Cleanup dependencies and fix documentation (#71)

* Cleanup dependencies and fix documentation

* Fix lintr issue

* Bump changed-files version

.github/workflows/build_docker_image.yml

@@ -32,7 +32,7 @@ jobs:
 
       - name: Get changed files in renv/profiles
         id: changed-files
-        uses: tj-actions/changed-files@v35
+        uses: tj-actions/changed-files@v41
         with:
           files: renv/profiles/**/renv.lock
 
@@ -86,7 +86,7 @@ jobs:
           else
               echo "platforms=linux/amd64" >> $GITHUB_OUTPUT
           fi
-          
+
 
       - name: Call deploy docker image action for every renv
         uses: insightsengineering/r-image-creator@v1

DESCRIPTION

@@ -36,27 +36,27 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 Depends: R (>= 4.2)
 Imports: 
-    admiraldev,
+    admiraldev (>= 1.1.0),
     dplyr (>= 1.0.0),
-    memoise,
-    assertthat,
-    purrr (>= 0.3.3),
-    rlang (>= 0.4.4),
+    purrr (>= 1.0.1),
+    rlang (>= 1.0.2),
+    tibble (>= 3.2.0),
+    vctrs (>= 0.5.0),
     stringr (>= 1.4.0),
-    tibble,
-    vctrs,
-    readr,
-    glue,
-    DT,
-    pillar
+    memoise (>= 2.0.1),
+    assertthat,
+    pillar,
+    cli
 Suggests:
     knitr,
     htmltools,
     lifecycle,
     magrittr,
     rmarkdown,
     spelling,
-    testthat (>= 3.1.7)
+    testthat (>= 3.1.7),
+    DT,
+    readr
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 Config/testthat/parallel: true

R/assertions.R

@@ -5,11 +5,7 @@ assert_logical_vector <- function(arg, optional = FALSE) {
   }
 
   if (!is.logical(arg)) {
-    err_msg <- sprintf(
-      "`arg` must be a logical vector but is %s.",
-      admiraldev::what_is_it(arg)
-    )
-    rlang::abort(err_msg)
+    cli::cli_abort("`arg` must be a logical vector but is {.obj_type_friendly {arg}}")
   }
 
   invisible(arg)

R/ct.R

@@ -103,11 +103,11 @@ assert_ct_spec <- function(ct_spec, optional = FALSE) {
   }
 
   if (!is.null(ct_spec) && anyNA(ct_spec[[ct_spec_vars("ct_clst")]])) {
-    rlang::abort(glue::glue("`{ct_spec_vars('ct_clst')}` can't have any NA values."))
+    rlang::abort(stringr::str_glue("`{ct_spec_vars('ct_clst')}` can't have any NA values."))
   }
 
   if (!is.null(ct_spec) && anyNA(ct_spec[[ct_spec_vars("to")]])) {
-    rlang::abort(glue::glue("`{ct_spec_vars('to')}` can't have any NA values."))
+    rlang::abort(stringr::str_glue("`{ct_spec_vars('to')}` can't have any NA values."))
   }
 
   invisible(ct_spec)
@@ -340,7 +340,8 @@ ct_map <-
 #'
 #' @export
 read_ct_spec <- function(file = stop("`file` must be specified")) {
-  ct_spec <- readr::read_csv(file = file, col_types = "c")
+  ct_spec <- utils::read.csv(file = file, na.strings = c("NA", ""), colClasses = "character") |>
+    tibble::as_tibble()
   assert_ct_spec(ct_spec)
 
   ct_spec
@@ -388,7 +389,7 @@ ct_spec_example <- function(example) {
 
   if (identical(local_path, "")) {
     stop(
-      glue::glue(
+      stringr::str_glue(
         "'{example}' does not match any ct spec files. Run `ct_spec_example()` for options."
       ),
       call. = FALSE

R/derive_blfl.R

@@ -54,6 +54,8 @@ dtc_datepart <- function(dtc, partial_as_na = TRUE) {
 #' @export
 #'
 #' @keywords internal
+#'
+#' @examples
 #' ## Partial or missing times set to NA and seconds ignored by default
 #' sdtm.oak:::dtc_timepart(
 #'   c(NA, "", "2021-12-25", "2021-12-25T12", "2021-12-25T12:30", "2021-12-25T12:30:59")

R/domain_example.R

@@ -80,7 +80,7 @@ domain_example <- function(example) {
 
   if (identical(local_path, "")) {
     stop(
-      glue::glue(
+      stringr::str_glue(
         "'{example}' does not match any domain example files. Run `domain_example()` for options."
       ),
       call. = FALSE
@@ -125,5 +125,8 @@ read_domain_example <- function(example) {
   }
 
   path <- domain_example(example)
-  readr::read_rds(file = path)
+  con <- file(path)
+  on.exit(close(con))
+
+  readRDS(con)
 }