Fix some R CMD CHK build error and warnings

.github/actions/spelling/expect.txt

@@ -94,6 +94,7 @@ itle
 iwalk
 jaccard
 jan
+jennifer
 jul
 keydate
 keyring
@@ -104,6 +105,8 @@ ltc
 ltcs
 lubridate
 magrittr
+Mcbride
+mcmahon
 MMMYY
 monthflag
 mpat
@@ -200,5 +203,6 @@ xintercept
 xlsx
 yearstay
 YYYYQX
+zihao
 zsav
 zstd

DESCRIPTION

@@ -28,6 +28,8 @@ Imports:
     dtplyr (>= 1.3.0),
     fs (>= 1.6.1),
     fst (>= 0.9.8),
+    future (>= 1.33.0),
+    future.callr (>= 0.8.1),
     glue (>= 1.6.2),
     haven (>= 2.5.2),
     hms (>= 1.1.0),

R/produce_test_comparison.R

@@ -23,7 +23,7 @@ produce_test_comparison <- function(old_data, new_data, recid = FALSE) {
       dplyr::mutate(
         difference = round(.data$value_new - .data$value_old, digits = 2L),
         pct_change = .data$difference / .data$value_old,
-        issue = !dplyr::between(pct_change, -0.05, 0.05)
+        issue = !dplyr::between(.data$pct_change, -0.05, 0.05)
       )
   } else {
     dplyr::full_join(old_data,
@@ -34,7 +34,7 @@ produce_test_comparison <- function(old_data, new_data, recid = FALSE) {
       dplyr::mutate(
         difference = round(.data$value_new - .data$value_old, digits = 2L),
         pct_change = .data$difference / .data$value_old,
-        issue = !dplyr::between(pct_change, -0.05, 0.05)
+        issue = !dplyr::between(.data$pct_change, -0.05, 0.05)
       )
   }
 }

R/run_episode_file.R

@@ -193,12 +193,12 @@
 fill_missing_cij_markers <- function(data) {
   fixable_data <- data %>%
     dplyr::filter(
       .data[["recid"]] %in% c("01B", "04B", "GLS", "02B", "DD") & !is.na(.data[["chi"]])
     )
 
   non_fixable_data <- data %>%
     dplyr::filter(
       !(.data[["recid"]] %in% c("01B", "04B", "GLS", "02B", "DD")) | is.na(.data[["chi"]])
     )
 
   fixed_data <- fixable_data %>%
@@ -331,8 +331,8 @@
   })
 
   # This 'blocks' the code until they have both finished executing
   value_demographic <- future::value(future_demographic)
   value_service_use <- future::value(future_service_use)
 
   return(data)
 }
@@ -340,6 +340,7 @@
 #' Join cohort lookups
 #'
 #' @inheritParams store_ep_file_vars
+#' @inheritParams get_demographic_cohorts_path
 #'
 #' @return The data including the Demographic and Service Use lookups.
 join_cohort_lookups <- function(data, year, update = latest_update()) {

R/write_tests_xlsx.R

@@ -42,12 +42,12 @@
 
     cli::cli_progress_bar(
       type = "iterator",
       format = "{cli::pb_spin} [{cli::pb_elapsed}] Waiting for {tests_workbook_name}..."
     )
     while (fs::file_exists(path = in_use_path) && seconds < max_wait) {
       # While the tests are in use (wait a random number of seconds from 1 to 30)
       cli::cli_progress_update()
-      wait <- round(runif(1, 1, 15))
+      wait <- sample(x = 3:15, size = 1)
 
       Sys.sleep(wait)
       seconds <- seconds + wait
@@ -56,7 +56,7 @@
   }
 
   # Final check to maybe avoid corrupting the workbook
-  Sys.sleep(round(runif(1, 1, 3)))
+  Sys.sleep(sample(x = 1:3, size = 1))
   if (!fs::file_exists(path = in_use_path)) {
     fs::file_create(path = in_use_path)
   } else {
@@ -79,7 +79,7 @@
   }
 
   # add a new sheet for tests
   date_today <- format(Sys.Date(), "%d_%b")
   sheet_name_dated <- ifelse(
     is.null(year),
     stringr::str_glue("{sheet_name}_{date_today}"),
@@ -185,7 +185,7 @@
   fs::file_delete(path = in_use_path)
 
   cli::cli_alert_success(
     "The tests for {year}{ifelse(is.null(year), '', '-')}{sheet_name} were written to {.file {fs::path_file(tests_workbook_path)}}"
   )
 
   return(comparison_data)