Closes #426 Removing unneeded dependencies (#431)

* removing unneeded dependencies * Update DESCRIPTION * Update DESCRIPTION * Update NEWS.md * Update test-assertions.R
pharmaverse · Apr 17, 2024 · 4886b5a · 4886b5a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -30,40 +30,29 @@ URL: https://pharmaverse.github.io/admiraldev/,
     https://github.com/pharmaverse/admiraldev/
 BugReports: https://github.com/pharmaverse/admiraldev/issues
 Depends: 
-    R (>= 3.5)
+    R (>= 4.0)
 Imports:
     cli,
     dplyr (>= 1.0.5),
     glue (>= 1.6.0),
-    hms (>= 0.5.3),
     lifecycle (>= 0.1.0),
     lubridate (>= 1.7.4),
-    magrittr (>= 1.5),
     purrr (>= 0.3.3),
     rlang (>= 0.4.4),
     stringr (>= 1.4.0),
     tidyr (>= 1.0.2),
     tidyselect (>= 1.0.0)
 Suggests:
-    covr,
-    devtools,
     diffdf,
     DT,
     htmltools,
     knitr,
-    lintr,
     methods,
-    miniUI,
     pharmaversesdtm,
-    pkgdown,
     rmarkdown,
-    roxygen2,
     rstudioapi,
     spelling,
-    styler,
-    testthat (>= 3.0.0),
-    tibble,
-    usethis
+    testthat (>= 3.2.0)
 VignetteBuilder: 
     knitr
 Config/testthat/edition: 3

diff --git a/NAMESPACE b/NAMESPACE
@@ -68,6 +68,7 @@ export(warn_if_vars_exist)
 export(what_is_it)
 importFrom(cli,cli_abort)
 importFrom(cli,cli_div)
+importFrom(dplyr,"%>%")
 importFrom(dplyr,across)
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_cols)
@@ -98,7 +99,6 @@ importFrom(dplyr,ungroup)
 importFrom(dplyr,union)
 importFrom(glue,glue)
 importFrom(glue,glue_collapse)
-importFrom(hms,as_hms)
 importFrom(lifecycle,deprecate_stop)
 importFrom(lifecycle,deprecate_warn)
 importFrom(lifecycle,deprecated)
@@ -118,7 +118,6 @@ importFrom(lubridate,weeks)
 importFrom(lubridate,years)
 importFrom(lubridate,ymd)
 importFrom(lubridate,ymd_hms)
-importFrom(magrittr,"%>%")
 importFrom(purrr,compose)
 importFrom(purrr,every)
 importFrom(purrr,flatten)

diff --git a/NEWS.md b/NEWS.md
@@ -27,6 +27,13 @@ strategy. (#353)
 
 - The "Release Strategy" vignette now contains a short new "Release Tracking" section linking to an external dashboard for CRAN packages that are awaiting release. (#358)
 
+## Other
+
+- Removed dependencies not needed to build package or package documentation. (#426)
+
+- Increased minimum R version required to 4.0 to match {admiral}. (#382)
+
+
 # admiraldev 1.0.0
 
 ## New Features

diff --git a/R/admiraldev-package.R b/R/admiraldev-package.R
@@ -2,8 +2,7 @@
 #' @importFrom dplyr across arrange bind_rows case_when desc ends_with filter
 #'   full_join group_by if_else mutate n pull rename row_number select slice
 #'   starts_with transmute ungroup n_distinct union distinct summarise coalesce
-#'   bind_cols na_if tibble
-#' @importFrom magrittr %>%
+#'   bind_cols na_if tibble %>%
 #' @importFrom rlang := abort arg_match as_function as_label as_name as_string
 #'   call2 caller_env call_name current_env .data enexpr enquo eval_bare
 #'   eval_tidy expr expr_interp expr_label exprs f_lhs f_rhs is_named inform missing_arg
@@ -21,7 +20,6 @@
 #'             time_length %--% ymd ymd_hms weeks years hours minutes
 #' @importFrom tidyr drop_na nest pivot_longer pivot_wider unnest
 #' @importFrom tidyselect all_of contains vars_select
-#' @importFrom hms as_hms
 #' @importFrom lifecycle deprecate_warn deprecated deprecate_stop
 #' @importFrom cli cli_abort cli_div
 #' @importFrom glue glue glue_collapse

diff --git a/R/assertions.R b/R/assertions.R
@@ -22,7 +22,6 @@
 #' @family assertion
 #'
 #' @examples
-#' library(tibble)
 #' library(dplyr)
 #' library(rlang)
 #' dm <- tribble(
@@ -1171,7 +1170,8 @@ assert_function_param <- function(arg, params) {
 #' @export
 #'
 #' @examples
-#' library(tibble)
+#' library(dplyr)
+#'
 #' advs <- tribble(
 #'   ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL,
 #'   "P01",    "WEIGHT",      80.1, "kg",      "WEIGHT",  80.1,
@@ -1244,7 +1244,8 @@ assert_unit <- function(dataset,
 #' @family assertion
 #'
 #' @examples
-#' library(tibble)
+#' library(dplyr)
+#'
 #' advs <- tribble(
 #'   ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL,
 #'   "P01",    "WEIGHT",      80.1, "kg",      "WEIGHT",  80.1,
@@ -1732,8 +1733,8 @@ assert_one_to_one <- function(dataset,
 #' @keywords assertion
 #'
 #' @examples
-#' library(tibble)
 #' library(lubridate)
+#' library(dplyr)
 #' library(rlang)
 #'
 #' example_fun <- function(dataset, var) {

diff --git a/R/expect_dfs_equal.R b/R/expect_dfs_equal.R
@@ -17,7 +17,6 @@
 #'
 #' @examples
 #' library(dplyr, warn.conflicts = FALSE)
-#' library(tibble)
 #'
 #' tbl1 <- tribble(
 #'   ~USUBJID, ~AGE, ~SEX,

diff --git a/R/process_set_values_to.R b/R/process_set_values_to.R
@@ -31,7 +31,7 @@
 #' @export
 #'
 #' @examples
-#' library(tibble)
+#' library(dplyr)
 #' data <- tribble(
 #'   ~AVAL,
 #'   20

diff --git a/man/assert_data_frame.Rd b/man/assert_data_frame.Rd
diff --git a/man/assert_date_var.Rd b/man/assert_date_var.Rd
diff --git a/man/assert_param_does_not_exist.Rd b/man/assert_param_does_not_exist.Rd
diff --git a/man/assert_unit.Rd b/man/assert_unit.Rd
diff --git a/man/expect_dfs_equal.Rd b/man/expect_dfs_equal.Rd
diff --git a/man/process_set_values_to.Rd b/man/process_set_values_to.Rd
diff --git a/tests/testthat/test-assertions.R b/tests/testthat/test-assertions.R
@@ -1,7 +1,7 @@
 # assert_has_variables ----
 ## Test 1: error if a required variable is missing (deprecation error) ----
 test_that("assert_has_variables Test 1: error if a required variable is missing (deprecation error)", { # nolint
-  data <- tibble::tribble(
+  data <- dplyr::tribble(
     ~USUBJID,
     "1"
   )
@@ -19,7 +19,7 @@ test_that("assert_has_variables Test 1: error if a required variable is missing
 
 ## Test 2: no error if a required variable exists (deprecation error) ----
 test_that("assert_has_variables Test 2: no error if a required variable exists (deprecation error)", { # nolint
-  data <- tibble::tribble(
+  data <- dplyr::tribble(
     ~USUBJID,
     "1"
   )
@@ -80,7 +80,7 @@ test_that("assert_data_frame Test 4: error if not a dataframe", {
 
 ## Test 5: assert_data_frame extract_vars() works as intended ----
 test_that("assert_data_frame Test 5: assert_data_frame extract_vars() works as intended", {
-  input <- tibble::tribble(
+  input <- dplyr::tribble(
     ~STUDYID, ~USUBJID, ~SEQ,
     "A",      "1",         1,
     "A",      "2",         2,
@@ -99,7 +99,7 @@ test_that("assert_data_frame Test 5: assert_data_frame extract_vars() works as i
 
 ## Test 6: assert_data_frame works if extract_vars() has NULL input ----
 test_that("assert_data_frame Test 6: assert_data_frame works if extract_vars() has NULL input", {
-  input <- tibble::tribble(
+  input <- dplyr::tribble(
     ~STUDYID, ~USUBJID, ~SEQ,
     "A",      "1",         1,
     "A",      "2",         2,
@@ -122,7 +122,7 @@ test_that("assert_data_frame Test 7: error if dataframe is grouped", {
     assert_data_frame(dataset, required_vars = exprs(STUDYID, USUBJID))
   }
 
-  data <- tibble::tribble(
+  data <- dplyr::tribble(
     ~STUDYID, ~USUBJID, ~ARMCD,
     "xyz",    "1",      "PLACEBO",
     "xyz",    "2",      "ACTIVE"
@@ -145,7 +145,7 @@ test_that("assert_data_frame Test 8: error if an expected variable is missing",
     assert_data_frame(dataset, required_vars = exprs(STUDYID, USUBJID))
   }
 
-  data <- tibble::tribble(
+  data <- dplyr::tribble(
     ~STUDYID, ~ARMCD,
     "xyz",    "PLACEBO",
     "xyz",    "ACTIVE"
@@ -167,7 +167,7 @@ test_that("assert_data_frame Test 9: error if expected variables are missing", {
     assert_data_frame(dataset, required_vars = exprs(STUDYID, USUBJID))
   }
 
-  data <- tibble::tribble(
+  data <- dplyr::tribble(
     ~ARMCD,
     "PLACEBO",
     "ACTIVE"
@@ -1004,7 +1004,7 @@ test_that("assert_function_param Test 63: error if expected function parameters
 # assert_unit ----
 ## Test 64: no error if the parameter is provided in the expected unit ----
 test_that("assert_unit Test 64: no error if the parameter is provided in the expected unit", {
-  advs <- tibble::tribble(
+  advs <- dplyr::tribble(
     ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL,
     "P01",    "WEIGHT",      80.1, "kg",      "WEIGHT",  80.1,
     "P02",    "WEIGHT",      85.7, "kg",      "WEIGHT",  85.7
@@ -1017,7 +1017,7 @@ test_that("assert_unit Test 64: no error if the parameter is provided in the exp
 
 ## Test 65: error if there are multiple units in the input dataset ----
 test_that("assert_unit Test 65: error if there are multiple units in the input dataset", {
-  advs <- tibble::tribble(
+  advs <- dplyr::tribble(
     ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL,
     "P01",    "WEIGHT",      80.1, "kg",      "WEIGHT",  80.1,
     "P02",    "WEIGHT",      85.7, "lb",      "WEIGHT",  85.7
@@ -1035,7 +1035,7 @@ test_that("assert_unit Test 65: error if there are multiple units in the input d
 
 ## Test 66: error if unexpected unit in the input dataset ----
 test_that("assert_unit Test 66: error if unexpected unit in the input dataset", {
-  advs <- tibble::tribble(
+  advs <- dplyr::tribble(
     ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL,
     "P01",    "WEIGHT",      80.1, "kg",      "WEIGHT",  80.1,
     "P02",    "WEIGHT",      85.7, "kg",      "WEIGHT",  85.7
@@ -1054,7 +1054,7 @@ test_that("assert_unit Test 66: error if unexpected unit in the input dataset",
 # assert_param_does_not_exist ----
 ## Test 67: error if parameter exists in the input dataset ----
 test_that("assert_param_does_not_exist Test 67: error if parameter exists in the input dataset", {
-  advs <- tibble::tribble(
+  advs <- dplyr::tribble(
     ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL,
     "P01",    "WEIGHT",      80.1, "kg",      "WEIGHT",  80.1,
     "P02",    "WEIGHT",      85.7, "kg",      "WEIGHT",  85.7
@@ -1073,7 +1073,7 @@ test_that("assert_param_does_not_exist Test 67: error if parameter exists in the
 
 ## Test 68: no error if the parameter exists in the dataset ----
 test_that("assert_param_does_not_exist Test 68: no error if the parameter exists in the dataset", {
-  advs <- tibble::tribble(
+  advs <- dplyr::tribble(
     ~USUBJID, ~VSTESTCD, ~VSTRESN, ~VSSTRESU, ~PARAMCD, ~AVAL,
     "P01",    "WEIGHT",      80.1, "kg",      "WEIGHT",  80.1,
     "P02",    "WEIGHT",      85.7, "kg",      "WEIGHT",  85.7
@@ -1291,7 +1291,7 @@ test_that("assert_one_to_one Test 85: error if there is a many to one mapping",
 
 ## Test 86: dataset is returned invisible if one-to-one ----
 test_that("assert_one_to_one Test 86: dataset is returned invisible if one-to-one", {
-  df <- tibble::tribble(
+  df <- dplyr::tribble(
     ~SPECIES, ~SPECIESN,
     "DOG",           1L,
     "CAT",           2L,
@@ -1313,7 +1313,7 @@ test_that("assert_date_var Test 87: error if variable is not a date or datetime
     assert_date_var(dataset = dataset, var = !!var)
   }
 
-  my_data <- tibble::tribble(
+  my_data <- dplyr::tribble(
     ~USUBJID, ~ADT,
     "1",      ymd("2020-12-06"),
     "2",      ymd("")

diff --git a/tests/testthat/test-dataset_vignette.R b/tests/testthat/test-dataset_vignette.R
@@ -4,7 +4,7 @@ test_that("dataset_vignette Test 1: A 'knitr_kable' object is outputted when run
   Sys.setenv(IN_PKGDOWN = "false") # nolint: undesirable_function_linter
   on.exit(Sys.setenv(IN_PKGDOWN = "")) # nolint: undesirable_function_linter
 
-  dm <- tibble::tribble(
+  dm <- dplyr::tribble(
     ~STUDYID, ~USUBJID, ~COUNTRY,
     "STUDY1", "1",      "USA",
     "STUDY1", "2",      "USA",
@@ -21,7 +21,7 @@ test_that("dataset_vignette Test 2: A 'shiny.tag.list' is outputted when run ins
   Sys.setenv(IN_PKGDOWN = "true") # nolint: undesirable_function_linter
   on.exit(Sys.setenv(IN_PKGDOWN = "")) # nolint: undesirable_function_linter
 
-  dm <- tibble::tribble(
+  dm <- dplyr::tribble(
     ~STUDYID, ~USUBJID, ~COUNTRY,
     "STUDY1", "1",      "USA",
     "STUDY1", "2",      "USA",
@@ -36,7 +36,7 @@ test_that("dataset_vignette Test 2: A 'shiny.tag.list' is outputted when run ins
 
 ## Test 3: An error is outputted when calling variable not in dataset ----
 test_that("dataset_vignette Test 3: An error is outputted when calling variable not in dataset", {
-  dm <- tibble::tribble(
+  dm <- dplyr::tribble(
     ~STUDYID, ~USUBJID, ~COUNTRY,
     "STUDY1", "1",      "USA",
     "STUDY1", "2",      "USA",

diff --git a/tests/testthat/test-dev_utilities.R b/tests/testthat/test-dev_utilities.R
@@ -27,7 +27,7 @@ test_that("convert_dtm_to_dtc Test 3: Error is thrown if dtm is not in correct f
 # filter_if ----
 ## Test 4: Input is returned as is if filter is NULL ----
 test_that("filter_if Test 4: Input is returned as is if filter is NULL", {
-  input <- tibble::tribble(
+  input <- dplyr::tribble(
     ~USUBJID, ~VSTESTCD, ~VSSTRESN,
     "P01",    "WEIGHT",       80.9,
     "P01",    "HEIGHT",      189.2
@@ -44,7 +44,7 @@ test_that("filter_if Test 4: Input is returned as is if filter is NULL", {
 
 ## Test 5: Input is filtered if filter is not NULL ----
 test_that("filter_if Test 5: Input is filtered if filter is not NULL", {
-  input <- tibble::tribble(
+  input <- dplyr::tribble(
     ~USUBJID, ~VSTESTCD, ~VSSTRESN,
     "P01",    "WEIGHT",       80.9,
     "P01",    "HEIGHT",      189.2

diff --git a/tests/testthat/test-get.R b/tests/testthat/test-get.R
@@ -1,7 +1,7 @@
 # get_constant_vars ----
 ## Test 1: without ignore_vars ----
 test_that("get_constant_vars Test 1: without ignore_vars", {
-  data <- tibble::tribble(
+  data <- dplyr::tribble(
     ~USUBJID, ~AGE, ~AVISIT,
     "1",      26,   "BASELINE",
     "1",      26,   "WEEK 1",
@@ -17,7 +17,7 @@ test_that("get_constant_vars Test 1: without ignore_vars", {
 
 ## Test 2: with ignore_vars ----
 test_that("get_constant_vars Test 2: with ignore_vars", {
-  data <- tibble::tribble(
+  data <- dplyr::tribble(
     ~USUBJID, ~AGE, ~WGTBL, ~HGTBL, ~AVISIT,
     "1",      26,   61,     172,    "BASELINE",
     "1",      26,   61,     172,    "WEEK 1",