Cran/description

DESCRIPTION

@@ -1,22 +1,24 @@
 Package: neotoma2
 Title: Working with the Neotoma Paleoecology Database
-Date: 2025-12-12
-Version: 1.0.11
+Date: 2026-04-23
+Version: 1.0.12
 Authors@R:
     c(person(given = "Dominguez Vidana",
              family = "Socorro",
              role = c("aut", "cre"),
              email = "dominguezvid@wisc.edu",
-             comment = structure("0000-0002-7926-4935", .Names = "ORCID")),
+             comment = c(ORCID="0000-0002-7926-4935")),
       person(given = "Simon",
              family = "Goring",
              role = c("aut"),
              email = "goring@wisc.edu",
-             comment = structure("0000-0002-2700-4605", .Names = "ORCID")))
+             comment = c(ORCID="0000-0002-2700-4605")))
 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

@@ -1,8 +1,16 @@
 # News neotoma2 R package
 
+## neotoma2 1.0.12
+Updated description file to match CRAN's comments.
+Now follows:
+ comment = c(ORCID = .......)
+
+
 ## 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") %>%

R/get_sites.R

@@ -62,42 +62,19 @@
 #'  * `loc` An `sf` object that describes site's location.
 #'  * `description`
 #'  * `collunits` limited information on collunits
-#' @examples
-#' \donttest{
+#' @examples \dontrun{
 #' ## Find sites with a min altitude of 12m and a max altitude of 25m
-#' tryCatch({
-#'   sites_12to25 <- get_sites(altmin=12, altmax=25)
-#' }, error = function(e) {
-#'   message("Neotoma server not responding. Try again later.")
-#' })
-#' ## Return all sites, using a minimum altitude of 2500m (returns >500 sites):
-#' tryCatch({
-#'   sites_2500 <- get_sites(altmin=2500, all_data = TRUE)
-#' }, error = function(e) {
-#'   message("Neotoma server not responding. Try again later.")
-#' })
-#'   ## To find sites in Brazil
+#' sites_12to25 <- get_sites(altmin=12, altmax=25)
+#' sites_2500 <- get_sites(altmin=2500, all_data = TRUE)
+#' ## To find sites in Brazil
 #' brazil <- '{"type": "Polygon",
 #' "coordinates": [[
 #'  [-73.125, -9.102096738726443],
 #'  [-56.953125,-33.137551192346145],
 #'  [-36.5625,-7.710991655433217],
 #'  [-68.203125,13.923403897723347],
 #'  [-73.125,-9.102096738726443]]]}'
-#' tryCatch({
 #' brazil_sites <- get_sites(loc = brazil[1])
-#' # Finding all sites with Liliaceae pollen in 1000 year bins:
-#' lilysites <- c()
-#' for (i in seq(0, 10000, by = 1000)) {
-#'   lily <- get_sites(taxa=c("Liliaceae"),
-#'                     ageyoung = i - 500,
-#'                     ageold = i + 500,
-#'                     all_data = TRUE)
-#'   lilysites <- c(lilysites, length(lily))
-#' }
-#' }, error = function(e) {
-#'   message("Neotoma server not responding. Try again later.")
-#' })
 #' }
 #' @md
 #' @export

R/get_speleothems.R

@@ -58,13 +58,9 @@ speleo_helper <- function(sites) {
 #'  * `x`  The unique dataset ID (integer) in Neotoma. Can be passed as a
 #' vector of dataset IDs.
 #'  * `sites`  A `sites` R object.
-#' @examples {
+#' @examples \dontrun{
 #' ## Find speleothems by numeric datasetid:
-#' tryCatch({
-#'   speleo <- get_speleothems(c(2,5))
-#' }, error = function(e) {
-#'   message("Neotoma server not responding. Try again later.")
-#' })
+#' speleo <- get_speleothems(c(2,5))
 #' }
 #' @md
 #' @export

R/get_stats.R

@@ -21,7 +21,7 @@
 #' added per month), and \code{dstypemonth} (the number of datasets added
 #' per dataset type per month). Default is \code{dsdbmonth}.
 #' @returns `data.frame` with summary statistics
-#' @examples \donttest{
+#' @examples \dontrun{
 #' tryCatch({
 #' last_month <- get_stats(start = 0, end = 1, type = "dsdbmonth")
 #' }, error = function(e) {

R/get_table.R

@@ -6,13 +6,9 @@
 #' @param limit Default 25 records
 #' @param offset Default 0.
 #' @returns selected `table` values from the Database.
-#' @examples {
+#' @examples \dontrun{
 #' # Returns only the first 25 specimen records.
-#' tryCatch({
 #' someSpec <- get_table('specimens')
-#' }, error = function(e) {
-#'  message("Neotoma server not responding. Try again later.")
-#' })
 #' }
 #' @importFrom dplyr bind_rows
 #' @importFrom purrr map

R/getids.r

@@ -9,13 +9,9 @@
 #' @param x A Neotoma2 \code{sites} or \code{collunits} object.
 #' @param order sort items by `siteid`, `collunitid`, `datasetid`
 #' @returns `data.frame` containing `siteid`, `datasetid`, and `collunitid`
-#' @examples \donttest{
-#' tryCatch({
+#' @examples \dontrun{
 #' marion <- get_sites(sitename = "Marion Lake")
 #' collunitids <- getids(collunits(marion))
-#' }, error = function(e) {
-#'  message("Neotoma server not responding. Try again later.")
-#' })
 #' }
 #' @md
 #' @export

R/pingNeotoma.r

@@ -8,7 +8,7 @@
 #' numeric port), \code{neotoma} or \code{dev}.
 #' @returns A valid HTTP status code or returns an error if a connection
 #' is refused.
-#' @examples {
+#' @examples \dontrun{
 #' test_connection <- pingNeotoma("neotoma")
 #' }
 #' @export

R/plotLeaflet.R

@@ -4,7 +4,7 @@
 #' @importFrom leaflet leaflet addTiles addCircleMarkers 
 #' @importFrom leaflet markerOptions markerClusterOptions
 #' @param object Sites object to plot
-#' @examples \donttest{
+#' @examples \dontrun{
 #' # Note that by default the limit for queries is 25 records:
 #' tryCatch({
 #' modernSites <- get_sites(keyword = "Modern")

R/samples.R

@@ -3,13 +3,10 @@
 #' @author Simon Goring \email{goring@wisc.edu}
 #' @param x sites object
 #' @description Obtain all samples within a sites object
-#' @examples {
-#' tryCatch({
+#' @examples \dontrun{
+#' # Get full data download from API and create a long table with samples data.
 #' dw <- get_downloads(1)
 #' pollen <- samples(dw)
-#' }, error = function(e) {
-#'  message("Neotoma server not responding. Try again later.")
-#' })
 #' }
 #' @importFrom dplyr bind_rows left_join rename mutate
 #' @importFrom purrr map

R/set_server.R

@@ -3,7 +3,7 @@
 #' @importFrom assertthat assert_that
 #' @param server One of \code{local} (when the API is running locally on
 #' port 3005), \code{neotoma} or \code{dev}.
-#' @examples \donttest{
+#' @examples \dontrun{
 #' # The user is running the API locally using the node/express API
 #' # cloned from github: https://github.com/NeotomaDB/api_nodetest
 #' set_server(server = "local")

R/site-methods.R

@@ -48,13 +48,9 @@ setMethod(f = "show",
 #' @description Obtain one of the elements within a `sites`,
 #' `collectionunits`, `datasets`, etc... Neotoma objects.
 #' @returns sliced `site` object
-#' @examples \donttest{
-#' tryCatch({
-#'   some_site <- get_sites(sitename = "Site%", limit=3)
-#'   some_site[[2]]
-#' }, error = function(e) {
-#'   message("Neotoma server not responding. Try again later.")
-#' })
+#' @examples \dontrun{
+#' some_site <- get_sites(sitename = "Site%", limit=3)
+#' some_site[[2]]
 #' }
 #' @aliases [[,sites,numeric-method
 #' @exportMethod [[
@@ -407,13 +403,10 @@ setMethod(f = "summary",
 #' @importFrom dplyr bind_rows full_join select arrange filter 
 #' @importFrom dplyr mutate group_by row_number
 #' @returns `data.frame` object with DOIs information.
-#' @examples {
-#' tryCatch({
+#' @examples \dontrun{
+#' # Get datasets metadata from API and retrieve DOIs
 #' ds <- get_datasets(1)
 #' doi(ds)
-#' }, error = function(e) {
-#' message("Neotoma server not responding. Try again later.")
-#' })
 #' }
 #' @aliases doi,sites-method
 #' @exportMethod doi
@@ -460,13 +453,9 @@ setMethod(f = "doi",
 #' @importFrom purrr map
 #' @importFrom dplyr bind_rows full_join select arrange filter
 #' @returns `data.frame` object with citation information.
-#' @examples {
-#' tryCatch({
+#' @examples \dontrun{
+#' # Get datasets metadata from API
 #' ds <- get_datasets(1)
-#' cite_data(ds)
-#' }, error = function(e) {
-#' message("Neotoma server not responding. Try again later.")
-#' })
 #' }
 #' @aliases cite_data,sites-method
 #' @exportMethod cite_data

R/speleothemdetails.R

@@ -7,16 +7,12 @@
 #' @returns `data.frame` with speleothem records
 #' @description Obtain elements on the speleothems level
 #' Experimental function: API and behavior may change.
-#' @examples \donttest{
-#' tryCatch({
+#' @examples \dontrun{
 #' kesang <- get_sites(sitename = "Kesang cave") %>%
 #'   get_datasets() %>%
 #'   filter(datasettype == "pollen") %>%
 #'   get_speleothems()
 #' sp <- speleothemdetails(kesang)
-#' }, error = function(e) {
-#' message("Neotoma server not responding. Try again later.")
-#' })
 #' }
 #' @md
 #' @export

R/speleothems.R

@@ -7,13 +7,9 @@
 #' @returns `data.frame` with sample records
 #' @description Obtain all speleothems within a sites object
 #' Experimental function: API and behavior may change.
-#' @examples {
-#' tryCatch({
+#' @examples \dontrun{
 #' ds <- get_datasets(37302)
 #' sp <- speleothems(ds)
-#' }, error = function(e) {
-#' message("Neotoma server not responding. Try again later.")
-#' })
 #' }
 #' @md
 #' @export

R/taxa.R

@@ -6,15 +6,11 @@
 #' @returns A \code{data.frame} reporting the taxa/data objects, units,
 #' elements and other features within a set of records.
 #' @description Extract taxonomic data from a set of sites.
-#' @examples \donttest{
-#' tryCatch({
+#' @examples \dontrun{
 #' somesites <- get_sites(datasettype = "diatom") %>%
 #'   get_downloads()
 #' diatomtaxa <- taxa(somesites)
-#' }, error = function(e) {
-#' message("Neotoma server not responding. Try again later.")
-#' })
-#'   }
+#' }
 #' @md
 #' @export
 setMethod(f = "taxa",

R/toWide.R

@@ -14,20 +14,15 @@
 #' @param operation label or vector of operations to be chosen from:
 #' 'prop', 'sum', 'presence'.
 #' @returns wide `data.frame` obtained from long `samples` `data.frame`
-#' @examples
-#' \donttest{
-#' tryCatch({
+#' @examples \dontrun{
 #' fc_sites <- neotoma2::get_datasets(limit=5, datasettype = "vertebrate fauna")
 #' fc_ds <- fc_sites %>%
 #'    neotoma2::get_downloads()
 #' fc_dl1 <- fc_dl[[1]]
 #' fc_smp <- samples(fc_dl1)
 #' toWide(fc_smp, ecologicalgroups=c('AVES', 'RODE'),
 #'        elementtypes='bone/tooth', unit='present/absent')
-#' }, error = function(e) {
-#' message("Neotoma server not responding. Try again later.")
-#' })
-#'}
+#' }
 #' @description Obtain a wide table with information regarding of
 #' samples grouped by variablename and depth/age.
 #' @export