v1.2.1
gsm.core v1.2.1
This patch release updates the GitHub action workflows to align with the new federated action framework in gsm.utils
What's Changed
- Main -> dev by Laura Maxwell (@lauramaxwell) in #137
- Update workflows by Jon Harmon (@jonthegeek) in #139
- Only check as public by Jon Harmon (@jonthegeek) in #142
- Delete requirement issue type by Jon Harmon (@jharmon-gilead) in #143
- gsm.core v1.2.1 release candidate by Laura Maxwell (@lauramaxwell) in #144
New Contributors
- Jon Harmon (@jharmon-gilead) made their first contribution in #143
Full Changelog: v1.2.0...v1.2.1
{qcthat} Reports
Completed Issues
✅ A qcthat issue test matrix with 5 milestones, 14 issues, and 20 tests
├─█─Milestone: v1.1.1 (4 issues, 6 tests)
│ ├─☑️─Issue 31: Feature/Bug - allow no params in workflow steps
│ │ └─✅─RunStep will run a function with no parameters (#31)
│ ├─☑️─Issue 23: Bugfix: Message out of `RunStep` related to vector arguments should not be vectorized.
│ │ └─✅─Passes direct value vector parameters correctly (#23)
│ ├─☑️─Issue 22: Feature: DATETIME data type
│ │ ├─✅─RunQuery applies schema appropriately (#22, #45)
│ │ └─✅─Validate column type works (#22)
│ └─☑️─Issue 21: QC: Warnings in Tests
│ ├─✅─Analyze_NormalApprox_PredictBounds processes data correctly (#21)
│ └─✅─rate output created as expected and has correct structure (#21)
├─█─Milestone: v1.1.2 (1 issue, 1 test)
│ └─☑️─Issue 28: Business Requirement: Update Accrual Thresholds for existing KRIs
│ └─✅─Function correctly applies accrual threshold (#7, #28)
├─█─Milestone: v1.1.4 (2 issues, 1 test)
│ ├─☑️─Bug 71: Bugfix: `RunQuery()` coerces undefined columns to `character`
│ │ └─✅─RunQuery applies incomplete schema appropriately (#70, #71)
│ └─☑️─Requirement 70: Business Requirement: Update `RunQuery` to not set `character` type if not specified
│ └─✅─RunQuery applies incomplete schema appropriately (#70, #71)
├─█─Milestone: v1.1.5 (1 issue, 1 test)
│ └─☑️─Technical Task 77: Add `RiskScoreWeight` info to `Analysis_Flagged` via the `Flag()` function
│ └─✅─Flag function adds RiskScoreWeight info to Analysis_Flagged (#77)
├─█─Milestone: v1.2.0 (2 issues, 9 tests)
│ ├─☑️─Bug 135: Negative flags aren't assigned correctly when `Score==Threshold`.
│ │ ├─✅─errors working as expected (#135)
│ │ └─✅─Flag correctly handles exact cut point values at negative and positive thresholds (#135)
│ └─☑️─Technical Task 116: Migrate appropriate qualification tests to gsm.core
│ ├─✅─Qual: Given raw participant-level data, a properly specified Workflow for a KRI creates summarized and flagged data (#116)
│ ├─✅─Qual: Given raw participant-level data with missingness,
a properly specified Workflow for a KRI creates summarized and flagged data (#116)
│ ├─✅─Qual: Given pre-processed input data, a properly specified Workflow for a KRI creates summarized and flagged data (#116)
│ ├─✅─Qual: Given appropriate metadata (i.e. vThresholds), flagged observations are properly marked in summary data (#116)
│ ├─✅─Qual: Given appropriate metadata (i.e. vThresholds), bounds are properly applied to generate flags (#116)
│ ├─✅─Qual: Given appropriate raw participant-level data, flag values can be correctly assigned to records that meet flagging criteria, including custom thresholding (#116)
│ └─✅─Qual: Given appropriate raw participant-level data, flag values are correctly assigned as NA for sites with low enrollment (#116)
└─█─Milestone: <none> (4 issues, 4 tests)
├─☑️─Issue 45: Feature: Support `logical` data type.
│ └─✅─RunQuery applies schema appropriately (#22, #45)
├─☑️─Issue 44: Bugfix: `RunQuery` throws an error on empty `Date` strings.
│ └─✅─RunQuery parses invalid date/times correctly (#44)
├─☑️─Technical Task 43: `MakeWorkflowList` doesn't work with packages that aren't installed.
│ └─✅─invalid data returns list NULL elements (#43)
└─☑️─Issue 7: Add generalized Accrual Threshold to Flag()
└─✅─Function correctly applies accrual threshold (#7, #28)
# Issue state: 📥 = open, ☑️ = closed (completed), ⛔ = closed (won't fix)
# Test disposition: ✅ = passed, ❌ = failed, 🚫 = skipped
🟢 All issues have at least one test
🙈 25 issues with label "qcthat-nocov" were ignored
This report was run locally by Laura Maxwell (@lauramaxwell) due to a bug in the qcthat package (Documented here)
Session Info
─ Session info ───────────────────────────────────────────────────────────────────────────! setting value
version R version 4.5.1 (2025-06-13 ucrt)
os Windows 11 x64 (build 26200)
system x86_64, mingw32
ui RStudio
language (EN)
collate English_Europe.utf8
ctype English_Europe.utf8
tz America/New_York
date 2026-05-18
rstudio 2025.09.2+418 Cucumberleaf Sunflower (desktop)
pandoc 3.9 @ C:\Users\Laura Maxwell\AppData\Local\Pandoc/ (via rmarkdown)
quarto @ C:\PROGRA1\RStudio\RESOUR1\app\bin\quarto\bin\quarto.exe
─ Packages ─────────────────────────────────────────────────────────────────────────────
! package * version date (UTC) lib source
askpass 1.2.1 2024-10-04 [1] CRAN (R 4.5.1)
brio 1.1.5 2024-04-24 [1] CRAN (R 4.5.1)
cli 3.6.6 2026-04-09 [1] CRAN (R 4.5.3)
credentials 2.0.3 2025-09-12 [1] CRAN (R 4.5.2)
curl 7.0.0 2025-08-19 [1] CRAN (R 4.5.1)
DBI 1.3.0 2026-02-25 [1] CRAN (R 4.5.3)
dbplyr 2.5.2 2026-02-13 [1] CRAN (R 4.5.3)
desc 1.4.3 2023-12-10 [1] CRAN (R 4.5.1)
digest 0.6.39 2025-11-19 [1] CRAN (R 4.5.3)
dplyr 1.2.1 2026-04-03 [1] CRAN (R 4.5.3)
DT 0.34.0 2025-09-02 [1] CRAN (R 4.5.1)
duckdb 1.5.2 2026-04-13 [1] CRAN (R 4.5.3)
emoji 16.0.0 2024-10-28 [1] CRAN (R 4.5.3)
evaluate 1.0.5 2025-08-27 [1] CRAN (R 4.5.1)
farver 2.1.2 2024-05-13 [1] CRAN (R 4.5.1)
fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.5.1)
fs 2.0.1 2026-03-24 [1] CRAN (R 4.5.3)
generics 0.1.4 2025-05-09 [1] CRAN (R 4.5.1)
gert 2.3.1 2026-01-11 [1] CRAN (R 4.5.2)
ggplot2 4.0.2 2026-02-03 [1] CRAN (R 4.5.3)
gh 1.5.0 2025-05-26 [1] CRAN (R 4.5.1)
gitcreds 0.1.2 2022-09-08 [1] CRAN (R 4.5.1)
glue 1.8.1 2026-04-17 [1] CRAN (R 4.5.1)
gsm.core * 1.2.1 2026-04-15 [1] Github (81ef8d2)
gsm.kri 1.5.1 2026-04-09 [1] Github (Gilead-BioStats/gsm.kri@8027935)
gsm.mapping * 1.1.4 2026-04-15 [1] Github (Gilead-BioStats/gsm.mapping@060720e)
gsm.reporting * 1.1.5 2026-04-17 [?] Github (Gilead-BioStats/gsm.reporting@e6bebde)
gt 1.3.0 2026-01-22 [1] CRAN (R 4.5.3)
gtable 0.3.6 2024-10-25 [1] CRAN (R 4.5.1)
htmltools 0.5.9 2025-12-04 [1] CRAN (R 4.5.3)
htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.5.1)
httr2 1.2.2 2025-12-08 [1] CRAN (R 4.5.2)
jsonlite 2.0.0 2025-03-27 [1] CRAN (R 4.5.1)
knitr 1.51 2025-12-20 [1] CRAN (R 4.5.2)
lifecycle 1.0.5 2026-01-08 [1] CRAN (R 4.5.1)
log4r 0.4.4 2024-10-12 [1] CRAN (R 4.5.1)
magrittr 2.0.5 2026-04-04 [1] CRAN (R 4.5.3)
openssl 2.4.0 2026-04-15 [1] CRAN (R 4.5.1)
otel 0.2.0 2025-08-29 [1] CRAN (R 4.5.2)
pak 0.9.2 2025-12-22 [1] CRAN (R 4.5.2)
pillar 1.11.1 2025-09-17 [1] CRAN (R 4.5.2)
pkgbuild 1.4.8 2025-05-26 [1] CRAN (R 4.5.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.5.1)
pkgload 1.5.2 2026-04-22 [1] CRAN (R 4.5.3)
purrr 1.2.2 2026-04-10 [1] CRAN (R 4.5.3)
qcthat 1.1.2.9000 2026-05-18 [1] Github (Gilead-Public/qcthat@038f5e7)
R6 2.6.1 2025-02-15 [1] CRAN (R 4.5.1)
rappdirs 0.3.4 2026-01-17 [1] CRAN (R 4.5.2)
RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.5.0)
rlang 1.2.0 2026-04-06 [1] CRAN (R 4.5.3)
rmarkdown 2.31 2026-03-26 [1] CRAN (R 4.5.3)
rprojroot 2.1.1 2025-08-26 [1] CRAN (R 4.5.1)
rstudioapi 0.18.0 2026-01-16 [1] CRAN (R 4.5.1)
S7 0.2.1-1 2025-11-14 [1] CRAN (R 4.5.1)
scales 1.4.0 2025-04-24 [1] CRAN (R 4.5.1)
sessioninfo 1.2.3 2025-02-05 [1] CRAN (R 4.5.1)
stringi 1.8.7 2025-03-27 [1] CRAN (R 4.5.0)
stringr 1.6.0 2025-11-04 [1] CRAN (R 4.5.2)
sys 3.4.3 2024-10-04 [1] CRAN (R 4.5.1)
testthat * 3.3.2 2026-01-11 [1] CRAN (R 4.5.2)
tibble 3.3.1 2026-01-11 [1] CRAN (R 4.5.3)
tidyr 1.3.2 2025-12-19 [1] CRAN (R 4.5.2)
tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.5.1)
utf8 1.2.6 2025-06-08 [1] CRAN (R 4.5.1)
vctrs 0.7.3 2026-04-11 [1] CRAN (R 4.5.3)
waldo 0.6.2 2025-07-11 [1] CRAN (R 4.5.1)
withr 3.0.2 2024-10-28 [1] CRAN (R 4.5.1)
xfun 0.57 2026-03-20 [1] CRAN (R 4.5.3)
xml2 1.5.2 2026-01-17 [1] CRAN (R 4.5.3)
yaml * 2.3.12 2025-12-10 [1] CRAN (R 4.5.3)
