Fixing issues with R CMD checks

LimaRAF · Apr 26, 2024 · b863587 · b863587
1 parent 545645c
commit b863587
Show file tree

Hide file tree

Showing 11 changed files with 47 additions and 37 deletions.
diff --git a/R/gbifNames.R b/R/gbifNames.R
@@ -19,8 +19,7 @@
 #' @source \url{https://hosted-datasets.gbif.org/datasets/backbone/current/}
 #' @evalRd .readScript("data-raw/gbif/last_update.txt", 
 #'  "Last update/change of the downloaded backbone (year-month-day):")
-#' @evalRd .readScript("data-raw/gbif/df_dim_Plantae.txt", 
-#'  "A data frame with:", "format")
+#' @format An object of class \code{data.frame} with 12 columns and over 1.9 million rows.
 #' @evalRd .readScript("data-raw/gbif/citation.txt", "", "references")
 #'  
 "gbifNamesPlantae"
@@ -46,8 +45,7 @@
 #' @source \url{https://hosted-datasets.gbif.org/datasets/backbone/current/}
 #' @evalRd .readScript("data-raw/gbif/last_update.txt", 
 #'  "Last update/change of the downloaded backbone (year-month-day):")
-#' @evalRd .readScript("data-raw/gbif/df_dim_Fungi.txt", 
-#'  "A data frame with:", "format")
+#' @format An object of class \code{data.frame} with 12 columns and almost 400 thousand rows.
 #' @evalRd .readScript("data-raw/gbif/citation.txt", "", "references")
 #'  
 "gbifNamesFungi"
@@ -73,8 +71,7 @@
 #' @source \url{https://hosted-datasets.gbif.org/datasets/backbone/current/}
 #' @evalRd .readScript("data-raw/gbif/last_update.txt", 
 #'  "Last update/change of the downloaded backbone (year-month-day):")
-#' @evalRd .readScript("data-raw/gbif/df_dim_Animalia.txt", 
-#'  "A data frame with:", "format")
+#' @format An object of class \code{data.frame} with 12 columns and over 3.7 million rows.
 #' @evalRd .readScript("data-raw/gbif/citation.txt", "", "references")
 #'  
 "gbifNamesAnimalia"
diff --git a/R/internals.R b/R/internals.R
@@ -89,6 +89,9 @@
 #'  
 #' @keywords internal
 #'
+#' @importFrom httr GET content
+#' @importFrom rvest html_element html_text html_text2
+#' 
 #' @noRd
 #' 
 .getUpdates <- function (url = NULL, source = NULL, pattern = NULL) {

diff --git a/R/wcvpNames.R b/R/wcvpNames.R
@@ -20,8 +20,7 @@
 #' @source \url{https://sftp.kew.org/pub/data-repositories/WCVP/}
 #' @evalRd .readScript("data-raw/wcvp/last_update.txt", 
 #'  "Last update/change of the downloaded backbone (year-month-day):")
-#' @evalRd .readScript("data-raw/wcvp/df_dim.txt", 
-#'  "A data frame with:", "format")
+#' @format An object of class \code{data.frame} with 10 columns and over 1.4 million rows.
 #' @references 
 #'   Govaerts, R., Nic Lughadha, E., Black, N. et al. (2021). The
 #'   World Checklist of Vascular Plants, a continuously updated

diff --git a/R/wfoNames.R b/R/wfoNames.R
@@ -19,13 +19,12 @@
 #' @usage data(wfoNames)
 #' @source \url{https://files.worldfloraonline.org/files/WFO_Backbone/_WFOCompleteBackbone/}
 #' @evalRd .readScript("data-raw/wfo/last_update.txt", 
-#'  "Last update/change of the downloaded backbone (year-month-day):")
-#' @evalRd .readScript("data-raw/wfo/df_dim.txt", 
-#'  "A data frame with:", "format")
+#'  "Last update of the downloaded backbone (month/day/year):")
+#' @format An object of class \code{data.frame} with 11 columns and over 1.5 million rows.
 #' @references 
 #'   Borsch, T., Berendsohn, W., Dalcin, E., et al. (2020). World
 #'   Flora Online: Placing taxonomists at the heart of a definitive
-#'   and comprehensive global resource on the world’s plants. Taxon,
-#'   69(6): 1311–1341. https://doi.org/10.1002/tax.12373
+#'   and comprehensive global resource on the world's plants. Taxon
+#'   69: 1311-1341. https://doi.org/10.1002/tax.12373
 #' 
 "wfoNames"
diff --git a/man/gbifNamesAnimalia.Rd b/man/gbifNamesAnimalia.Rd
diff --git a/man/gbifNamesFungi.Rd b/man/gbifNamesFungi.Rd
diff --git a/man/gbifNamesPlantae.Rd b/man/gbifNamesPlantae.Rd
diff --git a/man/plantRdata-package.Rd b/man/plantRdata-package.Rd
diff --git a/man/wcvpNames.Rd b/man/wcvpNames.Rd
diff --git a/man/wfoNames.Rd b/man/wfoNames.Rd
diff --git a/tests/testthat/tests.R b/tests/testthat/tests.R
@@ -13,10 +13,27 @@ test_that("Testing .buildName", {
 })
 
 test_that("Testing .readScript", {
-  x <- .readScript("data-raw/wfo/last_update.txt")
-  testthat::expect_false(is.null(x), FALSE)
   testthat::expect_error(.readScript())
   testthat::expect_warning(
-  testthat::expect_error(.readScript("data-raw/wfo/xuxu.txt"))
+  testthat::expect_error(.readScript("xuxu.txt"))
   )
 })
+
+test_that("Testing .getUpdates", {
+
+  url0 <- "https://files.worldfloraonline.org/files/WFO_Backbone/_WFOCompleteBackbone/"
+  zip <- "WFO_Backbone.zip"
+  last_updated <- .getUpdates(url0, "wfo", zip)
+  testthat::expect_equal(last_updated, "1/22/2024")
+
+  url0 <- "https://sftp.kew.org/pub/data-repositories/WCVP/"
+  zip <- "wcvp.zip"
+  last_updated <- .getUpdates(url0, "wcvp", zip)
+  testthat::expect_equal(last_updated, "2023-10-04")
+
+  url0 <- "https://hosted-datasets.gbif.org/datasets/backbone/current/"
+  zip <- "backbone.zip"
+  last_updated <- .getUpdates(url0, "gbif", zip)
+  testthat::expect_equal(last_updated, "2023-08-28")
+
+})