Fix some R CMD CHK build error and warnings (#743)

* Add {future} and {future.callr} as required packages * Use `.data$` * Document all parameters * Simplify the code and avoid using `runif` * [check-spelling] Update metadata Update for https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/5573642848/attempts/1 Accepted in #743 (comment) Signed-off-by: check-spelling-bot <[email protected]> --------- Signed-off-by: check-spelling-bot <[email protected]>
Public-Health-Scotland · Jul 17, 2023 · 3f86f89 · 3f86f89
1 parent 8e1bcc9
commit 3f86f89
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Showing 6 changed files with 13 additions and 4 deletions.
diff --git a/.github/actions/spelling/expect.txt b/.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
diff --git a/DESCRIPTION b/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),

diff --git a/R/produce_test_comparison.R b/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)
       )
   }
 }
diff --git a/R/run_episode_file.R b/R/run_episode_file.R
@@ -340,6 +340,7 @@ create_cohort_lookups <- function(data, year, update = latest_update()) {
 #' 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()) {

diff --git a/R/write_tests_xlsx.R b/R/write_tests_xlsx.R
@@ -47,7 +47,7 @@ write_tests_xlsx <- function(comparison_data, sheet_name, year = NULL) {
     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 @@ write_tests_xlsx <- function(comparison_data, sheet_name, year = NULL) {
   }
 
   # 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 {

diff --git a/man/join_cohort_lookups.Rd b/man/join_cohort_lookups.Rd