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Changes from villegar/v6.3.3-dev into v6.3.4-dev
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‎.github/workflows/dsBase_test_suite.yaml‎

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################################################################################
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# DataSHIELD GHA test suite - dsBase
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# Adapted from `azure-pipelines.yml` by Roberto Villegas-Diaz
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#
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# Inside the root directory $(Pipeline.Workspace) will be a file tree like:
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# /dsBase <- Checked out version of datashield/dsBase
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# /dsBase/logs <- Where results of tests and logs are collated
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# /testStatus <- Checked out version of datashield/testStatus
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#
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# As of Jul 2025 this takes ~ 9 mins to run.
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################################################################################
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name: dsBase tests' suite
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on:
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push:
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branches:
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- master
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- v6.3.3-dev
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schedule:
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- cron: '0 0 * * 0' # Weekly on master
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- cron: '0 1 * * *' # Nightly on v6.3.3-dev
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jobs:
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dsBase_test_suite:
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runs-on: ubuntu-latest
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timeout-minutes: 120
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# These should all be constant, except TEST_FILTER. This can be used to test
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# subsets of test files in the testthat directory. Options are like:
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# '*' <- Run all tests.
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# 'asNumericDS*' <- Run all asNumericDS tests, i.e. all the arg, etc. tests.
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# '*_smk_*' <- Run all the smoke tests for all functions.
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env:
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TEST_FILTER: '*'
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_r_check_system_clock_: 0
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WORKFLOW_ID: ${{ github.run_id }}-${{ github.run_attempt }}
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PROJECT_NAME: dsBase
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BRANCH_NAME: ${{ github.ref_name }}
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REPO_OWNER: ${{ github.repository_owner }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- name: Checkout dsBase
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uses: actions/checkout@v4
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with:
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path: dsBase
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- name: Checkout testStatus
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uses: actions/checkout@v4
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with:
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repository: ${{ env.REPO_OWNER }}/testStatus
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token: ${{ secrets.GH_TOKEN }}
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ref: master
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path: testStatus
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: release
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http-user-agent: release
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: |
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any::rcmdcheck
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cran::devtools
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cran::git2r
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cran::RCurl
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cran::readr
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cran::magrittr
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cran::xml2
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cran::purrr
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cran::dplyr
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cran::stringr
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cran::tidyr
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cran::quarto
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cran::knitr
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cran::kableExtra
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cran::rmarkdown
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cran::downlit
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needs: check
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- name: Check man files up-to-date
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run: |
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orig_sum=$(find man -type f | sort -u | xargs cat | md5sum)
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R -e "devtools::document()"
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new_sum=$(find man -type f | sort -u | xargs cat | md5sum)
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if [ "$orig_sum" != "$new_sum" ]; then
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echo "Your committed manual files (man/*.Rd) are out of sync with the R files. Run devtools::document() locally then commit."
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exit 1
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else
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echo "Documentation up-to-date."
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fi
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working-directory: dsBase
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continue-on-error: true
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- name: Run devtools::check
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run: |
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R -q -e "library('devtools'); devtools::check(args = c('--no-tests', '--no-examples'))" | tee ../check.Rout
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grep -q "^0 errors" ../check.Rout && grep -q " 0 warnings" ../check.Rout && grep -q " 0 notes" ../check.Rout
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working-directory: dsBase
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continue-on-error: true
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- name: Run tests with coverage & JUnit report
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run: |
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mkdir -p logs
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R -q -e "devtools::reload();"
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R -q -e '
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write.csv(
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covr::coverage_to_list(
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covr::package_coverage(
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type = c("none"),
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code = c('"'"'
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output_file <- file("test_console_output.txt");
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sink(output_file);
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sink(output_file, type = "message");
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junit_rep <- testthat::JunitReporter$new(file = file.path(getwd(), "test_results.xml"));
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progress_rep <- testthat::ProgressReporter$new(max_failures = 999999);
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multi_rep <- testthat::MultiReporter$new(reporters = list(progress_rep, junit_rep));
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testthat::test_package("${{ env.PROJECT_NAME }}", filter = "${{ env.TEST_FILTER }}", reporter = multi_rep, stop_on_failure = FALSE)'"'"'
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)
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)
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),
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"coveragelist.csv"
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)'
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mv coveragelist.csv logs/
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mv test_* logs/
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grep -q " FAIL 0 " logs/test_console_output.txt
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working-directory: dsBase
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- name: Check for JUnit errors
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run: |
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issue_count=$(sed 's/failures="0" errors="0"//' test_results.xml | grep -c errors= || true)
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echo "Number of testsuites with issues: $issue_count"
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sed 's/failures="0" errors="0"//' test_results.xml | grep errors= > issues.log || true
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cat issues.log || true
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exit $issue_count
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working-directory: dsBase/logs
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- name: Write versions to file
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run: |
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echo "branch:${{ env.BRANCH_NAME }}" > ${{ env.WORKFLOW_ID }}.txt
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echo "os:$(lsb_release -ds)" >> ${{ env.WORKFLOW_ID }}.txt
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echo "R:$(R --version | head -n1)" >> ${{ env.WORKFLOW_ID }}.txt
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working-directory: dsBase/logs
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- name: Parse results from testthat and covr
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run: |
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Rscript --verbose --vanilla ../testStatus/source/parse_test_report.R logs/
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working-directory: dsBase
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- name: Commit results to testStatus
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# if: github.repository == 'villegar/dsBase' && github.event_name != 'pull_request'
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run: |
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git config --global user.email "$GITHUB_ACTOR@users.noreply.github.com"
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git config --global user.name "$GITHUB_ACTOR"
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cd testStatus
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git checkout master
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git pull
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mkdir -p logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
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mkdir -p docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
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mkdir -p docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest/
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# clear the latest directory
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rm -rf docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest/*
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# Copy logs to new logs directory location
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cp -rv ../dsBase/logs/* logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
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cp -rv ../dsBase/logs/${{ env.WORKFLOW_ID }}.txt logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
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# Create symbolic links
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ln -sf ${{ env.WORKFLOW_ID }}/ logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/.LATEST
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# ln -sf docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/ docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/latest
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R -e 'input_dir <- file.path("../logs", Sys.getenv("PROJECT_NAME"), Sys.getenv("BRANCH_NAME"), Sys.getenv("WORKFLOW_ID")); quarto::quarto_render("source/test_report.qmd", execute_params = list(input_dir = input_dir))'
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mv source/test_report.html docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/index.html
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cp -r docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/* docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest
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git add .
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git commit -m "Auto test for ${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }} @ ${{ env.WORKFLOW_ID }}"
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git push
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env:
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PROJECT_NAME: ${{ env.PROJECT_NAME }}
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BRANCH_NAME: ${{ env.BRANCH_NAME }}
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WORKFLOW_ID: ${{ env.WORKFLOW_ID }}
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- name: Dump environment info
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run: |
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echo -e "\n#############################"
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echo -e "ls /: ######################"
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ls -al .
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echo -e "\n#############################"
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echo -e "lscpu: ######################"
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lscpu
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echo -e "\n#############################"
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echo -e "memory: #####################"
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free -m
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echo -e "\n#############################"
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echo -e "env: ########################"
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env
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echo -e "\n#############################"
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echo -e "R sessionInfo(): ############"
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R -e 'sessionInfo()'
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sudo apt install tree -y
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tree .
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‎.github/workflows/pkgdown.yaml‎

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

‎README.md‎

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dsBase
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======
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## dsBase: 'DataSHIELD' Server Side Base Functions
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DataSHIELD server side base R library.
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[![License](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.html)
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[![](https://www.r-pkg.org/badges/version/dsBase?color=black)](https://cran.r-project.org/package=dsBase)
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[![R build
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status](https://github.com/datashield/dsBase/workflows/R-CMD-check/badge.svg)](https://github.com/datashield/dsBase/actions)
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[![License](https://img.shields.io/badge/license-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.html)
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## Installation
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About
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=====
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You can install the released version of dsBase from
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[CRAN](https://cran.r-project.org/package=dsBase) with:
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``` r
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install.packages("dsBase")
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```
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And the development version from
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[GitHub](https://github.com/datashield/dsBase/) with:
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<!-- You can install the development version from [GitHub](https://github.com/) with: -->
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``` r
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install.packages("remotes")
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remotes::install_github("datashield/dsBase", "<BRANCH>")
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# Install v6.4.0 with the following
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remotes::install_github("datashield/dsBase", "v6.4.0-dev")
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```
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For a full list of development branches, checkout https://github.com/datashield/dsBase/branches
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## About
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DataSHIELD is a software package which allows you to do non-disclosive federated analysis on sensitive data. Our website (https://www.datashield.org) has in depth descriptions of what it is, how it works and how to install it. A key point to highlight is that DataSHIELD has a client-server infrastructure, so the dsBase package (https://github.com/datashield/dsBase) needs to be used in conjuction with the dsBaseClient package (https://github.com/datashield/dsBaseClient) - trying to use one without the other makes no sense.
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| obiba CRAN | Where you probably should install DataSHIELD from. |
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| releases | Stable releases. |
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| master branch | Mostly in sync with the latest release, changes rarely. |
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## References
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[1] Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R,
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Avraam D, Marcon Y, Bishop T, Gaye A, Escribà Montagut X, Wheater S (2025). _dsBase: 'DataSHIELD' Server Side Base Functions_. R
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package version 6.3.3. <https://doi.org/10.32614/CRAN.package.dsBase>.
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[2] Gaye A, Marcon Y, Isaeva J, LaFlamme P, Turner A, Jones E, Minion J, Boyd A, Newby C, Nuotio
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M, Wilson R, Butters O, Murtagh B, Demir I, Doiron D, Giepmans L, Wallace S, Budin-Ljøsne I,
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Oliver Schmidt C, Boffetta P, Boniol M, Bota M, Carter K, deKlerk N, Dibben C, Francis R,
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Hiekkalinna T, Hveem K, Kvaløy K, Millar S, Perry I, Peters A, Phillips C, Popham F, Raab G,
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Reischl E, Sheehan N, Waldenberger M, Perola M, van den Heuvel E, Macleod J, Knoppers B,
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Stolk R, Fortier I, Harris J, Woffenbuttel B, Murtagh M, Ferretti V, Burton P (2014).
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“DataSHIELD: taking the analysis to the data, not the data to the analysis.” _International
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Journal of Epidemiology_, *43*(6), 1929-1944. <https://doi.org/10.1093/ije/dyu188>.
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[3] Wilson R, W. Butters O, Avraam D, Baker J, Tedds J, Turner A, Murtagh M, R. Burton P (2017).
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“DataSHIELD – New Directions and Dimensions.” _Data Science Journal_, *16*(21), 1-21.
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<https://doi.org/10.5334/dsj-2017-021>.
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[4] Avraam D, Wilson R, Aguirre Chan N, Banerjee S, Bishop T, Butters O, Cadman T, Cederkvist L,
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Duijts L, Escribà Montagut X, Garner H, Gonçalves G, González J, Haakma S, Hartlev M,
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Hasenauer J, Huth M, Hyde E, Jaddoe V, Marcon Y, Mayrhofer M, Molnar-Gabor F, Morgan A,
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Murtagh M, Nestor M, Nybo Andersen A, Parker S, Pinot de Moira A, Schwarz F,
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Strandberg-Larsen K, Morris AvSwertz, Welten M, Wheater S, Burton P (2024). “DataSHIELD:
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mitigating disclosure risk in a multi-site federated analysis platform.” _Bioinformatics
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Advances_, *5*(1), 1-21. <https://doi.org/10.1093/bioadv/vbaf046>.

‎docs/authors.html‎

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