Skip to content

Main -> dev#146

Open
Laura Maxwell (lauramaxwell) wants to merge 5 commits into
devfrom
main
Open

Main -> dev#146
Laura Maxwell (lauramaxwell) wants to merge 5 commits into
devfrom
main

Conversation

@lauramaxwell
Copy link
Copy Markdown
Contributor

@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

@github-actions
Copy link
Copy Markdown

github-actions Bot commented May 15, 2026

✅ All workflows are up to date

Generated by this GitHub Action. Updated: 2026-05-15T13:45:57Z

@github-actions
Copy link
Copy Markdown

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 13:48:19 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

askpass 1.2.1 2024-10-04 [1] RSPM

astgrepr 0.1.1 2025-06-07 [1] RSPM

backports 1.5.1 2026-04-03 [1] RSPM

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

base64enc 0.1-6 2026-02-02 [1] RSPM

bigD 0.3.1 2025-04-03 [1] RSPM

bitops 1.0-9 2024-10-03 [1] RSPM

blob 1.3.0 2026-01-14 [1] RSPM

boot 1.3-32 2025-08-29 [3] CRAN (R 4.6.0)

brew 1.0-10 2023-12-16 [1] RSPM

brio 1.1.5 2024-04-24 [1] RSPM

broom 1.0.13 2026-05-14 [1] RSPM

bslib 0.10.0 2026-01-26 [1] RSPM

cachem 1.1.0 2024-05-16 [1] RSPM

callr 3.7.6 2024-03-25 [1] RSPM

checkmate 2.3.4 2026-02-03 [1] RSPM

class 7.3-23 2025-01-01 [3] CRAN (R 4.6.0)

cli 3.6.6 2026-04-09 [1] RSPM

clipr 0.8.0 2022-02-22 [1] RSPM

cluster 2.1.8.2 2026-02-05 [3] CRAN (R 4.6.0)

codetools 0.2-20 2024-03-31 [3] CRAN (R 4.6.0)

commonmark 2.0.0 2025-07-07 [1] RSPM

compiler 4.6.0 2026-04-24 [3] local

covr 3.6.5 2025-11-09 [1] RSPM

cpp11 0.5.4 2026-04-04 [1] CRAN (R 4.6.0)

crayon 1.5.3 2024-06-20 [1] RSPM

credentials 2.0.3 2025-09-12 [1] RSPM

crosstalk 1.2.2 2025-08-26 [1] RSPM

curl 7.1.0 2026-04-22 [1] RSPM

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

DBI 1.3.0 2026-02-25 [1] RSPM

dbplyr 2.5.2 2026-02-13 [1] RSPM

desc 1.4.3 2023-12-10 [1] RSPM

devtools 2.5.2 2026-04-30 [1] RSPM

diffobj 0.3.6 2025-04-21 [1] RSPM

digest 0.6.39 2025-11-19 [1] RSPM

downlit 0.4.5 2025-11-14 [1] RSPM

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

ellipsis 0.3.3 2026-04-04 [1] RSPM

emoji 16.0.0 2024-10-28 [1] RSPM

evaluate 1.0.5 2025-08-27 [1] RSPM

fansi 1.0.7 2025-11-19 [1] RSPM

farver 2.1.2 2024-05-13 [1] RSPM

fastmap 1.2.0 2024-05-15 [1] RSPM

fontawesome 0.5.3 2024-11-16 [1] RSPM

foreign 0.8-91 2026-01-29 [3] CRAN (R 4.6.0)

fs 2.1.0 2026-04-18 [1] RSPM

generics 0.1.4 2025-05-09 [1] RSPM

gert 2.3.1 2026-01-11 [1] RSPM

gh 1.5.0 2025-05-26 [1] RSPM

git2r 0.36.2 2025-03-29 [1] RSPM

gitcreds 0.1.2 2022-09-08 [1] RSPM

glue 1.8.1 2026-04-17 [1] RSPM

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

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

grid 4.6.0 2026-04-24 [3] local

gsm.core 1.2.0 2026-05-11 [1] local

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

gt 1.3.0 2026-01-22 [1] RSPM

here 1.0.2 2025-09-15 [1] RSPM

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

httpuv 1.6.17 2026-03-18 [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

juicyjuice 0.1.0 2022-11-10 [1] RSPM

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

knitr 1.51 2025-12-20 [1] RSPM

labeling 0.4.3 2023-08-29 [1] RSPM

lamW 2.2.7 2026-03-27 [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

litedown 0.9 2025-12-18 [1] RSPM

log4r 0.4.4 2024-10-12 [1] RSPM

magrittr 2.0.5 2026-04-04 [1] RSPM

markdown 2.0 2025-03-23 [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)

memoise 2.0.1 2021-11-26 [1] RSPM

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

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

mime 0.13 2025-03-17 [1] RSPM

miniUI 0.1.2 2025-04-17 [1] RSPM

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

nnet 7.3-20 2025-01-01 [3] CRAN (R 4.6.0)

openssl 2.4.1 2026-05-14 [1] RSPM

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

pillar 1.11.1 2025-09-17 [1] RSPM

pkgbuild 1.4.8 2025-05-26 [1] RSPM

pkgconfig 2.0.3 2019-09-22 [1] RSPM

pkgdown 2.2.0 2025-11-06 [1] RSPM

pkgload 1.5.2 2026-04-22 [1] RSPM

praise 1.0.0 2015-08-11 [1] RSPM

prettyunits 1.2.0 2023-09-24 [1] RSPM

processx 3.9.0 2026-04-22 [1] RSPM

profvis 0.4.0 2024-09-20 [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

R.cache 0.17.0 2025-05-02 [1] RSPM

R.methodsS3 1.8.2 2022-06-13 [1] RSPM

R.oo 1.27.1 2025-05-02 [1] RSPM

R.utils 2.13.0 2025-02-24 [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

rcmdcheck 1.4.0 2021-09-27 [1] RSPM

RColorBrewer 1.1-3 2022-04-03 [1] RSPM

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

RcppParallel 5.1.11-2 2026-03-05 [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

rlang 1.2.0 2026-04-06 [1] RSPM

rmarkdown 2.31 2026-03-26 [1] RSPM

roxygen2 8.0.0 2026-05-01 [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

rversions 3.0.0 2025-10-09 [1] RSPM

rvest 1.0.5 2025-08-29 [1] RSPM

sass 0.4.10 2025-04-11 [1] RSPM

scales 1.4.0 2025-04-24 [1] RSPM

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

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

shiny 1.13.0 2026-02-20 [1] RSPM

sourcetools 0.1.7-2 2026-03-28 [1] RSPM

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

styler 1.11.0 2025-10-13 [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

urlchecker 1.0.1 2021-11-30 [1] RSPM

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

V8 8.2.0 2026-04-21 [1] RSPM

vctrs 0.7.3 2026-04-11 [1] RSPM

viridisLite 0.4.3 2026-02-04 [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

xopen 1.0.1 2024-04-25 [1] RSPM

xtable 1.8-8 2026-02-22 [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.

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

@github-actions
Copy link
Copy Markdown

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 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 tests passed

🟢 All issues have at least one test

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

This report was generated by this GitHub Actions run.

Last updated: 2026-05-15 13:48:20 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

askpass 1.2.1 2024-10-04 [1] RSPM

astgrepr 0.1.1 2025-06-07 [1] RSPM

backports 1.5.1 2026-04-03 [1] RSPM

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

base64enc 0.1-6 2026-02-02 [1] RSPM

bigD 0.3.1 2025-04-03 [1] RSPM

bitops 1.0-9 2024-10-03 [1] RSPM

blob 1.3.0 2026-01-14 [1] RSPM

boot 1.3-32 2025-08-29 [3] CRAN (R 4.6.0)

brew 1.0-10 2023-12-16 [1] RSPM

brio 1.1.5 2024-04-24 [1] RSPM

broom 1.0.13 2026-05-14 [1] RSPM

bslib 0.10.0 2026-01-26 [1] RSPM

cachem 1.1.0 2024-05-16 [1] RSPM

callr 3.7.6 2024-03-25 [1] RSPM

checkmate 2.3.4 2026-02-03 [1] RSPM

class 7.3-23 2025-01-01 [3] CRAN (R 4.6.0)

cli 3.6.6 2026-04-09 [1] RSPM

clipr 0.8.0 2022-02-22 [1] RSPM

cluster 2.1.8.2 2026-02-05 [3] CRAN (R 4.6.0)

codetools 0.2-20 2024-03-31 [3] CRAN (R 4.6.0)

commonmark 2.0.0 2025-07-07 [1] RSPM

compiler 4.6.0 2026-04-24 [3] local

covr 3.6.5 2025-11-09 [1] RSPM

cpp11 0.5.4 2026-04-04 [1] CRAN (R 4.6.0)

crayon 1.5.3 2024-06-20 [1] RSPM

credentials 2.0.3 2025-09-12 [1] RSPM

crosstalk 1.2.2 2025-08-26 [1] RSPM

curl 7.1.0 2026-04-22 [1] RSPM

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

DBI 1.3.0 2026-02-25 [1] RSPM

dbplyr 2.5.2 2026-02-13 [1] RSPM

desc 1.4.3 2023-12-10 [1] RSPM

devtools 2.5.2 2026-04-30 [1] RSPM

diffobj 0.3.6 2025-04-21 [1] RSPM

digest 0.6.39 2025-11-19 [1] RSPM

downlit 0.4.5 2025-11-14 [1] RSPM

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

ellipsis 0.3.3 2026-04-04 [1] RSPM

emoji 16.0.0 2024-10-28 [1] RSPM

evaluate 1.0.5 2025-08-27 [1] RSPM

fansi 1.0.7 2025-11-19 [1] RSPM

farver 2.1.2 2024-05-13 [1] RSPM

fastmap 1.2.0 2024-05-15 [1] RSPM

fontawesome 0.5.3 2024-11-16 [1] RSPM

foreign 0.8-91 2026-01-29 [3] CRAN (R 4.6.0)

fs 2.1.0 2026-04-18 [1] RSPM

generics 0.1.4 2025-05-09 [1] RSPM

gert 2.3.1 2026-01-11 [1] RSPM

gh 1.5.0 2025-05-26 [1] RSPM

git2r 0.36.2 2025-03-29 [1] RSPM

gitcreds 0.1.2 2022-09-08 [1] RSPM

glue 1.8.1 2026-04-17 [1] RSPM

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

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

grid 4.6.0 2026-04-24 [3] local

gsm.core 1.2.0 2026-05-11 [1] local

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

gt 1.3.0 2026-01-22 [1] RSPM

here 1.0.2 2025-09-15 [1] RSPM

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

httpuv 1.6.17 2026-03-18 [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

juicyjuice 0.1.0 2022-11-10 [1] RSPM

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

knitr 1.51 2025-12-20 [1] RSPM

labeling 0.4.3 2023-08-29 [1] RSPM

lamW 2.2.7 2026-03-27 [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

litedown 0.9 2025-12-18 [1] RSPM

log4r 0.4.4 2024-10-12 [1] RSPM

magrittr 2.0.5 2026-04-04 [1] RSPM

markdown 2.0 2025-03-23 [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)

memoise 2.0.1 2021-11-26 [1] RSPM

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

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

mime 0.13 2025-03-17 [1] RSPM

miniUI 0.1.2 2025-04-17 [1] RSPM

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

nnet 7.3-20 2025-01-01 [3] CRAN (R 4.6.0)

openssl 2.4.1 2026-05-14 [1] RSPM

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

pillar 1.11.1 2025-09-17 [1] RSPM

pkgbuild 1.4.8 2025-05-26 [1] RSPM

pkgconfig 2.0.3 2019-09-22 [1] RSPM

pkgdown 2.2.0 2025-11-06 [1] RSPM

pkgload 1.5.2 2026-04-22 [1] RSPM

praise 1.0.0 2015-08-11 [1] RSPM

prettyunits 1.2.0 2023-09-24 [1] RSPM

processx 3.9.0 2026-04-22 [1] RSPM

profvis 0.4.0 2024-09-20 [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

R.cache 0.17.0 2025-05-02 [1] RSPM

R.methodsS3 1.8.2 2022-06-13 [1] RSPM

R.oo 1.27.1 2025-05-02 [1] RSPM

R.utils 2.13.0 2025-02-24 [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

rcmdcheck 1.4.0 2021-09-27 [1] RSPM

RColorBrewer 1.1-3 2022-04-03 [1] RSPM

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

RcppParallel 5.1.11-2 2026-03-05 [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

rlang 1.2.0 2026-04-06 [1] RSPM

rmarkdown 2.31 2026-03-26 [1] RSPM

roxygen2 8.0.0 2026-05-01 [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

rversions 3.0.0 2025-10-09 [1] RSPM

rvest 1.0.5 2025-08-29 [1] RSPM

sass 0.4.10 2025-04-11 [1] RSPM

scales 1.4.0 2025-04-24 [1] RSPM

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

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

shiny 1.13.0 2026-02-20 [1] RSPM

sourcetools 0.1.7-2 2026-03-28 [1] RSPM

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

styler 1.11.0 2025-10-13 [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

urlchecker 1.0.1 2021-11-30 [1] RSPM

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

V8 8.2.0 2026-04-21 [1] RSPM

vctrs 0.7.3 2026-04-11 [1] RSPM

viridisLite 0.4.3 2026-02-04 [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

xopen 1.0.1 2024-04-25 [1] RSPM

xtable 1.8-8 2026-02-22 [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.

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

@github-actions
Copy link
Copy Markdown

github-actions Bot commented May 15, 2026

🌐 PR pkgdown deployed: https://Gilead-BioStats.github.io/gsm.core/pr/146/dev

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

@github-actions
Copy link
Copy Markdown

github-actions Bot commented May 15, 2026

📊 Test coverage: 88.03%

Per-file coverage
File Coverage
R/Analyze_Fisher.R 100%
R/Analyze_Identity.R 100%
R/Analyze_NormalApprox_PredictBounds.R 87.5%
R/Analyze_NormalApprox.R 100%
R/Analyze_Poisson_PredictBounds.R 94.4%
R/Analyze_Poisson.R 100%
R/data-specs.R 0%
R/Flag.R 100%
R/Input_Rate.R 100%
R/RunQuery.R 90.7%
R/RunStep.R 92.3%
R/RunWorkflow.R 68.8%
R/RunWorkflows.R 100%
R/Summarize.R 69.2%
R/Transform_Count.R 100%
R/Transform_Rate.R 100%
R/util-checkSpec.R 100%
R/util-cli_logger_wrappers.R 88.2%
R/util-func-namespace.R 87.5%
R/util-logger.R 75%
R/util-MakeWorkflowList.R 83.3%
R/util-ParseThreshold.R 100%
R/zzz.R 0%

Generated by this GitHub Action. Updated: 2026-05-15T13:49:30Z

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

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

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

3 participants

@lauramaxwell @jharmon-gilead @jonthegeek