V6.3.4 dev

.github/workflows/dsBase_test_suite.yaml

@@ -0,0 +1,210 @@
+################################################################################
+# 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:
+    branches: [master, v6.3.4-dev]
+  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
+
+    steps:
+      - name: Checkout dsBase
+        uses: actions/checkout@v4
+        with:
+          path: dsBase
+
+      - name: Checkout testStatus
+        uses: actions/checkout@v4
+        with:
+          repository: ${{ env.REPO_OWNER }}/testStatus
+          token: ${{ secrets.GH_TOKEN }}
+          ref: master
+          path: testStatus
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: release
+          http-user-agent: release
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::rcmdcheck
+            cran::devtools
+            cran::git2r
+            cran::RCurl
+            cran::readr
+            cran::magrittr
+            cran::xml2
+            cran::purrr
+            cran::dplyr
+            cran::stringr
+            cran::tidyr
+            cran::quarto
+            cran::knitr
+            cran::kableExtra
+            cran::rmarkdown
+            cran::downlit
+          needs: check
+
+      - name: Check man files up-to-date
+        run: |
+          orig_sum=$(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)" >> ${{ env.WORKFLOW_ID }}.txt
+        working-directory: dsBase/logs
+
+      - name: Parse results from testthat and covr
+        run: |
+          Rscript --verbose --vanilla ../testStatus/source/parse_test_report.R logs/
+        working-directory: dsBase
+
+      - name: Commit results to testStatus
+        # if: github.repository == 'villegar/dsBase' && github.event_name != 'pull_request'
+        run: |
+          git config --global user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git config --global user.name "$GITHUB_ACTOR"
+          cd testStatus
+          git checkout master
+          git pull
+
+          mkdir -p logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
+          mkdir -p docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
+          mkdir -p docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest/
+          # clear the latest directory 
+          rm -rf docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest/*
+
+          # Copy logs to new logs directory location
+          cp -rv ../dsBase/logs/* logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
+          cp -rv ../dsBase/logs/${{ env.WORKFLOW_ID }}.txt logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
+
+          # Create symbolic links
+          ln -sf ${{ env.WORKFLOW_ID }}/ logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/.LATEST
+          # ln -sf docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/ docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/latest
+
+          R -e 'input_dir <- file.path("../logs", Sys.getenv("PROJECT_NAME"), Sys.getenv("BRANCH_NAME"), Sys.getenv("WORKFLOW_ID")); quarto::quarto_render("source/test_report.qmd", execute_params = list(input_dir = input_dir))'
+          mv source/test_report.html docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/index.html
+          cp -r docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/* docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest
+
+          git add .
+          git commit -m "Auto test for ${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }} @ ${{ env.WORKFLOW_ID }}"
+          git push
+
+        env:
+          PROJECT_NAME: ${{ env.PROJECT_NAME }}
+          BRANCH_NAME: ${{ env.BRANCH_NAME }}
+          WORKFLOW_ID: ${{ env.WORKFLOW_ID }}
+
+      - 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

.github/workflows/test-coverage.yaml

@@ -0,0 +1,62 @@
+# 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: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          print(cov)
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v5
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: 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

DESCRIPTION

@@ -1,23 +1,27 @@
 Package: dsBase
-Title: 'DataSHIELD' Server Site Base Functions
+Title: 'DataSHIELD' Server Side Base Functions
 Description: Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a software package which allows
     you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have
     been designed to only share non disclosive summary statistics, with built in automated output
     checking based on statistical disclosure control. With data sites setting the threshold values for
     the automated output checks. For more details, see 'citation("dsBase")'.
-Version: 6.3.3
+Version: 6.3.4-9000
 Authors@R: c(person(given = "Paul",
                     family = "Burton",
-                    role = c("aut")),
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0001-5799-9634")),
              person(given = "Rebecca",
                     family = "Wilson",
-                    role = c("aut")),
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0003-2294-593X")),
              person(given = "Olly",
                     family = "Butters",
-                    role = c("aut")),
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0003-0354-8461")),
              person(given = "Patricia",
                     family = "Ryser-Welch",
-                    role = c("aut")),
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0002-0070-0264")),
              person(given = "Alex",
                     family = "Westerberg",
                     role = c("aut")),
@@ -37,6 +41,17 @@ Authors@R: c(person(given = "Paul",
                     role = c("aut"),
                     email = "yannick.marcon@obiba.org",
                     comment = c(ORCID = "0000-0003-0138-2023")),
+             person(given = "Tom",
+                    family = "Bishop",
+                    role = c("aut")),
+             person(given = "Amadou",
+                    family = "Gaye",
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0002-1180-2792")),
+             person(given = "Xavier",
+                    family = "Escribà-Montagut",
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0003-2888-8948")),
              person(given = "Stuart",
                     family = "Wheater",
                     role = c("aut", "cre"),

R/BooleDS.R

@@ -28,7 +28,7 @@
 BooleDS <- function(V1.name=NULL, V2.name=NULL, Boolean.operator.n=NULL, na.assign.text, numeric.output=TRUE){
 
   # Check Permissive Privacy Control Level.
-  dsBase::checkPermissivePrivacyControlLevel(c('permissive', 'banana'))
+  dsBase::checkPermissivePrivacyControlLevel(c('permissive', 'banana', 'carrot'))
 
 #########################################################################
 # DataSHIELD MODULE: CAPTURE THE nfilter SETTINGS                       #

R/blackBoxDS.R

@@ -67,8 +67,11 @@ blackBoxDS <- function(input.var.name=NULL,
   ########################################################
 
   # back-up current .Random.seed and revert on.exit
-  old_seed <- .Random.seed
-  on.exit(.Random.seed <- old_seed, add = TRUE)
+  if (exists(x = ".Random.seed", envir = globalenv())) {
+      assign(x = "old_seed", value = .Random.seed, envir = parent.frame());
+      on.exit({ assign(x = ".Random.seed", value = old_seed, envir = globalenv()); remove("old_seed", envir = parent.frame()) }, add = TRUE)
+  } else
+      on.exit(if (exists(x = ".Random.seed", envir = globalenv())) remove(".Random.seed", envir = globalenv()), add = TRUE)
 
  input.var <- eval(parse(text=input.var.name), envir = parent.frame())