Cran/description by sedv8808 · Pull Request #54 · NeotomaDB/neotoma2

sedv8808 · 2026-04-23T19:23:03Z

Modified Description to match the new CRAN requirements

…t all

Modified description file for ORCIDs

Fixed some of the links to point to the right workshop links.

Copilot

Pull request overview

Updates the package’s metadata and documentation to comply with CRAN requirements around internet access (API-backed examples/vignettes) and corrects the Authors@R ORCID formatting per CRAN feedback.

Changes:

Updated DESCRIPTION (version/date, Authors@R ORCID format, and expanded Description text).
Converted many examples to \dontrun{} and set vignette chunks to not evaluate during checks.
Updated ancillary release/CRAN docs (NEWS, cran-comments, codemeta) and some workshop links.

Reviewed changes

Copilot reviewed 51 out of 52 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
vignettes/neotoma2-package.Rmd	Adds CRAN internet-access note; disables chunk evaluation globally; updates chunk headers/links.
DESCRIPTION	Bumps version/date; changes `Authors@R` ORCID formatting; adds CRAN-related Description sentences.
NEWS.md	Adds 1.0.12 notes and updates prior release notes for CRAN behavior.
cran-comments.md	Adds notes about CRAN feedback and summarizes the CRAN-related adjustments.
codemeta.json	Updates version and expands description to mention CRAN check behavior.
R/toWide.R	Switches roxygen examples to `\dontrun{}`.
R/taxa.R	Switches roxygen examples to `\dontrun{}`.
R/speleothems.R	Switches roxygen examples to `\dontrun{}`.
R/speleothemdetails.R	Switches roxygen examples to `\dontrun{}`.
R/site-methods.R	Switches roxygen examples to `\dontrun{}` for `[[`, `doi`, `cite_data`.
R/set_server.R	Switches roxygen examples to `\dontrun{}`.
R/samples.R	Switches roxygen examples to `\dontrun{}`.
R/plotLeaflet.R	Switches roxygen examples to `\dontrun{}`.
R/pingNeotoma.r	Switches roxygen examples to `\dontrun{}`.
R/getids.r	Switches roxygen examples to `\dontrun{}`.
R/get_table.R	Switches roxygen examples to `\dontrun{}`.
R/get_stats.R	Switches roxygen examples to `\dontrun{}`.
R/get_speleothems.R	Switches roxygen examples to `\dontrun{}`.
R/get_sites.R	Switches roxygen examples to `\dontrun{}` and simplifies example content.
R/get_publications.R	Switches roxygen examples to `\dontrun{}`.
R/get_manual.R	Switches roxygen examples to `\dontrun{}`.
R/get_downloads.R	Switches roxygen examples to `\dontrun{}`.
R/get_documentation.R	Switches roxygen examples to `\dontrun{}`.
R/get_datasets.R	Switches roxygen examples to `\dontrun{}`.
R/filter.R	Switches roxygen examples to `\dontrun{}`.
R/clean.R	Switches roxygen examples to `\dontrun{}`.
R/01_classDefinitions.R	Wraps class example in braces.
man/toWide.Rd	Converts example to `\dontrun{}` and removes tryCatch wrapper.
man/taxa-sites-method.Rd	Converts example to `\dontrun{}` and removes tryCatch wrapper.
man/sub-sub.Rd	Converts example to `\dontrun{}` and removes tryCatch wrapper.
man/speleothems-sites-method.Rd	Converts example to `\dontrun{}` and removes tryCatch wrapper.
man/speleothemdetails-sites-method.Rd	Converts example to `\dontrun{}` and removes tryCatch wrapper.
man/set_server.Rd	Converts example to `\dontrun{}`.
man/samples-sites-method.Rd	Converts example to `\dontrun{}` and removes tryCatch wrapper.
man/plotLeaflet-sites-method.Rd	Converts example to `\dontrun{}` (keeps tryCatch).
man/pingNeotoma.Rd	Converts example to `\dontrun{}`.
man/getids.Rd	Converts example to `\dontrun{}` and removes tryCatch wrapper.
man/get_table.Rd	Converts example to `\dontrun{}` and removes tryCatch wrapper.
man/get_stats.Rd	Converts example to `\dontrun{}`.
man/get_speleothems.Rd	Converts example to `\dontrun{}` and removes tryCatch wrapper.
man/get_sites.Rd	Converts example to `\dontrun{}` and simplifies example content.
man/get_publications.Rd	Converts example to `\dontrun{}`.
man/get_manual.Rd	Converts example to `\dontrun{}`.
man/get_downloads.Rd	Converts example to `\dontrun{}`.
man/get_documentation.Rd	Converts example to `\dontrun{}`.
man/get_datasets.Rd	Converts example to `\dontrun{}`.
man/filter.Rd	Converts example to `\dontrun{}`.
man/doi-sites-method.Rd	Converts example to `\dontrun{}` and removes tryCatch wrapper.
man/contacts_classes.Rd	Wraps class example in braces.
man/clean.Rd	Converts example to `\dontrun{}`.
man/cite_data-sites-method.Rd	Converts example to `\dontrun{}` but no longer calls `cite_data()`.

Comments suppressed due to low confidence (1)

vignettes/neotoma2-package.Rmd:32

The setup_md chunk defines safe_eval, but it won’t run because chunk evaluation is globally disabled immediately before this (and the function is not used elsewhere in the vignette). Either remove this helper or explicitly set this chunk to eval=TRUE and use it for inline fallbacks, to avoid dead/unreachable setup code.

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Copilot · 2026-04-23T19:27:45Z

+> **Note**
+> This package is an interface to an external web API.
+> To comply with CRAN policies on Internet access, code examples in this vignette
+> are shown but not executed during CRAN checks.
+> Users can run all examples locally after installation.
+
 ```{r setOpts, include = FALSE}
-knitr::opts_chunk$set(
-  collapse = TRUE,
-  comment = "#>"
-)
-api_available <- FALSE
-res <- pingNeotoma()
-if (res$status_code == 200) {
-    api_available <- TRUE
-  }
-# Disable evaluation globally if API is down
 knitr::opts_chunk$set(eval = FALSE,
                      error = TRUE)


knitr::opts_chunk$set(eval = FALSE) disables evaluation for all vignette builds, not just CRAN checks. This contradicts the note that examples are only not executed during CRAN checks. Consider gating eval on an environment signal (e.g., Sys.getenv("NOT_CRAN") / isTRUE(getOption("pkg.build_vignettes"))) so local vignette builds can still run while CRAN remains non-executing.

Copilot · 2026-04-23T19:27:46Z

-#' tryCatch({
+#' @examples \dontrun{
+#' # Get datasets metadata from API
 #' ds <- get_datasets(1)


The cite_data roxygen example no longer demonstrates the function being documented (it only assigns ds <- get_datasets(1) and then stops). Add a call to cite_data(ds) (or an equivalent minimal usage) so the generated Rd example remains meaningful, even when wrapped in \dontrun{}.

Suggested change

#' ds <- get_datasets(1)

#' ds <- get_datasets(1)

#' cite_data(ds)

Copilot · 2026-04-23T19:27:46Z

 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.


The added DESCRIPTION text focuses on CRAN-check behavior (and includes multiple long lines). CRAN may flag non-functional/administrative content in the package Description and/or lines >80 characters. Consider keeping Description focused on what the package does, moving CRAN-check specifics to cran-comments/README, and reflowing Description lines to stay within recommended width.

Suggested change

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.

Description: Access and manipulate data from the Neotoma Paleoecology

Database. See <https://api.neotomadb.org/api-docs/>.

Copilot · 2026-04-23T19:27:47Z

    c(person(given = "Dominguez Vidana",
             family = "Socorro",


In Authors@R, the first author’s given/family names appear swapped (given = "Dominguez Vidana", family = "Socorro"). Other project metadata (e.g., CITATION.cff) lists given-names: Socorro and family-names: Dominguez Vidana, so DESCRIPTION likely should match to ensure correct author display on CRAN.

Suggested change

c(person(given = "Dominguez Vidana",

family = "Socorro",

c(person(given = "Socorro",

family = "Dominguez Vidana",

sedv8808 added 3 commits December 13, 2025 22:11

Uploading examples to include dontrun instead to avoid touching api a…

b1e0e3f

…t all

NRP-80 Fixed structore to match CRAN's policies

da06917

Modified description file for ORCIDs

NRP-80 CRAN sub prep

1a69886

Fixed some of the links to point to the right workshop links.

Copilot AI review requested due to automatic review settings April 23, 2026 19:23

Copilot started reviewing on behalf of sedv8808 April 23, 2026 19:23 View session

Copilot AI reviewed Apr 23, 2026

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kurtlindberg mentioned this pull request May 5, 2026

Update Authors@R formatting #55

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	#' ds <- get_datasets(1)
	#' ds <- get_datasets(1)
	#' cite_data(ds)

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Pull request overview

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