Finally made it through the automated CRAN checks. Data.table caused …

…issues with using too many cores. Fixed tests, examples and vignette
OskarGauffin · Jan 12, 2024 · abdb0fe · abdb0fe
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diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
 Version: 0.0.1
-Date: 2024-01-12 12:49:03 UTC
-SHA: af9c5217de39fdca012e03540660464fbe197d98
+Date: 2024-01-12 20:49:19 UTC
+SHA: 3a20f21681a92d66a1a7240916bc7c27bc7f4076
diff --git a/R/lower_level_disprop_analysis.R b/R/lower_level_disprop_analysis.R
@@ -171,8 +171,9 @@ count_expected_ror <- function(count_dt) {
 #' @return A tibble with three columns (point estimate and credibility bounds).
 #'
 #' @examples
+#' \dontrun{
 #' ic(obs = 20, exp = 10)
-#'
+#' }
 #' # Note that obs and exp can be vectors (of equal length, no recycling allowed)
 #' ic(obs = c(20, 30), exp = c(10, 10))
 #' @importFrom Rdpack reprompt
@@ -254,21 +255,23 @@ ic <- function(obs = NULL,
 #' Number of rows equals length of inputs obs, n_drug, n_event_prr and n_tot_prr.
 #'
 #' @examples
-#'
-#' pvda::prr(
+#' \dontrun{
+#' prr(
 #'   obs = 5,
 #'   n_drug = 10,
 #'   n_event_prr = 20,
 #'   n_tot_prr = 10000
 #' )
 #'
+#'
 #' # Note that input parameters can be vectors (of equal length, no recycling)
 #' pvda::prr(
 #'   obs = c(5, 10),
 #'   n_drug = c(10, 20),
 #'   n_event_prr = c(15, 30),
 #'   n_tot_prr = c(10000, 10000)
 #' )
+#' }
 #' @references
 #' \insertRef{Montastruc_2011}{pvda}
 #'
@@ -348,7 +351,8 @@ prr <- function(obs = NULL,
 #'
 #' @examples
 #'
-#' pvda::ror(
+#' \dontrun{
+#' ror(
 #'   a = 5,
 #'   b = 10,
 #'   c = 20,
@@ -362,6 +366,7 @@ prr <- function(obs = NULL,
 #'   c = c(15, 30),
 #'   d = c(10000, 10000)
 #' )
+#' }
 #' @references
 #' \insertRef{Montastruc_2011}{pvda}
 #' @export
@@ -407,7 +412,9 @@ ror <- function(a = NULL,
 #' Default is 0.95 (i.e. 95 \% confidence interval).
 #' @return A list with two numerical vectors, "lower" and "upper".
 #' @examples
+#' \dontrun{
 #' conf_lvl_to_quantile_prob(0.95)
+#' }
 #' @export
 conf_lvl_to_quantile_prob <- function(conf_lvl = 0.95) {
   checkmate::qassert(conf_lvl, "N1[0,1]")

diff --git a/R/onLoad.R b/R/onLoad.R
@@ -2,8 +2,9 @@
 #   base::packageStartupMessage("Under development. Report issues at https://github.com/OskarGauffin/pvda")
 # }
 
-.onLoad <- function(libname, pkgname) {
-  # CRAN OMP THREAD LIMIT
-  Sys.setenv("OMP_THREAD_LIMIT" = 2)
-
-}
+# .onLoad <- function(libname, pkgname) {
+#   # CRAN OMP THREAD LIMIT
+#   # This did not, on it's own, prevent NOTEs about too many cores being used by data.table, when
+#   # submitting to CRAN.
+#   Sys.setenv("OMP_THREAD_LIMIT" = 2)
+# }
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,25 +1,10 @@
 ## Resubmission
 
-This is a resubmission. In this version I have: 
+This is a resubmission. In this version I have tried to adress NOTES about data.table using too many cores, e.g. "Re-building vignettes had CPU time 7.4 times elapsed time" by: 
 
-* Adressed the first NOTE by wrapping time consuming examples in the noted functions with \dontrun. 
-
-* For the other two notes: 
-
-"Running R code in ‘testthat.R’ had CPU time 10.2 times elapsed time" 
-"Re-building vignettes had CPU time 7.3 times elapsed time"
-
-I've followed advice from stack overflow and included an onLoad-function which limits the number of cores used (OMP_THREAD_LIMIT" = 2). 
-
-For completeness, this is the post I followed https://stackoverflow.com/questions/77323811/r-package-to-cran-had-cpu-time-5-times-elapsed-time 
-and this post suggests that it should cover the vignette note as well:
-https://www.mail-archive.com/r-package-devel@r-project.org/msg08734.html
-
-I've also:
-
-* Corrected four URLs in the README.md file. An old github repo name caused an "possibly invalid URL" as those URLs were redirected automatically to the new github repo name.
-
-* Listed a misplaced Rmd-file in .RBuildignore (it was not noted as a problem.)
+* Wrapping all examples with \dontrun. 
+* Set the Sys.setenv("OMP_THREAD_LIMIT" = 2) in my testthat.R-file
+* Set data.table::setDTthreads(1) in the beginning of the vignette.
 
 ------------------------------------------------------
 

diff --git a/man/conf_lvl_to_quantile_prob.Rd b/man/conf_lvl_to_quantile_prob.Rd
diff --git a/man/ic.Rd b/man/ic.Rd
diff --git a/man/prr.Rd b/man/prr.Rd
diff --git a/man/ror.Rd b/man/ror.Rd
diff --git a/tests/testthat.R b/tests/testthat.R
@@ -6,6 +6,8 @@
 # * https://r-pkgs.org/tests.html
 # * https://testthat.r-lib.org/reference/test_package.html#special-files
 
+Sys.setenv("OMP_THREAD_LIMIT" = 2)
+
 library(testthat)
 library(pvda)
 

diff --git a/tests/testthat/test-disprop_analysis.R b/tests/testthat/test-disprop_analysis.R
@@ -12,6 +12,7 @@ test_that("1-3. Function ic works", {
   expect_equal(test_df[, 2], expected_output[, 2])
   expect_equal(test_df[, 3], expected_output[, 3])
 })
+
 test_that("4. Function ror works", {
   test_df <- ror(1:2, 2:3, 3:4, 4:5)
 
@@ -25,6 +26,7 @@ test_that("4. Function ror works", {
   expect_equal(test_df[, 2], expected_output[, 2])
   # expect_equal(test_df[, 3], expected_output[, 3])
 })
+
 test_that("5-10. Function add_expected_count works", {
   df_colnames <- list(
     report_id = "report_id",
@@ -39,9 +41,9 @@ test_that("5-10. Function add_expected_count works", {
   })
 
   produced_output <- pvda::add_expected_counts(pvda::drug_event_df,
-    df_colnames,
-    df_syms = df_syms,
-    expected_count_estimators = c("rrr", "prr", "ror")
+                                               df_colnames,
+                                               df_syms = df_syms,
+                                               expected_count_estimators = c("rrr", "prr", "ror")
   )
 
   # Should return as many rows as there are unique report_ids in drug_event_df
@@ -59,6 +61,7 @@ test_that("5-10. Function add_expected_count works", {
   expect_equal(first_row$n_event_prr, first_row$c)
   expect_equal(first_row$n_tot_prr, diff(as.numeric(first_row[, c("n_drug", "n_tot")])))
 })
+
 test_that("11. The whole disproportionality function chain runs without NA output except in PRR and ROR", {
   output <- pvda::drug_event_df |>
     pvda::da() |>
@@ -69,6 +72,7 @@ test_that("11. The whole disproportionality function chain runs without NA outpu
 
   expect_equal(FALSE, any(is.na(output)))
 })
+
 test_that("12. The grouping functionality runs", {
   drug_event_df_with_grouping <- pvda::drug_event_df |>
     dplyr::mutate("group" = report_id %% 2)
@@ -91,6 +95,7 @@ test_that("12. The grouping functionality runs", {
 
   expect_equal(first_row_ic_group_0, manual_calc_ic_first_row_group_0)
 })
+
 test_that("13. Custom column names can be passed through the df_colnames list", {
   drug_event_df_custom_names <- pvda::drug_event_df |>
     dplyr::rename(RepId = report_id, Drug = drug, Event = event)
@@ -107,6 +112,7 @@ test_that("13. Custom column names can be passed through the df_colnames list",
 
   expect_equal(custom_colnames, c("Drug", "Event"))
 })
+
 test_that("14. Sorting works as expected", {
   # Repeated from test above on grouping
   da_1 <- drug_event_df |>
@@ -144,26 +150,29 @@ test_that("14. Sorting works as expected", {
     dplyr::pull("ic2.5") |>
     (\(x){
       all(x == da_1 |>
-        dplyr::filter(n == 1) |>
-        dplyr::pull(ic2.5))
+            dplyr::filter(n == 1) |>
+            dplyr::pull(ic2.5))
     })()
   expect_equal(c(desc_order_status, group_order_status), c(TRUE, TRUE))
 })
+
 test_that("15. Summary table contains a prr2.5 by default", {
   suppressMessages(invisible(capture.output(summary_output <- summary.da(pvda::drug_event_df |> pvda::da()))))
   has_prr2.5 <- as.character(summary_output[, 1]) |> stringr::str_detect("prr2.5")
 
   expect_equal(has_prr2.5, TRUE)
 })
 test_that("16. print function runs and has the same number of characters in first row as it has before", {
+
+
   suppressMessages(invisible(printed <- capture.output(print(pvda::drug_event_df |> pvda::da()))))
   expect_equal(nchar(printed[2]), 80L)
 })
 
 test_that("17. Grouped output from summary function works.", {
   summary_output <- pvda::drug_event_df |>
-      da(df_colnames = list(group_by = "group"))  |>
-      summary(print = FALSE)
+    da(df_colnames = list(group_by = "group"))  |>
+    summary(print = FALSE)
 
   expect_equal(2L, ncol(summary_output))
 })
diff --git a/vignettes/Disproportionality_analysis.Rmd b/vignettes/Disproportionality_analysis.Rmd
@@ -13,6 +13,11 @@ editor_options:
 ---
 # Introduction
 ```{r, include=FALSE}
+
+# There are notes about data.table using too many cores when you try to submit a table with data.table-dependencies
+# to cran. This is supposed to prevent that note. Also included in tests. 
+data.table::setDTthreads(1)
+
 library(pvda)
 knitr::opts_chunk$set(echo = FALSE)
 ```