geom_3.3-2.tar.gz \
-# /opt/pkgs/spatstat.random_3.3-1.tar.gz \
-# /opt/pkgs/spatstat.explore_3.1-0.tar.gz \
-# /opt/pkgs/spatstat.univar_3.0-0.tar.gz \
-
-#      /opt/pkgs/spatstat.geom_3.2-1.tar.gz \
-#      /opt/pkgs/spatstat.data_3.1-2.tar.gz \
-#      /opt/pkgs/spatstat.data_2.1-2.tar.gz \
-#      /opt/pkgs/spatstat.random_3.1-5.tar.gz \
-#      /opt/pkgs/spatstat.geom_2.3-2.tar.gz \
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
-      /opt/pkgs/spatstat.utils_3.1-0.tar.gz \
-      /opt/pkgs/spatstat.data_3.0-0.tar.gz \
-      /opt/pkgs/deldir_2.0-4.tar.gz \
-      /opt/pkgs/polyclip_1.10-7.tar.gz \
-      /opt/pkgs/spatstat.univar_2.0-3.tar.gz \
-      /opt/pkgs/spatstat.geom_3.0-3.tar.gz \
-      /opt/pkgs/spatstat.random_2.2-0.tar.gz \
-      /opt/pkgs/abind_1.4-5.tar.gz \
-      /opt/pkgs/tensor_1.5.tar.gz \
-      /opt/pkgs/goftest_1.2-3.tar.gz \
-      /opt/pkgs/spatstat.sparse_3.1-0.tar.gz 
-
-#      /opt/pkgs/spatstat.explore_3.0-3.tar.gz \
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
-      /opt/pkgs/spatstat.core_2.4-2.tar.gz \
-      /opt/pkgs/spatstat.linnet_2.2-1.tar.gz 
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/RSpectra_0.16-1.tar.gz \
- /opt/pkgs/dotCall64_1.1-1.tar.gz \
- /opt/pkgs/spam_2.11-0.tar.gz  \
- /opt/pkgs/RcppHNSW_0.4.1.tar.gz \
- /opt/pkgs/leidenbase_0.1.30.tar.gz 
-
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/fastDummies_1.7.3.tar.gz \
- /opt/pkgs/sp_1.5-0.tar.gz \
- /opt/pkgs/rgeos_0.5-9.tar.gz \
- /opt/pkgs/SeuratObject_4.1.1.tar.gz \
- /opt/pkgs/Seurat_4.1.1.tar.gz \
- /opt/pkgs/XML_3.99-0.14.tar.gz \
- /opt/pkgs/anndata_0.7.5.2.tar.gz \
- /opt/pkgs/annotate_1.72.0.tar.gz \
- /opt/pkgs/ash_1.0-15.tar.gz 
-
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/beeswarm_0.4.0.tar.gz \
- /opt/pkgs/filelock_1.0.3.tar.gz \
- /opt/pkgs/BiocFileCache_2.2.1.tar.gz \
- /opt/pkgs/BiocManager_1.30.26.tar.gz \
- /opt/pkgs/BiocNeighbors_1.12.0.tar.gz \
- /opt/pkgs/BiocVersion_3.14.0.tar.gz \
- /opt/pkgs/bluster_1.4.0.tar.gz \
- /opt/pkgs/bslib_0.5.0.tar.gz \
- /opt/pkgs/cachem_1.1.0.tar.gz \
- /opt/pkgs/Cairo_1.6-0.tar.gz \
- /opt/pkgs/desc_1.4.2.tar.gz \
- /opt/pkgs/pkgload_1.3.0.tar.gz \
- /opt/pkgs/brio_1.1.3.tar.gz
-
-#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/BiocManager_1.30.26.tar.gz
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/zip_2.3.3.tar.gz \
- /opt/pkgs/openxlsx_4.2.5.2.tar.gz \
- /opt/pkgs/praise_1.0.0.tar.gz \
- /opt/pkgs/diffobj_0.3.5.tar.gz \
- /opt/pkgs/waldo_0.5.1.tar.gz \
- /opt/pkgs/testthat_3.1.6.tar.gz \
- /opt/pkgs/nloptr_2.0.3.tar.gz \
- /opt/pkgs/minqa_1.2.5.tar.gz \
- /opt/pkgs/lme4_1.1-33.tar.gz \
- /opt/pkgs/MatrixModels_0.5-1.tar.gz \
- /opt/pkgs/SparseM_1.81.tar.gz \
- /opt/pkgs/quantreg_5.95.tar.gz \
- /opt/pkgs/numDeriv_2016.8-1.1.tar.gz \
- /opt/pkgs/pbkrtest_0.5.2.tar.gz \
- /opt/pkgs/maptools_1.1-7.tar.gz \
- /opt/pkgs/carData_3.0-5.tar.gz \
- /opt/pkgs/rio_0.5.29.tar.gz \
- /opt/pkgs/car_3.0-0.tar.gz 
-
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/pROC_1.18.2.tar.gz \
- /opt/pkgs/proxy_0.4-27.tar.gz \
- /opt/pkgs/e1071_1.7-13.tar.gz \
- /opt/pkgs/ModelMetrics_1.2.2.2.tar.gz \
- /opt/pkgs/SummarizedExperiment_1.24.0.tar.gz \
- /opt/pkgs/SingleCellExperiment_1.16.0.tar.gz 
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/clock_0.7.0.tar.gz \
- /opt/pkgs/shinyjs_2.1.0.tar.gz \
- /opt/pkgs/colourpicker_1.2.0.tar.gz \
- /opt/pkgs/combinat_0.0-8.tar.gz \
- /opt/pkgs/conquer_1.3.3.tar.gz \
- /opt/pkgs/corrplot_0.92.tar.gz \
- /opt/pkgs/cpp11_0.4.7.tar.gz \
- /opt/pkgs/diagram_1.6.5.tar.gz \
- /opt/pkgs/DT_0.28.tar.gz \
- /opt/pkgs/Rttf2pt1_1.3.12.tar.gz \
- /opt/pkgs/extrafontdb_1.0.tar.gz \
- /opt/pkgs/extrafont_0.18.tar.gz \
- /opt/pkgs/vipor_0.4.7.tar.gz \
- /opt/pkgs/ggbeeswarm_0.7.2.tar.gz \
- /opt/pkgs/ggrastr_1.0.2.tar.gz \
- /opt/pkgs/fastICA_1.2-3.tar.gz \
- /opt/pkgs/gdata_2.18.0.1.tar.gz \
- /opt/pkgs/ggExtra_0.10.1.tar.gz
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/ggsci_3.0.0.tar.gz \
- /opt/pkgs/ggsignif_0.6.3.tar.gz \
- /opt/pkgs/gower_1.0.1.tar.gz \
- /opt/pkgs/graph_1.72.0.tar.gz \
- /opt/pkgs/gridBase_0.4-7.tar.gz \
- /opt/pkgs/GSEABase_1.56.0.tar.gz \
- /opt/pkgs/hardhat_1.3.0.tar.gz \
- /opt/pkgs/RhpcBLASctl_0.23-42.tar.gz \
- /opt/pkgs/hdf5r_1.3.5.tar.gz \
- /opt/pkgs/hexbin_1.28.3.tar.gz \
- /opt/pkgs/interactiveDisplayBase_1.32.0.tar.gz \
- /opt/pkgs/survival_3.2-13.tar.gz \
- /opt/pkgs/MASS_7.3.55-tar.gz \
- /opt/pkgs/SQUAREM_2021.1.tar.gz \
- /opt/pkgs/lava_1.7.2.1.tar.gz \
- /opt/pkgs/lobstr_1.1.2.tar.gz \
- /opt/pkgs/lsei_1.3-0.tar.gz \
- /opt/pkgs/markdown_1.13.tar.gz \
- /opt/pkgs/MAST_1.20.0.tar.gz 
-
-# /opt/pkgs/zip_2.3.3.tar.gz \
-
-RUN set -eux; \
-    R CMD INSTALL -l /usr/local/lib/R/site-library \
- /opt/pkgs/lpSolve_5.6.16.tar.gz \
- /opt/pkgs/mclust_6.0.0.tar.gz \
- /opt/pkgs/metapod_1.2.0.tar.gz \
- /opt/pkgs/npsurv_0.5-0.tar.gz \
- /opt/pkgs/pheatmap_1.0.12.tar.gz \
- /opt/pkgs/polynom_1.4-1.tar.gz \
- /opt/pkgs/proj4_1.0-12.tar.gz \
- /opt/pkgs/pryr_0.1.5.tar.gz \
- /opt/pkgs/ps_1.8.1.tar.gz \
- /opt/pkgs/RcppParallel_5.1.6.tar.gz \
- /opt/pkgs/Rhdf5lib_1.16.0.tar.gz \
- /opt/pkgs/rstatix_0.7.0.tar.gz \
- /opt/pkgs/scuttle_1.4.0.tar.gz
-
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/scater_1.22.0.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/statmod_1.5.0.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/scran_1.22.1.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/SingleR_1.8.1.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/svglite_2.1.0.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/svMisc_1.2.3.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/sys_3.4.2.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/timeDate_4022.108.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/TrajectoryUtils_1.2.0.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/TSCAN_1.32.0.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/xts_0.12.2.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/TTR_0.24.3.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/xml2_1.3.3.tar.gz
-
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/maps_3.4.1.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/ggpubr_0.4.0.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/harmony_0.1.1.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/prodlim_2023.03.31.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/ipred_0.9-14.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/recipes_1.0.6.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/caret_6.0-94.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/quantmod_0.4.20.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/rhdf5filters_1.6.0.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/rhdf5_2.38.1.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/HDF5Array_1.22.1.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/GSVA_1.42.0.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/AnnotationHub_3.2.2.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/ExperimentHub_2.2.1.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/celldex_1.4.0.tar.gz
-
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/xgboost_1.7.8.1.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/scDblFinder_1.8.0.tar.gz
-# new
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/profvis_0.3.7.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/sessioninfo_1.2.3.tar.gz
-
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/downlit_0.4.2.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/whisker_0.4.1.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/pkgdown_2.0.7.tar.gz
-
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/pkgbuild_1.4.8.tar.gz
-
-
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/brew_1.0-8.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/roxygen2_7.2.3.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/urlchecker_1.0.1.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/rversions_2.1.2.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/xopen_1.0.0.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/rcmdcheck_1.4.0.tar.gz
-
-
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/credentials_1.3.2.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/gert_1.9.2.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/gitcreds_0.1.2.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/httr2_0.2.3.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/ini_0.3.1.tar.gz
-
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/gh_1.4.0.tar.gz
-
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/usethis_3.1.0.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/devtools_2.4.5.tar.gz
-
-#deprecated
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/ggalt_0.4.0.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/EnhancedVolcano_1.12.0.tar.gz
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/nidapFunctions_0.7.8.tar.gz
-
-# RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/SparseArray_1.2.0.tar.gz
-
-# _______ end 
-
-# hold off for now 
-#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/SCWorkflow_NA.tar.gz
-
-# hard  - difficult dependencies
-#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/litedown_0.1.tar.gz
-#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/litedown_0.7.tar.gz
-#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/SparseArray_1.8.0.tar.gz
-# genomation ?  what for? it's just data for genomation
-#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/genomationData_1.24.0.tar.gz
-
-# not quite version ... use older version 
-#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/xgboost_1.7.8.1.tar.gz
-
-# RUN R -e "install.packages('https://github.com/NIDAP-Community/nidapFunctions/raw/main/nidapFunctions_0.7.8.tar.gz', repos=NULL)"
-
-# problems:
-# RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/vector_0.0.2.tar.gz   NO 
-# RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/arrow_4.0.1.tar.gz   NO 
-# RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/FoundryObjects_0.86.0.tar.gz   NO 
-# RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/FoundrySparkR_0.2.0.tar.gz   NO 
-# RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/SparkR_3.4.1.tar.gz   NO 
-
-#dupes:
-# /opt/pkgs/viridis_0.6.5.tar.gz \
-# RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/plotly_4.10.4.tar.gz
-# RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/dplyr_1.1.4.tar.gz
-#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/GenomeInfoDbData_1.2.7.tar.gz
-
-#RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/SCWorkflow_NA.tar.gz
-
-RUN R CMD INSTALL -l /usr/local/lib/R/site-library /opt/pkgs/remotes_2.5.0.tar.gz
-#        RUN R -e "remotes::install_github('NIDAP-Community/SCWorkflow/tree/GalaxyCLI')"
-# worked RUN R -e "remotes::install_github('https://github.com/NIDAP-Community/SCWorkflow/tree/GalaxyCLI')"
-
-RUN R -e "remotes::install_github('NIDAP-Community/SCWorkflow', ref = 'GalaxyCLI')"
+# Install remaining specialized packages
+RUN R --vanilla --slave -e " \
+  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) \
+    }) \
+  }"
 
 COPY Dockerfile /
 
-RUN rm -rf /opt/pkgs
-
 

From 79e5d3720c457a5d81ce5398af0840308d08b0cd Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 17 Feb 2026 16:52:02 -0500
Subject: [PATCH 15/18] chore(docker): use heredoc syntax to reduce line length

---
 Dockerfile | 883 +++++++++++++++++++++++++++--------------------------
 1 file changed, 445 insertions(+), 438 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index f08ed89..d44695e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -46,263 +46,264 @@ RUN R -q -e " \
   }"
 
 # Install packages with specific versions from CRAN and Bioconductor
-RUN R --vanilla --slave -e " \
-  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) \
-    }) \
-  }; \
-  \
-  message('All packages installed successfully')"
+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)
+  })
+}
+
+message('All packages installed successfully')
+EOF
 
 
 # Additional packages that need special installation
@@ -311,189 +312,195 @@ RUN R --vanilla --slave -e " \
 RUN R --vanilla --slave -e "remotes::install_github('NIDAP-Community/SCWorkflow', ref = 'GalaxyCLI', quiet = TRUE)"
 
 # Install spatstat family packages with specific versions
-RUN R --vanilla --slave -e " \
-  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) \
-    }) \
-  }"
+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 R --vanilla --slave -e " \
-  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) \
-    }) \
-  }"
+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
 
 COPY Dockerfile /
 

From dfb55641c3a85d0ae57ebee43e589a3f93e12bc8 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 18 Feb 2026 11:47:47 -0500
Subject: [PATCH 16/18] ci(docker): install local SCWorkflow

---
 Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index d44695e..e331ac4 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -309,7 +309,8 @@ EOF
 # Additional packages that need special installation
 
 # Install SCWorkflow from GitHub
-RUN R --vanilla --slave -e "remotes::install_github('NIDAP-Community/SCWorkflow', ref = 'GalaxyCLI', quiet = TRUE)"
+COPY . /opt/SCWorkflow
+RUN R --vanilla --slave -e "remotes::install_local('/opt/SCWorkflow', quiet = TRUE, upgrade='never')"
 
 # Install spatstat family packages with specific versions
 RUN cat > /tmp/install_spatstat.R << 'EOFSPAT'

From e65f98a496762378cf765bcbe5aac06e42785f63 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 18 Feb 2026 12:19:59 -0500
Subject: [PATCH 17/18] ci(docker): install dev deps

---
 Dockerfile | 20 +++++++++++++++++---
 1 file changed, 17 insertions(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index e331ac4..6d7ae3b 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -301,8 +301,6 @@ for (pkg in names(bioc_versions)) {
     BiocManager::install(pkg, ask = FALSE, quiet = TRUE)
   })
 }
-
-message('All packages installed successfully')
 EOF
 
 
@@ -310,7 +308,7 @@ EOF
 
 # Install SCWorkflow from GitHub
 COPY . /opt/SCWorkflow
-RUN R --vanilla --slave -e "remotes::install_local('/opt/SCWorkflow', quiet = TRUE, upgrade='never')"
+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'
@@ -503,6 +501,22 @@ 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
 COPY Dockerfile /
 
 

From ec9ee480632beafa167036ad3a2b3036216979e8 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 18 Feb 2026 12:42:10 -0500
Subject: [PATCH 18/18] ci(docker): check that all deps installed

---
 Dockerfile | 28 +++++++++++++++++++++++++++-
 1 file changed, 27 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 6d7ae3b..e957f2a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -517,6 +517,32 @@ for (pkg in dev_dependencies) {
 EOFDEV
 
 RUN R --vanilla --slave --file=/tmp/install_dev_dependencies.R
-COPY Dockerfile /
 
+# 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 /