Fix gh-pages build issues (#125)

* Fix GH Action dependency issue

This temporary fix resolves the failing website build and deployment to the gh-pages branch of the EMLassemblyline GitHub (GH) repository. This GH Action is defined in pkgdown.yml. More information on the fix is at r-lib/actions#559.

* Tag internal only funcs for doc build

Internal only use functions should be tagged or pkgdown fails.

.github/workflows/pkgdown.yaml

@@ -32,6 +32,7 @@ jobs:
         with:
           extra-packages: any::pkgdown, local::.
           needs: website
+          pak-version: devel # See https://github.com/r-lib/actions/issues/559
 
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)

DESCRIPTION

@@ -30,7 +30,7 @@ Suggests: testthat
 License: MIT
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.0
 Remotes:
     EDIorg/taxonomyCleanr
 URL: https://github.com/EDIorg/EMLassemblyline,

NAMESPACE

@@ -1,9 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
 export(annotate_eml)
-export(api_get_provenance_metadata)
-export(detect_delimeter)
-export(detect_os)
 export(eml2eal)
 export(eml2eal_losses)
 export(issues)
@@ -18,8 +15,4 @@ export(template_geographic_coverage)
 export(template_provenance)
 export(template_table_attributes)
 export(template_taxonomic_coverage)
-export(url_env)
-export(validate_file_names)
-export(validate_path)
 export(view_unit_dictionary)
-export(vocab_lter_scope)

R/annotate_eml.R

@@ -407,6 +407,8 @@ annotate_eml <- function(
 #' elements only supported through ID references are added to 
 #' /eml/dataset/annotations (e.g. ResponsibleParty).
 #' 
+#' @keywords internal
+#' 
 annotate_element <- function(element, eml, anno, rp) {
 
   if (element == "dataset") {
@@ -520,6 +522,8 @@ annotate_element <- function(element, eml, anno, rp) {
 #'     \item{responsible.party}{(emld list) Annotated responsible party node}
 #'     \item{rp}{(data.frame) the rp object}
 #' 
+#' @keywords internal
+#' 
 append_rp <- function(responsible.party, annotations.template) {
 
   subject <- paste(
@@ -588,6 +592,8 @@ append_rp <- function(responsible.party, annotations.template) {
 #'     \item{responsible.party}{(emld list) Annotated responsible party node}
 #'     \item{rp}{(data.frame) the rp object}
 #' 
+#' @keywords internal
+#' 
 assign_responsible_party_id <- function(responsible.party, anno, rp) {
 
   r <- lapply(