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Laura Maxwell (lauramaxwell) wants to merge 8 commits into
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Main -> dev#127
Laura Maxwell (lauramaxwell) wants to merge 8 commits into
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@lauramaxwell Laura Maxwell (lauramaxwell) commented May 15, 2026

Overview

Catch dev up to the newest release in main

Test Notes/Sample Code

Connected Issues

  • Closes #XXX

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github-actions Bot commented May 15, 2026

✅ All workflows are up to date

Generated by this GitHub Action. Updated: 2026-05-15T13:46:20Z

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github-actions Bot commented May 15, 2026

{qcthat} Report: User Acceptance

No issues are awaiting UAT.

This report was generated by this GitHub Actions run.

Last updated: 2026-05-15 13:49:05 UTC

Session Info ─ Session info ───────────────────────────────────────────────────────────────

setting value

version R version 4.6.0 (2026-04-24)

os Ubuntu 24.04.4 LTS

system x86_64, linux-gnu

ui X11

language (EN)

collate C.UTF-8

ctype C.UTF-8

tz UTC

date 2026-05-15

pandoc 3.1.3 @ /usr/bin/pandoc

quarto NA

─ Packages ───────────────────────────────────────────────────────────────────

package * version date (UTC) lib source

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astgrepr 0.1.1 2025-06-07 [1] RSPM

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dplyr 1.2.1 2026-04-03 [1] RSPM

DT 0.34.0 2025-09-02 [1] RSPM

duckdb 1.5.2 2026-04-13 [1] RSPM

emoji 16.0.0 2024-10-28 [1] RSPM

evaluate 1.0.5 2025-08-27 [1] RSPM

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fastmap 1.2.0 2024-05-15 [1] RSPM

fontawesome 0.5.3 2024-11-16 [1] RSPM

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gh 1.5.0 2025-05-26 [1] RSPM

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grid 4.6.0 2026-04-24 [3] local

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gsm.utils 0.3.0.9000 2026-05-11 [1] Github (Gilead-BioStats/gsm.utils@586c827)

highr 0.12 2026-03-06 [1] RSPM

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lazyeval 0.2.3 2026-04-04 [1] RSPM

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magrittr 2.0.5 2026-04-04 [1] RSPM

MASS 7.3-65 2025-02-28 [3] CRAN (R 4.6.0)

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qcthat 1.1.2 2026-05-15 [1] Github (Gilead-BioStats/qcthat@d0958dc)

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rex 1.2.2 2026-03-28 [1] RSPM

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rprojroot 2.1.1 2025-08-26 [1] RSPM

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[3] /opt/R/4.6.0/lib/R/library

  • ── Packages attached to the search path.

──────────────────────────────────────────────────────────────────────────────

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github-actions Bot commented May 15, 2026

{qcthat} Reports

PR-Associated Issues

█ A qcthat issue test matrix with 0 milestones, 0 issues, and 0 tests 
# Issue state: 📥 = open, ☑️ = closed (completed), ⛔ = closed (won't fix)
# Test disposition: ✅ = passed, ❌ = failed, 🚫 = skipped

Completed Issues

✅ A qcthat issue test matrix with 3 milestones, 29 issues, and 11 tests 
├─█─Milestone: v1.1.0 (4 issues, 0 tests)
│ ├─☑️─Requirement 62: Business Requirement:  Add AE domains to data model
│ │ └─(no tests)
│ ├─☑️─Issue 61: Request New Domain or Variable: Dates
│ │ └─(no tests)
│ ├─☑️─Issue 35: Feature: Additional AE fields
│ │ └─(no tests)
│ └─☑️─Issue 34: Feature: Add "category" to PD.yaml
│   └─(no tests)
├─█─Milestone: v1.1.2 (2 issues, 0 tests)
│ ├─☑️─Feature 104: Make modifications to `EXCLUSION.yaml` to tweak text of ineligibility related components for legibility
│ │ └─(no tests)
│ └─☑️─Technical Task 91: Add `db_lock_dt` to `STUDY` domain
│   └─(no tests)
├─█─Milestone: v1.1.3 (4 issues, 3 tests)
│ ├─☑️─Technical Task 114: Add a new `death_days` column to `DEATH` domain
│ │ ├─✅─Qual: mappings now done by individual domain, test that inputs and outputs of priority 1 mappings are completed as expected (#97, #114)
│ │ └─✅─Qual: mappings now done by individual domain, test that inputs and outputs of priority 2 mappings are completed as expected (#97, #114)
│ ├─☑️─Bug 112: Remove `setdiff` call for `db_lock_dt`
│ │ └─(no tests)
│ ├─☑️─Bug 101: Fix data types in AE, PK and SUBJ
│ │ └─(no tests)
│ └─☑️─Technical Task 97: Migrate appropriate qualification tests to gsm.mapping
│   ├─✅─Qual: mappings now done by individual domain, test that inputs and outputs of priority 1 mappings are completed as expected (#97, #114)
│   ├─✅─Qual: mappings now done by individual domain, test that inputs and outputs of priority 2 mappings are completed as expected (#97, #114)
│   └─✅─Qual: mappings now done by individual domain, test that inputs and outputs of priority 3 mappings are completed as expected (#97)
└─█─Milestone: <none> (19 issues, 8 tests)
  ├─☑️─Issue 72: Feature: Include study ID in all data specifications.
  │ └─(no tests)
  ├─☑️─Issue 29: Feature: Create Issue templates for adding and editing new domain
  │ └─(no tests)
  ├─☑️─Issue 28: Feature: Add  `{gsm.endpoints}` mapping workflows
  │ └─(no tests)
  ├─☑️─Issue 25: Updates to Mapping Specification VIgnette
  │ └─(no tests)
  ├─☑️─Issue 24: Remove `util-` from file names
  │ └─(no tests)
  ├─☑️─Issue 21: refactor yamls to remove `_all` param/field
  │ └─(no tests)
  ├─☑️─Issue 20: Move additional data wrangling functions from gsm
  │ └─(no tests)
  ├─☑️─Issue 6: Feature: Expand AE.yaml
  │ └─(no tests)
  ├─☑️─Issue 5: Feature: Expand SUBJ.yaml
  │ └─(no tests)
  ├─☑️─Issue 2: Add ingestion-related functions
  │ ├─✅─Combining multiple specs with overlapping dfs, deduplicating cols (#2)
  │ ├─✅─Combining specs with non-overlapping dfs (#2)
  │ ├─✅─Combining specs with some empty dfs (#2)
  │ ├─✅─Combining empty list of specs returns an empty list (#2)
  │ ├─✅─Combining a single spec returns the same spec (#2)
  │ ├─✅─Combining specs with NULL entries is handled correctly (#2)
  │ ├─✅─warning if type doesn't match first instance (#2)
  │ └─✅─Ingest works with optional columns (#2)
  ├─☑️─Issue 1: Add mapping yamls from `{gsm}` 
  │ └─(no tests)
  ├─☑️─Bug 70: Data specification of `_all` coerces all columns to character.
  │ └─(no tests)
  ├─☑️─Technical Task 58: Request New Domain or Variable:  IE domain
  │ └─(no tests)
  ├─☑️─Issue 55: Keep Specified Columns
  │ └─(no tests)
  ├─☑️─Issue 53: Feature: Merge visit schedule onto PK domain.
  │ └─(no tests)
  ├─☑️─Issue 50: Bugfix: Fix source column names for endpoints mappings
  │ └─(no tests)
  ├─☑️─Issue 38: Add PK yaml
  │ └─(no tests)
  ├─☑️─Issue 37: Feature: Swap clindata with gsm.datasim
  │ └─(no tests)
  └─☑️─Issue 30: QC: Namespace all functions in workflow yamls
    └─(no tests)
# Issue state: 📥 = open, ☑️ = closed (completed), ⛔ = closed (won't fix)
# Test disposition: ✅ = passed, ❌ = failed, 🚫 = skipped
✅ All tests passed

⭕ 26 issues lack tests

🙈 12 issues with label "qcthat-nocov" were ignored

This report was generated by this GitHub Actions run.

Last updated: 2026-05-15 13:49:06 UTC

Session Info ─ Session info ───────────────────────────────────────────────────────────────

setting value

version R version 4.6.0 (2026-04-24)

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language (EN)

collate C.UTF-8

ctype C.UTF-8

tz UTC

date 2026-05-15

pandoc 3.1.3 @ /usr/bin/pandoc

quarto NA

─ Packages ───────────────────────────────────────────────────────────────────

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astgrepr 0.1.1 2025-06-07 [1] RSPM

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clipr 0.8.0 2022-02-22 [1] RSPM

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diffobj 0.3.6 2025-04-21 [1] RSPM

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downlit 0.4.5 2025-11-14 [1] RSPM

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DT 0.34.0 2025-09-02 [1] RSPM

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gsm.utils 0.3.0.9000 2026-05-11 [1] Github (Gilead-BioStats/gsm.utils@586c827)

highr 0.12 2026-03-06 [1] RSPM

htmltools 0.5.9 2025-12-04 [1] RSPM

htmlwidgets 1.6.4 2023-12-06 [1] RSPM

httr 1.4.8 2026-02-13 [1] RSPM

httr2 1.2.2 2025-12-08 [1] RSPM

ini 0.3.1 2018-05-20 [1] RSPM

jquerylib 0.1.4 2021-04-26 [1] RSPM

jsonlite 2.0.0 2025-03-27 [1] RSPM

KernSmooth 2.23-26 2025-01-01 [3] CRAN (R 4.6.0)

knitr 1.51 2025-12-20 [1] RSPM

later 1.4.8 2026-03-05 [1] RSPM

lattice 0.22-9 2026-02-09 [3] CRAN (R 4.6.0)

lazyeval 0.2.3 2026-04-04 [1] RSPM

lifecycle 1.0.5 2026-01-08 [1] RSPM

log4r 0.4.4 2024-10-12 [1] RSPM

magrittr 2.0.5 2026-04-04 [1] RSPM

MASS 7.3-65 2025-02-28 [3] CRAN (R 4.6.0)

Matrix 1.7-5 2026-03-21 [3] CRAN (R 4.6.0)

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mgcv 1.9-4 2025-11-07 [3] CRAN (R 4.6.0)

mime 0.13 2025-03-17 [1] RSPM

nlme 3.1-169 2026-03-27 [3] CRAN (R 4.6.0)

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otel 0.2.0 2025-08-29 [1] RSPM

pak 0.9.5 2026-04-27 [2] local

parallel 4.6.0 2026-04-24 [3] local

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pkgdown 2.2.0 2025-11-06 [1] RSPM

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praise 1.0.0 2015-08-11 [1] RSPM

processx 3.9.0 2026-04-22 [1] RSPM

promises 1.5.0 2025-11-01 [1] RSPM

ps 1.9.3 2026-04-20 [1] RSPM

purrr 1.2.2 2026-04-10 [1] RSPM

qcthat 1.1.2 2026-05-15 [1] Github (Gilead-BioStats/qcthat@d0958dc)

quarto 1.5.1 2025-09-04 [1] RSPM

R6 2.6.1 2025-02-15 [1] RSPM

ragg 1.5.2 2026-03-23 [1] RSPM

rappdirs 0.3.4 2026-01-17 [1] RSPM

Rcpp 1.1.1-1.1 2026-04-24 [1] RSPM

reactable 0.4.5 2025-12-01 [1] RSPM

reactR 0.6.1 2024-09-14 [1] RSPM

rex 1.2.2 2026-03-28 [1] RSPM

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rmarkdown 2.31 2026-03-26 [1] RSPM

rpart 4.1.27 2026-03-27 [3] CRAN (R 4.6.0)

rprojroot 2.1.1 2025-08-26 [1] RSPM

rrapply 1.2.8 2025-11-25 [1] RSPM

rstudioapi 0.18.0 2026-01-16 [1] RSPM

rvest 1.0.5 2025-08-29 [1] RSPM

sass 0.4.10 2025-04-11 [1] RSPM

selectr 0.5-1 2025-12-17 [1] RSPM

sessioninfo 1.2.3 2025-02-05 [1] any (@1.2.3)

spatial 7.3-18 2025-01-01 [3] CRAN (R 4.6.0)

splines 4.6.0 2026-04-24 [3] local

stats * 4.6.0 2026-04-24 [3] local

stats4 4.6.0 2026-04-24 [3] local

stringi 1.8.7 2025-03-27 [1] RSPM

stringr 1.6.0 2025-11-04 [1] RSPM

survival 3.8-6 2026-01-16 [3] CRAN (R 4.6.0)

sys 3.4.3 2024-10-04 [1] RSPM

systemfonts 1.3.2 2026-03-05 [1] RSPM

tcltk 4.6.0 2026-04-24 [3] local

testthat 3.3.2 2026-01-11 [1] RSPM

textshaping 1.0.5 2026-03-06 [1] RSPM

tibble 3.3.1 2026-01-11 [1] RSPM

tidyr 1.3.2 2025-12-19 [1] RSPM

tidyselect 1.2.1 2024-03-11 [1] RSPM

tinytex 0.59 2026-03-28 [1] RSPM

tools 4.6.0 2026-04-24 [3] local

usethis 3.2.1 2025-09-06 [1] RSPM

utf8 1.2.6 2025-06-08 [1] RSPM

utils * 4.6.0 2026-04-24 [3] local

vctrs 0.7.3 2026-04-11 [1] RSPM

waldo 0.6.2 2025-07-11 [1] RSPM

whisker 0.4.1 2022-12-05 [1] RSPM

withr 3.0.2 2024-10-28 [1] RSPM

xfun 0.57 2026-03-20 [1] RSPM

xml2 1.5.2 2026-01-17 [1] RSPM

yaml 2.3.12 2025-12-10 [1] RSPM

zip 2.3.3 2025-05-13 [1] RSPM

[1] /home/runner/work/_temp/Library

[2] /opt/R/4.6.0/lib/R/site-library

[3] /opt/R/4.6.0/lib/R/library

  • ── Packages attached to the search path.

──────────────────────────────────────────────────────────────────────────────

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github-actions Bot commented May 15, 2026

📊 Test coverage: 84.00%

Per-file coverage
File Coverage
R/ApplySpec.R 66.7%
R/CalculatePercentage.R 66.7%
R/CombineSpecs.R 95.8%
R/complete_death.R 87.5%
R/Ingest.R 100%
R/MakeLongMeta.R 100%
R/zzz.R 0%

Generated by this GitHub Action. Updated: 2026-05-15T13:49:07Z

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github-actions Bot commented May 15, 2026

🌐 PR pkgdown deployed: https://Gilead-BioStats.github.io/gsm.mapping/pr/127/dev

Generated by this GitHub Action. Updated: 2026-05-15T13:49:11Z

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@jharmon-gilead Jon Harmon (jharmon-gilead) jharmon-gilead approved these changes

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@lauramaxwell @jharmon-gilead @jonthegeek