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Merge of changes made to 'v6.3.5-dev'
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‎.Rbuildignore‎

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@@ -9,4 +9,5 @@
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^pkgdown$
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^\.circleci$
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^\.circleci/config\.yml$
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^\.github$
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^\.github$
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^cran-comments\.md$

‎.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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schedule:
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- cron: '0 0 * * 0' # Weekly
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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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permissions:
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contents: write
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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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GITHUB_TOKEN: ${{ github.token || 'placeholder-token' }}
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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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if: ${{ github.actor != 'nektos/act' }} # for local deployment only
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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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ref: master
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path: testStatus
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persist-credentials: false
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token: ${{ env.GITHUB_TOKEN }}
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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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- name: Install dsBase
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run: |
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Rscript -e 'install.packages(c("RANN", "stringr", "lme4", "dplyr", "reshape2", "polycor", "gamlss", "gamlss.dist", "mice", "childsds", "usethis", "devtools"), dependencies = TRUE)'
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R CMD INSTALL ./dsBase
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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dependencies: 'c("Imports")'
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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)" >> ${{ env.WORKFLOW_ID }}.txt
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Rscript --vanilla -e 'sessionInfo()' >> session_info_${{ 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/ logs/ https://github.com/datashield/${{ env.PROJECT_NAME }}/blob/${{ env.BRANCH_NAME }} '[^-:.]+' '(?<=::)[^:]+(?=::)'
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working-directory: dsBase
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env:
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PROJECT_NAME: ${{ env.PROJECT_NAME }}
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BRANCH_NAME: ${{ env.BRANCH_NAME }}
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- name: Render report
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run: |
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cd testStatus
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mkdir -p new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
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mkdir -p new/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 ../${{ env.PROJECT_NAME }}/logs/* new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
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cp -rv ../${{ env.PROJECT_NAME }}/logs/${{ env.WORKFLOW_ID }}.txt new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
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R -e 'input_dir <- file.path("../new/logs", Sys.getenv("PROJECT_NAME"), Sys.getenv("BRANCH_NAME"), Sys.getenv("WORKFLOW_ID")); quarto::quarto_render("source/test_report.qmd", execute_params = list(input_dir = input_dir))'
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mv source/test_report.html new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest/index.html
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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: Upload test logs
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uses: actions/upload-artifact@v4
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with:
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name: dsbase-logs
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path: testStatus/new
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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

‎.github/workflows/test-coverage.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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name: test-coverage.yaml
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permissions: read-all
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jobs:
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test-coverage:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v4
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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::covr, any::xml2
28+
needs: coverage
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- name: Test coverage
31+
run: |
32+
cov <- covr::package_coverage(
33+
quiet = FALSE,
34+
clean = FALSE,
35+
install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
36+
)
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print(cov)
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covr::to_cobertura(cov)
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shell: Rscript {0}
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- uses: codecov/codecov-action@v5
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with:
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# Fail if error if not on PR, or if on PR and token is given
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fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
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files: ./cobertura.xml
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plugins: noop
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disable_search: true
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token: ${{ secrets.CODECOV_TOKEN }}
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- name: Show testthat output
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if: always()
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run: |
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## --------------------------------------------------------------------
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find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload test results
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if: failure()
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uses: actions/upload-artifact@v4
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with:
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name: coverage-test-failures
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path: ${{ runner.temp }}/package

‎DESCRIPTION‎

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11
Package: dsBase
2-
Title: 'DataSHIELD' Server Site Base Functions
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Title: 'DataSHIELD' Server Side Base Functions
33
Description: Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a software package which allows
44
you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have
55
been designed to only share non disclosive summary statistics, with built in automated output
66
checking based on statistical disclosure control. With data sites setting the threshold values for
7-
the automated output checks.
8-
Version: 6.4.0-9000
7+
the automated output checks. For more details, see 'citation("dsBase")'.
8+
Version: 6.4.0.9000
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Authors@R: c(person(given = "Paul",
1010
family = "Burton",
11-
role = c("aut")),
11+
role = c("aut"),
12+
comment = c(ORCID = "0000-0001-5799-9634")),
1213
person(given = "Rebecca",
1314
family = "Wilson",
14-
role = c("aut")),
15+
role = c("aut"),
16+
comment = c(ORCID = "0000-0003-2294-593X")),
1517
person(given = "Olly",
1618
family = "Butters",
17-
role = c("aut")),
19+
role = c("aut"),
20+
comment = c(ORCID = "0000-0003-0354-8461")),
1821
person(given = "Patricia",
1922
family = "Ryser-Welch",
20-
role = c("aut")),
23+
role = c("aut"),
24+
comment = c(ORCID = "0000-0002-0070-0264")),
2125
person(given = "Alex",
2226
family = "Westerberg",
2327
role = c("aut")),
@@ -37,6 +41,17 @@ Authors@R: c(person(given = "Paul",
3741
role = c("aut"),
3842
email = "yannick.marcon@obiba.org",
3943
comment = c(ORCID = "0000-0003-0138-2023")),
44+
person(given = "Tom",
45+
family = "Bishop",
46+
role = c("aut")),
47+
person(given = "Amadou",
48+
family = "Gaye",
49+
role = c("aut"),
50+
comment = c(ORCID = "0000-0002-1180-2792")),
51+
person(given = "Xavier",
52+
family = "Escribà-Montagut",
53+
role = c("aut"),
54+
comment = c(ORCID = "0000-0003-2888-8948")),
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person(given = "Stuart",
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family = "Wheater",
4257
role = c("aut", "cre"),
@@ -62,6 +77,8 @@ Imports:
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tidyselect,
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tidytable
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Suggests:
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spelling,
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testthat
66-
RoxygenNote: 7.3.2
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RoxygenNote: 7.3.3
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Encoding: UTF-8
84+
Language: en-GB

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