fix some warnings and notes from package check

Author: nuest

DESCRIPTION

@@ -29,7 +29,6 @@ Depends: R (>= 4.0.0), gh, R.cache, parsedate
 Imports: 
     dplyr,
     tidyr,
-    magrittr,
     yaml,
     xtable,
     stringr,

NAMESPACE

@@ -40,6 +40,7 @@ importFrom(rmarkdown,render)
 importFrom(rorcid,check_dois)
 importFrom(stringr,str_match)
 importFrom(stringr,str_replace_all)
+importFrom(utils,askYesNo)
 importFrom(utils,capture.output)
 importFrom(utils,read.csv)
 importFrom(utils,tail)

R/codecheck.R

@@ -271,24 +271,27 @@ cite_certificate <- function(metadata) {
 
 # Zenodo records interaction ----
 
-##' Create a new Zenodo record and return its pre-assigned DOI
-##'
-##' Run this only once per new codecheck.
-##' @title Create a new Zenodo record and return its pre-assigned DOI
-##' @param zen - Object from zen4R to interact with Zenodo
-##' @return Number of zenodo record created.
-##' @author Stephen Eglen
-##' @importFrom zen4R ZenodoRecord
-##' 
-##' @export
+#' Create a new Zenodo record and return its pre-assigned DOI
+#'
+#' Run this only once per new codecheck.
+#' @title Create a new Zenodo record and return its pre-assigned DOI
+#' @param zen Object from zen4R to interact with Zenodo
+#' @param metadata codecheck.yml file
+#' @param warn Ask for user input before creating a new record
+#' @return Number of Zenodo record created
+#' @author Stephen Eglen
+#' @importFrom zen4R ZenodoRecord
+#' @importFrom utils askYesNo
+#' 
+#' @export
 get_or_create_zenodo_record <- function(zen, metadata, warn=TRUE) {
   id <- get_zenodo_record(metadata$report)
   if (!is.na(id)) {
     my_rec <- zen$getDepositionById(id)
   } else {
     ## no record, create a new one.
     if(warn) { 
-      proceed <- askYesNo("You do not have a zenodo record; I can fix this for you but please make sure your codecheck.yaml is saved, as I will need to update it.  Proceed?")
+      proceed <- askYesNo("You do not have a Zenodo record yet; I can fix this for you but please make sure your codecheck.yaml is saved, as I will need to update it. Proceed?")
       stopifnot(proceed==TRUE)
     }
     my_rec <- zen$createEmptyRecord()
@@ -330,17 +333,17 @@ get_zenodo_id <- function(report) {
   as.integer(result)
 }
 
-##' Get the full Zenodo record from the metadata
-##'
-##' Retrieve the zenodo record, if one exists.
-##' If no record number is currently  listed in the metadata (i.e. the "FIXME" tag is still there)
-##' then the code returns NULL and an empty record should be created.
-##' @title Get the full zenodo record using the record number stored in the metadata.
-##' @param zenodo 
-##' @param metadata 
-##' @return The Zenodo record, or NULL.
-##' @author Stephen Eglen
-##' @export
+#' Get the full Zenodo record from the metadata
+#'
+#' Retrieve the Zenodo record, if one exists.
+#' If no record number is currently  listed in the metadata (i.e. the "FIXME" tag is still there)
+#' then the code returns NULL and an empty record should be created.
+#' @title Get the full zenodo record using the record number stored in the metadata.
+#' @param zenodo An object from zen4R to connect with Zenodo
+#' @param metadata A codecheck configuration (likely read from a codecheck.yml)
+#' @return The Zenodo record, or NULL.
+#' @author Stephen Eglen
+#' @export
 get_zenodo_record <- function(zenodo, metadata) {
   id <- get_zenodo_id(metadata$report)
   if (is.na(id)) {
@@ -350,18 +353,18 @@ get_zenodo_record <- function(zenodo, metadata) {
   }
 }
 
-##' Upload codecheck metadata to Zenodo.
-##'
-##' The contents of codecheck.yml are uploaded to Zenodo using this funciton.
-##' 
-##' @title Upload metadata to Zenodod
-##' @param zen 
-##' @param myrec 
-##' @param metadata 
-##' @return rec -- the updated record.
-##' @author Stephen Eglen
-##' @export
-upload_zenodo_metadata <- function(zen, myrec, metadata) {
+#' Upload codecheck metadata to Zenodo.
+#'
+#' The contents of codecheck.yml are uploaded to Zenodo using this funciton.
+#' 
+#' @title Upload metadata to Zenodod
+#' @param zenodo object from zen4R to connect with Zenodo
+#' @param myrec a Zenodo record object
+#' @param metadata codecheck metadata, likely loaded from a codecheck.yml file
+#' @return rec -- the updated record.
+#' @author Stephen Eglen
+#' @export
+upload_zenodo_metadata <- function(zenodo, myrec, metadata) {
   ##draft$setPublicationType("report")
   ##draft$setCommunities(communities = c("codecheck"))
   myrec$metadata <- NULL
@@ -394,23 +397,23 @@ upload_zenodo_metadata <- function(zen, myrec, metadata) {
   ##myrec$addRelatedIdentifier(relation = "isSupplementTo", identifier = metadata$repository)
   ##myrec$addRelatedIdentifier(relation = "isSupplementTo", identifier = metadata$paper$reference)
   cat(paste0("Check your record online at ",  myrec$links$self_html, "\n"))
-  myrec <- zen$depositRecord(myrec)
+  myrec <- zenodo$depositRecord(myrec)
 
 }
 
 
-##' Upload the CODECHECK certificate to Zenodo.
-##'
-##' Upload the CODECHECK certificate to Zenodo as a draft.  Warning: if
-##' the file has already been uploaded once, you will need to delete it via
-##' the web interface before being able to upload a new versin.
-##' @title Upload the CODECHECK certificate to Zenodo.
-##' @param zen - Object from zen4R to interact with Zenodo
-##' @param record - string containing the report URL on Zenodo.
-##' @param certificate name of the PDF file.
-##' @return NULL
-##' @author Stephen Eglen
-##' @export
+#' Upload the CODECHECK certificate to Zenodo.
+#'
+#' Upload the CODECHECK certificate to Zenodo as a draft.  Warning: if
+#' the file has already been uploaded once, you will need to delete it via
+#' the web interface before being able to upload a new versin.
+#' @title Upload the CODECHECK certificate to Zenodo.
+#' @param zen - Object from zen4R to interact with Zenodo
+#' @param record - string containing the report URL on Zenodo.
+#' @param certificate name of the PDF file.
+#' @return NULL
+#' @author Stephen Eglen
+#' @export
 set_zenodo_certificate <- function(zen, record, certificate) {
   draft <- zen$getDepositionById(record)
   stopifnot(file.exists(certificate))
@@ -426,7 +429,7 @@ add_id_to_yml <- function(id, yml_file) {
   ## Add id to the yaml file.
   data1 <- readLines(yml_file)
   data2 <- gsub(pattern = "zenodo.FIXME$",
-                replace = paste0("zenodo.",id),
+                replacement = paste0("zenodo.",id),
                 x = data1)
   writeLines(data2, yml_file)
 }

R/register.R

@@ -6,6 +6,7 @@
 #' - `.md``
 #'
 #' @param register A `data.frame` with all required information for the register's view
+#' @param filter_by The filter or list o filters (if applicable)
 #' @param outputs The output formats to create
 #' @param config A list of configuration files to be sourced at the beginning of the rending process
 #'

R/utils_preprocess_register.R

@@ -202,7 +202,10 @@ create_temp_register_with_codechecker <- function(register_table){
 }
 
 #' Function for preprocessing the register to create and return the preprocessed register table.
-#' @param register The register
+#' 
+#' @param register The register.
+#' @param filter_by The filter (if applicable).
+#' 
 #' @return The preprocessed register table
 preprocess_register <- function(register, filter_by) {
     register_table <- register
@@ -220,4 +223,4 @@ preprocess_register <- function(register, filter_by) {
     register_table <- add_check_time(register_table, register)
     register_table <- add_paper_links(register_table, register)
     return(register_table)
-}
+}

R/utils_render_cert_md.R

@@ -254,6 +254,7 @@ create_cert_md <- function(cert_id, repo_link, download_cert_status){
 #'
 #' @param md_content A character string containing the Markdown template content with placeholders.
 #' @param repo_link A character string containing the repository link associated with the certificate.
+#' @param download_cert_status An integer (0 or 1) indicating whether the certificate PDF was downloaded (1) or not (0).
 #' @return The markdown content, with paper details placeholders filled.
 add_paper_details_md <- function(md_content, repo_link, download_cert_status){
   config_yml <- get_codecheck_yml(repo_link)

R/utils_render_table_non_registers.R

@@ -172,7 +172,7 @@ generate_html_title_non_registers <- function(filter, subcat){
 #' There is only extra text for the codecheckers HTML page to explain
 #' the reason for discrepancy between total_codechecks != SUM(no.of codechecks)
 #' 
-#' @param filter The filter
+#' @param filter A string specifying the filter applied (e.g., "venues", "codecheckers").
 #' @return The extra text to place under the table
 generate_html_extra_text_non_register <- function(filter){
   extra_text <- ""
@@ -188,8 +188,8 @@ generate_html_extra_text_non_register <- function(filter){
 #' the number of codechecks and number of codechecks/ venues etc.
 #' 
 #' @param table The table to showcase in the html
-#' @param page_type The HTML page type that needs to rendered
-#' @param table_name The name of the table
+#' @param filter A string specifying the filter applied (e.g., "venues", "codecheckers").
+#' @param subcat An optional string for the subcategory (if applicable).
 #' @return The subtext to put under the html title
 generate_html_subtext_non_register <- function(table, filter, subcat = NULL){
   # The filter is in the CONFIG$NON_REG_SUBTEXT

inst/extdata/config.R

@@ -1,5 +1,7 @@
 CONFIG <- new.env()
 
+utils::globalVariables(c("CONFIG"))
+
 # REGISTER TABLE
 
 # Specifying the register table column widths