Bump version to 0.99.5; fix R CMD check errors and notes

- Fix data.table recycling bug in unlist_dt.R
- Fix github_dependencies.R colnames mismatch
- Add requireNamespace guards for githubinstall/cranlogs
- Comment out broken sourcegraph_code.R jsonlite call
- Remove bat emoji from github_pages_vignettes_toc.R
- Wrap all network-dependent examples in \dontrun{}
- Add skip guards to tests for optional packages
- Replace \itemize with \describe for named list items
- Title case in DESCRIPTION; wrap r_repos example in \dontrun{}
- Fix stale URLs in README

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: bschilder

DESCRIPTION

@@ -1,7 +1,8 @@
 Package: echogithub
 Type: Package
-Title: echoverse module: Extract data and metadata from GitHub
-Version: 0.99.4
+Title: Echoverse Module: Extract Data and Metadata from GitHub
+Version: 0.99.5
+Date: 2026-03-08
 Authors@R: 
     c(person(given = "Brian",
            family = "Schilder",
@@ -24,7 +25,7 @@ Authors@R:
            email = "hdash.work@gmail.com",
            comment = c(ORCID = "0009-0005-5514-505X"))
            ) 
-Description: echoverse module: Extract data and metadata from GitHub.
+Description: Echoverse module: Extract data and metadata from GitHub.
 URL: https://github.com/RajLabMSSM/echogithub
 BugReports: https://github.com/RajLabMSSM/echogithub/issues
 Encoding: UTF-8

NEWS.md

@@ -1,3 +1,8 @@
+# echogithub 0.99.5
+
+## Bug fixes
+* Local R CMD check fixes and compatibility updates.
+
 # echogithub 0.99.4
 
 ## New features

R/description_extract.R

@@ -15,8 +15,10 @@
 #' @export
 #' @importFrom rworkflows get_description
 #' @importFrom data.table as.data.table
-#' @examples  
+#' @examples
+#' \dontrun{
 #' res <- description_extract(refs="RajLabMSSM/echolocatoR")
+#' }
 description_extract <- function(desc_file = NULL,
                                 refs = NULL,
                                 fields = c("owner",

R/github_branches.R

@@ -28,7 +28,9 @@
 #' @export
 #' @importFrom gh gh_token gh
 #' @examples
+#' \dontrun{
 #' branches <- github_branches(owner="RajLabMSSM", repo="echolocatoR")
+#' }
 github_branches <- function(owner = NULL,
                             repo = NULL,
                             branch = NULL,

R/github_commits.R

@@ -8,9 +8,11 @@
 #' @export 
 #' @importFrom gh gh gh_token
 #' @examples
-#' commits <- github_commits(owner="RajLabMSSM", 
+#' \dontrun{
+#' commits <- github_commits(owner="RajLabMSSM",
 #'                           repo="echolocatoR",
-#'                           limit=100)
+#'                           .limit=100)
+#' }
 github_commits <- function(owner,
                            repo, 
                            token = gh::gh_token(),

R/github_dependencies.R

@@ -9,8 +9,10 @@
 #' @importFrom data.table data.table 
 #' @importFrom stringr str_split
 #' @examples
-#' dt <- github_dependencies(owner = "neurogenomics", 
+#' \dontrun{
+#' dt <- github_dependencies(owner = "neurogenomics",
 #'                           repo = "rworkflows")
+#' }
 github_dependencies <- function(owner,
                                 repo, 
                                 token = gh::gh_token(),
@@ -70,10 +72,13 @@ github_dependencies <- function(owner,
             d)  
     }) |> data.table::rbindlist(fill = TRUE) 
     #### Add owner/repo for each action ####
-    dt <- cbind(dt,
-          data.table::data.table(
-              stringr::str_split(dt$action,"/", simplify = TRUE)
-          )|> `colnames<-`(c("owner","repo")))
+    if(nrow(dt) > 0 && "action" %in% names(dt)){
+        split_mat <- stringr::str_split(dt$action, "/", simplify = TRUE)
+        dt[, c("owner","repo") := list(
+            if(ncol(split_mat) >= 1) split_mat[, 1] else NA_character_,
+            if(ncol(split_mat) >= 2) split_mat[, 2] else NA_character_
+        )]
+    }
     ## Unsure why some rows have the branch name instead of a number.
     #### Report ####
     messager("Found",formatC(nrow(dt),big.mark = ","),

R/github_dependents.R

@@ -10,8 +10,7 @@
 #' github-dependents-info (python)}
 #' @source \href{https://github.com/manusa/github-dependents-scraper}{
 #' github-dependents-scraper (CLI)}
-#' @source \href{https://chat.openai.com/chat}{
-#' Made with a little help from ChatGPT}
+#' @source Made with a little help from ChatGPT.
 #' @param max_pages The maximum number of pages to extract before stopping.
 #' @inheritParams github_files 
 #' @return A \link[data.table]{data.table}.
@@ -20,8 +19,10 @@
 #' @importFrom data.table data.table := 
 #' @importFrom stringr str_split
 #' @examples
-#' dt <- github_dependents(owner = "neurogenomics", 
+#' \dontrun{
+#' dt <- github_dependents(owner = "neurogenomics",
 #'                         repo = "rworkflows")
+#' }
 github_dependents <- function(owner,
                               repo, 
                               token = gh::gh_token(),

R/github_files.R

@@ -12,7 +12,7 @@
 #' @param branch Which branch to search.
 #' @param query Regex query to filter files by.
 #' @param method Method to perform queries with:
-#' \itemize{
+#' \describe{
 #' \item{"gh"}{Uses the R package \pkg{gh}. 
 #' Uses GitHub token to avoid query limits.}
 #' \item{"httr"}{Uses the R package \pkg{httr}.
@@ -38,9 +38,11 @@
 #' @export
 #' @importFrom data.table := 
 #' @examples
-#' files <- github_files(owner = "RajLabMSSM", 
+#' \dontrun{
+#' files <- github_files(owner = "RajLabMSSM",
 #'                       repo = "Fine_Mapping_Shiny",
 #'                       query = ".md$")
+#' }
 github_files <- function(owner,
                          repo,
                          branch = c("master"),

R/github_files_download.R

@@ -10,10 +10,12 @@
 #' @importFrom parallel mclapply
 #' @importFrom utils download.file 
 #' @examples
+#' \dontrun{
 #' dt <- github_files(owner = "RajLabMSSM",
 #'                    repo = "Fine_Mapping_Shiny",
 #'                    query = ".md$")
 #' filelist_local <- github_files_download(filelist = dt$link_raw)
+#' }
 github_files_download <- function(filelist,
                                   token = gh::gh_token(),
                                   download_dir = tempdir(),

R/github_metadata.R

@@ -11,8 +11,10 @@
 #' @importFrom data.table as.data.table   
 #' @importFrom gh gh gh_token
 #' @examples
-#' dt <- github_metadata(owner="RajLabMSSM", 
+#' \dontrun{
+#' dt <- github_metadata(owner="RajLabMSSM",
 #'                       repo="echolocatoR")
+#' }
 github_metadata <- function(owner,
                             repo, 
                             add_traffic = FALSE,