Merge pull request #68 from olivroy/cran-check

Cran check
ropensci · Oct 27, 2023 · 7508525 · 7508525
2 parents 05fcd88 + 49c3f56
commit 7508525
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -22,21 +22,19 @@ RoxygenNote: 7.2.3
 Imports:
     ape,
     beautier (>= 2.6.9),
-    devtools,
     phangorn,
     rappdirs,
     readr,
     rJava,
+    rlang (>= 1.1.0),
+    sessioninfo,
     stringr,
     tibble,
     xml2
 Suggests:
-    hunspell,
     knitr,
-    markdown,
     rmarkdown,
     spelling,
-    testit,
     testthat (>= 2.1.0),
     tracerer (>= 2.2.3)
 URL: https://docs.ropensci.org/beastier/ (website)

diff --git a/NAMESPACE b/NAMESPACE
@@ -99,6 +99,7 @@ export(run_beast2_from_options)
 export(save_lines)
 export(save_nexus_as_fasta)
 export(uninstall_beast2)
+import(rlang)
 importFrom(beautier,check_rename_fun)
 importFrom(beautier,create_alpha_param)
 importFrom(beautier,create_bd_tree_prior)

diff --git a/R/are_beast2_input_lines.R b/R/are_beast2_input_lines.R
@@ -27,20 +27,20 @@ are_beast2_input_lines <- function(
     stop("'method' must be \"deep\" or \"fast\", value was '", method, "'")
   }
   if (method == "deep") {
-    filename <- beastier::get_beastier_tempfilename()
+    filename <- get_beastier_tempfilename()
     dir.create(dirname(filename), showWarnings = FALSE, recursive = TRUE)
-    beastier::save_lines(filename = filename, lines = lines)
-    is_valid <- beastier::are_beast2_input_lines_deep(
+    save_lines(filename = filename, lines = lines)
+    is_valid <- are_beast2_input_lines_deep(
       lines = lines,
       verbose = verbose,
       beast2_path = beast2_path
     )
     file.remove(filename)
     return(is_valid)
   } else {
-    testit::assert(method == "fast")
+    check_true(method == "fast")
     return(
-      beastier::are_beast2_input_lines_fast(lines) # nolint internal function
+      are_beast2_input_lines_fast(lines) # nolint internal function
     )
   }
 }
@@ -67,10 +67,10 @@ are_beast2_input_lines_deep <- function(
   verbose = FALSE,
   beast2_path = get_default_beast2_path()
 ) {
-  filename <- beastier::create_temp_input_filename()
+  filename <- create_temp_input_filename()
   dir.create(dirname(filename), recursive = TRUE, showWarnings = FALSE)
-  beastier::save_lines(filename = filename, lines = lines)
-  is_valid <- beastier::is_beast2_input_file(
+  save_lines(filename = filename, lines = lines)
+  is_valid <- is_beast2_input_file(
     filename = filename,
     verbose = verbose,
     beast2_path = beast2_path
@@ -97,5 +97,5 @@ are_beast2_input_lines_deep <- function(
 are_beast2_input_lines_fast <- function(
   lines
 ) {
-  beastier::has_unique_ids(lines)
+  has_unique_ids(lines)
 }
diff --git a/R/are_identical_alignments.R b/R/are_identical_alignments.R
@@ -5,10 +5,10 @@
 #' @author Richèl J.C. Bilderbeek
 #' @export
 are_identical_alignments <- function(p, q) {
-  if (!beastier::is_alignment(p)) {
+  if (!is_alignment(p)) {
     stop("p must be an alignment")
   }
-  if (!beastier::is_alignment(q)) {
+  if (!is_alignment(q)) {
     stop("q must be an alignment")
   }
   return(identical(p, q))

diff --git a/R/beast2_options_to_table.R b/R/beast2_options_to_table.R
@@ -9,7 +9,7 @@
 #' @author Richèl J.C. Bilderbeek
 #' @export
 beast2_options_to_table <- function(beast2_options) {
-  beastier::check_beast2_options(beast2_options)
+  check_beast2_options(beast2_options)
   tibble::tibble(
     parameter = names(beast2_options),
     value = unlist(beast2_options)

diff --git a/R/beastier-package.R b/R/beastier-package.R
@@ -159,5 +159,6 @@
 "_PACKAGE"
 
 ## usethis namespace: start
+#' @import rlang
 ## usethis namespace: end
 NULL
diff --git a/R/beastier_report.R b/R/beastier_report.R
@@ -21,7 +21,7 @@ beastier_report <- function(
   message("***********")
   message("OS: ", os)
   message("beast2_folder: ", beast2_folder)
-  beast2_path <- beastier::get_default_beast2_path(
+  beast2_path <- get_default_beast2_path(
     beast2_folder = beast2_folder
   )
   message("beast2_path: ", beast2_path)
@@ -33,23 +33,23 @@ beastier_report <- function(
   message("**********")
   message("* BEAST2 *")
   message("**********")
-  message("Java version: ", beastier::get_java_version())
+  message("Java version: ", get_java_version())
   message(
     "Is BEAST2 installed: ",
-    beastier::is_beast2_installed(folder_name = beast2_folder)
+    is_beast2_installed(folder_name = beast2_folder)
   )
-  if (beastier::is_beast2_installed(folder_name = beast2_folder)) {
+  if (is_beast2_installed(folder_name = beast2_folder)) {
     message(
       "BEAST2 version: ",
-      beastier::get_beast2_version(beast2_path = beast2_path)
+      get_beast2_version(beast2_path = beast2_path)
     )
     message(
       "BEAST2 default path: ",
-      beastier::get_default_beast2_bin_path(beast2_folder = beast2_folder)
+      get_default_beast2_bin_path(beast2_folder = beast2_folder)
     )
   }
   message("****************")
   message("* session info *")
   message("****************")
-  message(paste0(devtools::session_info(), collapse = "\n"))
+  message(paste0(sessioninfo::session_info(), collapse = "\n"))
 }
diff --git a/R/check_beast2.R b/R/check_beast2.R
@@ -11,11 +11,11 @@
 #' @author Richèl J.C. Bilderbeek
 #' @export
 check_beast2 <- function(
-  beast2_path = beastier::get_default_beast2_path()
+  beast2_path = get_default_beast2_path()
 ) {
   tryCatch({
-    beastier::is_beast2_input_file(
-      filename = beastier::get_beastier_path("anthus_2_4.xml"),
+    is_beast2_input_file(
+      filename = get_beastier_path("anthus_2_4.xml"),
       beast2_path = beast2_path
     )
   }, error = function(e) {

diff --git a/R/check_beast2_options.R b/R/check_beast2_options.R
@@ -17,12 +17,12 @@
 check_beast2_options <- function(
   beast2_options
 ) {
-  beastier::check_beast2_options_names(beast2_options)
-  beastier::check_beast2_options_data_types(beast2_options)
+  check_beast2_options_names(beast2_options)
+  check_beast2_options_data_types(beast2_options)
   # Do not check if the BEAST2 path already/still exist.
   # It shouldn't be checked by here, only when actually running BEAST2.
   # By doing so, data with beast2_options can be analysed on different computers
-  beastier::check_beast2_options_filenames_differ(beast2_options)
+  check_beast2_options_filenames_differ(beast2_options)
 }
 
 #' Check if the \code{beast2_options}, which is a list,
@@ -67,17 +67,17 @@ check_beast2_options_names <- function( # nolint long function name indeed, whic
 check_beast2_options_data_types <- function( # nolint long function name indeed, which is fine for an internal function
   beast2_options
 ) {
-  testthat::expect_true(beautier::is_one_string(beast2_options$input_filename))
-  testthat::expect_true(beautier::is_one_string(beast2_options$output_state_filename))
-  beastier::check_rng_seed(beast2_options$rng_seed)
-  beastier::check_n_threads(beast2_options$n_threads)
+  check_true(beautier::is_one_string(beast2_options$input_filename))
+  check_true(beautier::is_one_string(beast2_options$output_state_filename))
+  check_rng_seed(beast2_options$rng_seed)
+  check_n_threads(beast2_options$n_threads)
   if (!beautier::is_one_bool(beast2_options$use_beagle)) {
     stop("'use_beagle' must be one boolean")
   }
   if (!beautier::is_one_bool(beast2_options$overwrite)) {
     stop("'overwrite' must be one boolean")
   }
-  testthat::expect_true(beautier::is_one_string(beast2_options$beast2_path))
+  check_true(beautier::is_one_string(beast2_options$beast2_path))
   if (!beautier::is_one_bool(beast2_options$verbose)) {
     stop("'verbose' must be one boolean")
   }

diff --git a/R/check_beast2_options_do_not_overwrite_existing_files.R b/R/check_beast2_options_do_not_overwrite_existing_files.R
@@ -19,7 +19,7 @@
 check_beast2_options_do_not_overwrite_existing_files <- function( # nolint indeed a long function name, which is fine for internal functions
   beast2_options
 ) {
-  beastier::check_beast2_options(beast2_options)
+  check_beast2_options(beast2_options)
   if (beast2_options$overwrite) {
     return(invisible(beast2_options))
   }

diff --git a/R/check_beast2_optionses.R b/R/check_beast2_optionses.R
@@ -22,6 +22,6 @@ check_beast2_optionses <- function(
   }
   for (i in seq_along(beast2_optionses)) {
     # Stub with too simple error message
-    beastier::check_beast2_options(beast2_optionses[[i]])
+    check_beast2_options(beast2_optionses[[i]])
   }
 }
diff --git a/R/check_can_create_dir_for_state_output_file.R b/R/check_can_create_dir_for_state_output_file.R
@@ -19,7 +19,7 @@
 check_can_create_dir_for_state_output_file <- function( # nolint indeed a long function name
   beast2_options
 ) {
-  beastier::check_beast2_options(beast2_options)
+  check_beast2_options(beast2_options)
   folder <- dirname(beast2_options$output_state_filename)
 
   # If it exists, that folder can be created

diff --git a/R/check_can_create_file.R b/R/check_can_create_file.R
@@ -28,7 +28,7 @@ check_can_create_file <- function(
     } else {
       # Delete the file
       file.remove(filename)
-      testthat::expect_true(
+      check_true(
         !file.exists(filename),
         info = paste0(
           "Cannot delete the file already present at location ", filename
@@ -58,7 +58,7 @@ check_can_create_file <- function(
   }
 
 
-  testthat::expect_true(
+  check_true(
     !file.exists(filename),
     info = paste0(
       "Cannot delete the temporary file created at location ", filename

diff --git a/R/check_can_create_screenlog_file.R b/R/check_can_create_screenlog_file.R
@@ -11,18 +11,18 @@ check_can_create_screenlog_file <- function( # nolint indeed a long function nam
   beast2_options
 ) {
   # Extract the screenlog file
-  testthat::expect_true(file.exists(beast2_options$input_filename))
+  check_true(file.exists(beast2_options$input_filename))
   text <- readr::read_lines(beast2_options$input_filename, progress = FALSE)
   screenlog_line <- stringr::str_subset(
     string = text,
     pattern = "<logger id=\"screenlog\""
   )
-  testthat::expect_equal(length(screenlog_line), 1)
+  check_true(length(screenlog_line) == 1)
   matches <- stringr::str_match(
     string = screenlog_line,
     pattern = "fileName=\\\"([:graph:]+)\\\" "
   )
-  testthat::expect_equal(ncol(matches), 2)
+  check_true(ncol(matches) == 2)
   screenlog_filename <- matches[1, 2]
 
   if (is.na(screenlog_filename)) return()
@@ -32,7 +32,7 @@ check_can_create_screenlog_file <- function( # nolint indeed a long function nam
   }
 
   tryCatch(
-    beastier::check_can_create_file(
+    check_can_create_file(
       filename = screenlog_filename, overwrite = FALSE
     ),
     error = function(e) {

diff --git a/R/check_can_create_state_output_file.R b/R/check_can_create_state_output_file.R
@@ -10,8 +10,8 @@
 check_can_create_state_output_file <- function( # nolint indeed a long function name
   beast2_options
 ) {
-  beastier::check_beast2_options(beast2_options)
-  beastier::check_can_create_dir_for_state_output_file(beast2_options)
+  check_beast2_options(beast2_options)
+  check_can_create_dir_for_state_output_file(beast2_options)
   if (file.exists(beast2_options$output_state_filename)) {
     return(invisible(beast2_options))
   }
@@ -24,7 +24,7 @@ check_can_create_state_output_file <- function( # nolint indeed a long function
 
   # Use a more precise error message
   tryCatch(
-    beastier::check_can_create_file(
+    check_can_create_file(
       filename = beast2_options$output_state_filename,
       overwrite = FALSE
     ),

diff --git a/R/check_can_create_tracelog_file.R b/R/check_can_create_tracelog_file.R
@@ -13,8 +13,8 @@
 check_can_create_tracelog_file <- function(
   beast2_options
 ) {
-  testthat::expect_true(file.exists(beast2_options$input_filename))
-  tracelog_filename <- beastier::extract_tracelog_filename_from_beast2_input_file( # nolint indeed a long internal function name
+  check_true(file.exists(beast2_options$input_filename))
+  tracelog_filename <- extract_tracelog_filename_from_beast2_input_file( # nolint indeed a long internal function name
     input_filename = beast2_options$input_filename
   )
 
@@ -24,7 +24,7 @@ check_can_create_tracelog_file <- function(
   }
 
   tryCatch(
-    beastier::check_can_create_file(
+    check_can_create_file(
       filename = tracelog_filename, overwrite = FALSE
     ),
     error = function(e) {

diff --git a/R/check_can_create_treelog_file.R b/R/check_can_create_treelog_file.R
@@ -11,8 +11,8 @@ check_can_create_treelog_file <- function(
   beast2_options
 ) {
   # Extract the treelog file
-  testthat::expect_true(file.exists(beast2_options$input_filename))
-  treelog_filename <- beastier::extract_treelog_filename_from_beast2_input_file(
+  check_true(file.exists(beast2_options$input_filename))
+  treelog_filename <- extract_treelog_filename_from_beast2_input_file(
     input_filename = beast2_options$input_filename
   )
 
@@ -22,7 +22,7 @@ check_can_create_treelog_file <- function(
   }
 
   tryCatch(
-    beastier::check_can_create_file(
+    check_can_create_file(
       filename = treelog_filename, overwrite = FALSE
     ),
     error = function(e) {

diff --git a/R/check_input_filename.R b/R/check_input_filename.R
@@ -44,7 +44,7 @@ check_input_filename_validity <- function(
   verbose <- beast2_options$verbose
 
   if (
-    !beastier::is_beast2_input_file(
+    !is_beast2_input_file(
       filename = input_filename,
       verbose = verbose,
       beast2_path = beast2_path
@@ -53,7 +53,7 @@ check_input_filename_validity <- function(
     stop(
       "'input_filename' must be a valid BEAST2 XML file. ",
       "File '", input_filename, "' is not a valid BEAST2 file. ",
-      beastier::is_beast2_input_file(
+      is_beast2_input_file(
         input_filename,
         verbose = verbose,
         beast2_path = beast2_path

diff --git a/R/check_rng_seed.R b/R/check_rng_seed.R
@@ -30,7 +30,7 @@ check_rng_seed <- function(rng_seed) {
       "Actual value: ", rng_seed
     )
   }
-  testthat::expect_true(beautier::is_one_int(rng_seed))
+  check_true(beautier::is_one_int(rng_seed))
   if (rng_seed <= 0) {
     stop(
       "'rng_seed' should be one NA or one non-zero positive value.\n",