Update to align with V6.3.5 dev changes

.Rbuildignore

@@ -7,3 +7,7 @@
 ^data$
 ^docs$
 ^pkgdown$
+^\.circleci$
+^\.circleci/config\.yml$
+^\.github$
+^cran-comments\.md$

.circleci/config.yml

@@ -0,0 +1,51 @@
+# Copyright (c) 2024 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
+
+version: 2.1
+
+jobs:
+  dsbase:
+    docker:
+      - image: cimg/base:current
+    resource_class: small
+    steps:
+      - checkout
+      - setup_remote_docker:
+          docker_layout_caching: true
+      - run: |
+          echo "Building"
+          echo "  Repo Name: " $CIRCLE_PROJECT_REPONAME
+          echo "  Branch:    " $CIRCLE_BRANCH
+          echo "  Tag:       " $CIRCLE_TAG
+      - run:
+          command: |
+              sudo apt-get update -y
+              sudo apt-get install -y r-base-core cmake
+      - run:
+          command: |
+              sudo apt-get install -y libxml2-dev
+      - run:
+          command: |
+              echo "options(Ncpus=4)" >> ~/.Rprofile
+              sudo Rscript -e "install.packages('RANN', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('stringr', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('lme4', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('dplyr', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('reshape2', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('polycor', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('splines', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('gamlss', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('gamlss.dist', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('mice', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('childsds', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('xml2', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('covr', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('devtools', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('DSI', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('DSLite', dependencies=TRUE)"
+      - run:
+          command: |
+              sudo Rscript -e 'library(covr); covr::codecov(token = "'$CODECOV_TOKEN'")'
+workflows:
+  build:
+    jobs:
+      - dsbase

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,51 @@
+# 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:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual", "--compact-vignettes=gs+qpdf")'

.github/workflows/dsBase_test_suite.yaml

@@ -0,0 +1,209 @@
+################################################################################
+# DataSHIELD GHA test suite - dsBase
+# Adapted from `azure-pipelines.yml` by Roberto Villegas-Diaz
+#
+# Inside the root directory $(Pipeline.Workspace) will be a file tree like:
+# /dsBase               <- Checked out version of datashield/dsBase
+# /dsBase/logs          <- Where results of tests and logs are collated
+# /testStatus           <- Checked out version of datashield/testStatus
+#
+# As of Jul 2025 this takes ~ 9 mins to run.
+################################################################################
+name: dsBase tests' suite
+
+on:
+  push:
+  schedule:
+    - cron: '0 0 * * 0'   # Weekly
+    - cron: '0 1 * * *'   # Nightly
+
+jobs:
+  dsBase_test_suite:
+    runs-on: ubuntu-latest
+    timeout-minutes: 120
+    permissions:
+      contents: write
+
+    # These should all be constant, except TEST_FILTER. This can be used to test 
+    # subsets of test files in the testthat directory. Options are like:
+    # '*'               <- Run all tests.
+    # 'asNumericDS*'    <- Run all asNumericDS tests, i.e. all the arg, etc. tests.
+    # '*_smk_*'         <- Run all the smoke tests for all functions.
+    env:
+      TEST_FILTER: '*'
+      _r_check_system_clock_: 0
+      WORKFLOW_ID: ${{ github.run_id }}-${{ github.run_attempt }}
+      PROJECT_NAME: dsBase
+      BRANCH_NAME: ${{ github.ref_name }}
+      REPO_OWNER: ${{ github.repository_owner }}
+      R_KEEP_PKG_SOURCE: yes
+      GITHUB_TOKEN: ${{ github.token || 'placeholder-token' }}
+
+    steps:
+      - name: Checkout dsBase
+        uses: actions/checkout@v4
+        with:
+          path: dsBase
+
+      - name: Checkout testStatus
+        if: ${{ github.actor != 'nektos/act' }} # for local deployment only
+        uses: actions/checkout@v4
+        with:
+          repository: ${{ env.REPO_OWNER }}/testStatus
+          ref: master
+          path: testStatus
+          persist-credentials: false
+          token: ${{ env.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: release
+          http-user-agent: release
+          use-public-rspm: true
+
+      - name: Install dsBase
+        run: |
+          Rscript -e 'install.packages(c("RANN", "stringr", "lme4", "dplyr", "reshape2", "polycor", "gamlss", "gamlss.dist", "mice", "childsds", "usethis", "devtools"), dependencies = TRUE)'
+          R CMD INSTALL ./dsBase
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: 'c("Imports")'
+          extra-packages: | 
+            any::rcmdcheck 
+            cran::devtools 
+            cran::git2r 
+            cran::RCurl 
+            cran::readr 
+            cran::magrittr 
+            cran::xml2 
+            cran::purrr 
+            cran::dplyr 
+            cran::stringr 
+            cran::tidyr 
+            cran::quarto 
+            cran::knitr 
+            cran::kableExtra 
+            cran::rmarkdown 
+            cran::downlit 
+          needs: check
+
+      - name: Check man files up-to-date
+        run: |
+          orig_sum=$(find man -type f | sort -u | xargs cat | md5sum)
+          R -e "devtools::document()"
+          new_sum=$(find man -type f | sort -u | xargs cat | md5sum)
+          if [ "$orig_sum" != "$new_sum" ]; then
+            echo "Your committed manual files (man/*.Rd) are out of sync with the R files. Run devtools::document() locally then commit."
+            exit 1
+          else
+            echo "Documentation up-to-date."
+          fi
+        working-directory: dsBase
+        continue-on-error: true
+
+      - name: Run devtools::check
+        run: |
+          R -q -e "library('devtools'); devtools::check(args = c('--no-tests', '--no-examples'))" | tee ../check.Rout
+          grep -q "^0 errors" ../check.Rout && grep -q " 0 warnings" ../check.Rout && grep -q " 0 notes" ../check.Rout
+        working-directory: dsBase
+        continue-on-error: true
+
+      - name: Run tests with coverage & JUnit report
+        run: |
+          mkdir -p logs
+          R -q -e "devtools::reload();"
+          R -q -e '
+            write.csv(
+              covr::coverage_to_list(
+                covr::package_coverage(
+                  type = c("none"),
+                  code = c('"'"'
+                    output_file <- file("test_console_output.txt");
+                    sink(output_file);
+                    sink(output_file, type = "message");
+                    junit_rep <- testthat::JunitReporter$new(file = file.path(getwd(), "test_results.xml"));
+                    progress_rep <- testthat::ProgressReporter$new(max_failures = 999999);
+                    multi_rep <- testthat::MultiReporter$new(reporters = list(progress_rep, junit_rep));
+                    testthat::test_package("${{ env.PROJECT_NAME }}", filter = "${{ env.TEST_FILTER }}", reporter = multi_rep, stop_on_failure = FALSE)'"'"'
+                  )
+                )
+              ),
+              "coveragelist.csv"
+            )'
+
+          mv coveragelist.csv logs/
+          mv test_* logs/
+          grep -q " FAIL 0 " logs/test_console_output.txt
+        working-directory: dsBase
+
+      - name: Check for JUnit errors
+        run: |
+          issue_count=$(sed 's/failures="0" errors="0"//' test_results.xml | grep -c errors= || true)
+          echo "Number of testsuites with issues: $issue_count"
+          sed 's/failures="0" errors="0"//' test_results.xml | grep errors= > issues.log || true
+          cat issues.log || true
+          exit $issue_count
+        working-directory: dsBase/logs
+
+      - name: Write versions to file
+        run: |
+          echo "branch:${{ env.BRANCH_NAME }}" > ${{ env.WORKFLOW_ID }}.txt
+          echo "os:$(lsb_release -ds)" >> ${{ env.WORKFLOW_ID }}.txt
+          echo "R:$(R --version | head -n1)" >> ${{ env.WORKFLOW_ID }}.txt
+        working-directory: dsBase/logs
+
+      - name: Parse results from testthat and covr
+        run: |
+          Rscript --verbose --vanilla ../testStatus/source/parse_test_report.R logs/
+        working-directory: dsBase
+
+      - name: Render report
+        run: |
+          cd testStatus
+
+          mkdir -p new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
+          mkdir -p new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
+          mkdir -p new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest/
+
+          # Copy logs to new logs directory location
+          cp -rv ../${{ env.PROJECT_NAME }}/logs/* new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
+          cp -rv ../${{ env.PROJECT_NAME }}/logs/${{ env.WORKFLOW_ID }}.txt new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
+
+          R -e 'input_dir <- file.path("../new/logs", Sys.getenv("PROJECT_NAME"), Sys.getenv("BRANCH_NAME"), Sys.getenv("WORKFLOW_ID")); quarto::quarto_render("source/test_report.qmd", execute_params = list(input_dir = input_dir))'
+          mv source/test_report.html new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/index.html
+          cp -r new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/* new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest
+
+        env:
+          PROJECT_NAME: ${{ env.PROJECT_NAME }}
+          BRANCH_NAME: ${{ env.BRANCH_NAME }}
+          WORKFLOW_ID: ${{ env.WORKFLOW_ID }}
+
+      - name: Upload test logs
+        uses: actions/upload-artifact@v4
+        with:
+          name: dsbase-logs
+          path: testStatus/new
+
+      - name: Dump environment info
+        run: |
+          echo -e "\n#############################"
+          echo -e "ls /: ######################"
+          ls -al .
+          echo -e "\n#############################"
+          echo -e "lscpu: ######################"
+          lscpu
+          echo -e "\n#############################"
+          echo -e "memory: #####################"
+          free -m
+          echo -e "\n#############################"
+          echo -e "env: ########################"
+          env
+          echo -e "\n#############################"
+          echo -e "R sessionInfo(): ############"
+          R -e 'sessionInfo()'
+          sudo apt install tree -y
+          tree .
+

.github/workflows/pkgdown.yaml

@@ -0,0 +1,49 @@
+# 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:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs