Merge pull request #38 from Merck/rcmdcheck

Fix `R CMD check` notes

.github/workflows/R-CMD-check.yaml

@@ -29,7 +29,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -47,3 +47,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -22,7 +22,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,7 +41,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/style.yaml

@@ -9,11 +9,13 @@ name: Style
 jobs:
   style:
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -46,7 +48,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache styler
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ steps.styler-location.outputs.location }}
           key: ${{ runner.os }}-styler-${{ github.sha }}

.github/workflows/test-coverage.yaml

@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -31,20 +31,20 @@ jobs:
           covr::codecov(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
         shell: Rscript {0}
 
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -48,4 +48,4 @@ VignetteBuilder:
     knitr
 Config/testthat/edition: 3
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

R/calc_seq_p.R

@@ -44,6 +44,7 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' calc_seq_p(
 #'   test_analysis = 2,
 #'   test_hypothesis = "H1, H2, H3",
@@ -77,6 +78,7 @@
 #'   info_frac = c(0.5, 1),
 #'   interval = c(1e-4, 0.2)
 #' )
+#' }
 calc_seq_p <- function(
     test_analysis = 2,
     test_hypothesis = "H1, H2, H3",

R/globals.R

@@ -19,6 +19,8 @@
 utils::globalVariables(
   unique(
     c(
+      # From `calc_seq_p()`
+      c("analysis"),
       # From `closed_test()`
       c("Analysis"),
       # From `generate_bounds()`

vignettes/adj-seq-p.Rmd

@@ -16,13 +16,11 @@ vignette: >
 ---
 
 ```{r, message = FALSE, warning = FALSE}
+library(wpgsd)
+library(gsDesign)
 library(tibble)
 library(gt)
-library(gsDesign)
 library(dplyr)
-library(mvtnorm)
-library(ggplot2)
-library(wpgsd)
 ```
 
 # Example overview
@@ -790,23 +788,23 @@ ans %>%
     `Sequential p-values of Weighted Bonferroni`, `Adjusted-sequential p-values of Weighted Bonferroni`,
     `Sequential p-values of WPGSD`, `Adjusted-sequential p-values of WPGSD`
   ) %>%
-  gt::gt() %>%
-  gt::tab_spanner(
+  gt() %>%
+  tab_spanner(
     label = "Weighted Bonferroni",
     columns = c(`Sequential p-values of Weighted Bonferroni`, `Adjusted-sequential p-values of Weighted Bonferroni`)
   ) %>%
-  gt::tab_spanner(
+  tab_spanner(
     label = "WPGSD",
     columns = c(`Sequential p-values of WPGSD`, `Adjusted-sequential p-values of WPGSD`)
   ) %>%
-  gt::tab_style_body(
+  tab_style_body(
     columns = where(is.numeric),
     style = cell_fill(color = "pink"),
     fn = function(x) x <= 0.025
   ) %>%
-  gt::fmt_number(columns = 3:6, decimals = 4) %>%
-  gt::tab_header(
+  fmt_number(columns = 3:6, decimals = 4) %>%
+  tab_header(
     title = "(Adjusted-) sequential p-values",
     subtitle = "Multiple populations"
-  ) # %>% gt::as_latex()
+  ) # %>% as_latex()
 ```