Uploading examples to include dontrun instead to avoid touching api at all

Author: sedv8808

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: neotoma2
 Title: Working with the Neotoma Paleoecology Database
-Date: 2025-12-12
+Date: 2025-12-13
 Version: 1.0.11
 Authors@R:
     c(person(given = "Dominguez Vidana",
@@ -17,6 +17,8 @@ URL: https://github.com/NeotomaDB/neotoma2
 BugReports: https://github.com/NeotomaDB/neotoma2/issues
 Description: Access and manipulation of data using the Neotoma Paleoecology Database.
         <https://api.neotomadb.org/api-docs/>.
+        Examples in functions that require API access are not executed during CRAN checks.
+        Vignettes do not execute as to avoid API calls during CRAN checks.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

NEWS.md

@@ -2,7 +2,9 @@
 
 ## neotoma2 1.0.11
 
-Added flag error=True to all vignette codechunks to not run when API is down in case API comes down in between a knitting.
+Set examples to \dontrun{} to avoid violating CRAN's policy that allows access to internet.
+Set vignettes to `eval=FALSE` as to avoid calling APIs that require access to internet.
+Set all tests that require API call to `skip on CRAN`.
 
 ## neotoma2 1.0.10
 

R/01_classDefinitions.R

@@ -7,8 +7,9 @@ setClassUnion("id", c("character", "integer", "numeric"))
 #' @name contacts_classes
 #' @description An unordered list of individual S4 `contact` objects.
 #' @export
-#' @examples
+#' @examples {
 #' new("contact", familyname = "Goring", givennames = "Simon J.")
+#' }
 #' @returns object of class `contact`
 #' @aliases contact-class
 #' @md

R/clean.R

@@ -16,7 +16,7 @@
 #'   * After: \{site: 1, dataset: \[1, 2\]\}
 #' So the site is gathered, and the datasets are now part of an
 #' array of datasets.
-#' @examples \donttest{
+#' @examples \dontrun{
 #' tryCatch({
 #'   alex <- get_sites(sitename = "Alex%")
 #'   alex2 <- get_sites(24)

R/filter.R

@@ -49,7 +49,7 @@
 #' @param .by (only used for filtering `data.frame` objects)
 #' @param .preserve (only used for filtering `data.frame` objects)
 #' @returns filtered `sites` object
-#' @examples \donttest{
+#' @examples \dontrun{
 #' # Download 10 sites, but only keep the sites that are close to sea level.
 #' tryCatch({
 #'  some_sites <- get_sites(sitename = "Lake%", limit = 3)

R/get_datasets.R

@@ -60,7 +60,7 @@
 #' record.
 #'  * `all_data` The API only downloads the first 25 records of the query. 
 #'  For the complete records, use `all_data=TRUE`
-#' @examples \donttest{
+#' @examples \dontrun{
 #' tryCatch({
 #'   random_sites <- get_sites(1)
 #'   allds <- get_datasets(random_sites, limit=3)

R/get_documentation.R

@@ -4,7 +4,7 @@
 #' @importFrom utils browseURL
 #' @importFrom rlang is_interactive
 #' @returns NULL
-#' @examples \donttest{
+#' @examples \dontrun{
 #' if (interactive()) {
 #'  get_documentation()
 #' }

R/get_downloads.R

@@ -48,7 +48,7 @@
 #' \item{ \code{pi list} }{P.I. info}
 #' \item{ \code{analyst} }{analyst info}
 #' \item{ \code{metadata} }{dataset metadata}
-#' @examples \donttest{
+#' @examples \dontrun{
 #' # To find the downloads object of dataset 24:
 #' tryCatch({
 #'   downloads24 <- get_downloads(24)

R/get_manual.R

@@ -3,7 +3,7 @@
 #' @description Open up the Neotoma manual homepage.
 #' @importFrom utils browseURL
 #' @importFrom rlang is_interactive
-#' @examples {
+#' @examples \dontrun{
 #' # This call does not work from `source()` calls or in testing.
 #' # interactive() just lets us know you are interacting with the console:
 #' if (interactive()) {

R/get_publications.R

@@ -17,7 +17,7 @@
 #' `year` The year the publication was released.
 #' `search` A plain text search string used to search the citation.
 #' @returns `publications` object
-#' @examples \donttest{
+#' @examples \dontrun{
 #' # How old are the papers in Neotoma that include the term "mammut"?
 #' tryCatch({
 #'   mammoth_papers <- get_publications(search="mammut") %>%