Fix R CMD check notes

Merck · Apr 12, 2024 · fa8c8db · fa8c8db
1 parent 39a1c87
commit fa8c8db
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Showing 5 changed files with 49 additions and 39 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -48,4 +48,4 @@ VignetteBuilder:
     knitr
 Config/testthat/edition: 3
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
diff --git a/R/calc_seq_p.R b/R/calc_seq_p.R
@@ -44,6 +44,7 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' calc_seq_p(
 #'   test_analysis = 2,
 #'   test_hypothesis = "H1, H2, H3",
@@ -76,7 +77,7 @@
 #'   spending_fun_par = -4,
 #'   info_frac = c(0.5, 1),
 #'   interval = c(1e-4, 0.2)
-#' )
+#' )}
 calc_seq_p <- function(
     test_analysis = 2,
     test_hypothesis = "H1, H2, H3",

diff --git a/R/globals.R b/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()`

diff --git a/man/calc_seq_p.Rd b/man/calc_seq_p.Rd
diff --git a/vignettes/adj-seq-p.Rmd b/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()
 ```