Fix BiocCheck errors and notes for examples and vignette

- Replace \dontrun with runnable examples for read_counts(),
  read_mod_annotations(), and compute_odds_ratios() using new small
  example data files in inst/extdata/ecoli/
- Convert \dontrun to \donttest for fetch_modomics_mods() (needs network)
- Guard \donttest examples for plot_arc_diagram() and structure_to_png()
  with requireNamespace() checks for suggested packages
- Add chunk label to first vignette code chunk
- Refactor suppressWarnings(as.numeric()) in plot-chord.R to use grepl
- Wrap long example file paths to stay under 80 characters

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

Author: jayhesselberth

DESCRIPTION

@@ -15,8 +15,9 @@ Description: Analyze direct tRNA sequencing data. Provides differential
     expression, modification, and tools for visualization.
 License: MIT + file LICENSE
 URL: https://rnabioco.github.io/clover, https://github.com/rnabioco/clover
+BugReports: https://github.com/rnabioco/clover/issues
 Depends:
-    R (>= 4.3.0)
+    R (>= 4.5.0)
 Imports:
     Biostrings,
     cli,
@@ -55,11 +56,11 @@ Suggests:
     testthat (>= 3.0.0),
     tidygraph,
     withr
-LinkingTo: 
+LinkingTo:
     cpp11
-VignetteBuilder: 
+VignetteBuilder:
     knitr
-bioCViews: RNASeq, Visualization
+biocViews: RNASeq, Visualization
 Config/Needs/dev: devtools, roxygen2, pkgdown
 Config/Needs/website: rnabioco/rbitemplate
 Config/testthat/edition: 3

R/clover-se.R

@@ -134,9 +134,8 @@ read_fasta <- function(fa) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
-#' read_mod_annotations("modifications.tsv")
-#' }
+#' path <- clover_example("ecoli/mod_annotations.tsv")
+#' read_mod_annotations(path)
 read_mod_annotations <- function(mods) {
   readr::read_tsv(mods, show_col_types = FALSE)
 }

R/modomics.R

@@ -181,7 +181,7 @@ load_cached_sequences <- function(organism) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' fa <- clover_example("ecoli/validated.fa.gz")
 #' mods <- fetch_modomics_mods(fa, "Escherichia coli")
 #' mods

R/odds-ratios.R

@@ -317,9 +317,8 @@ compute_ror <- function(
 #' @export
 #'
 #' @examples
-#' \dontrun{
-#' compute_odds_ratios("sample.mod_calls.tsv.gz")
-#' }
+#' path <- clover_example("ecoli/mod_calls.tsv.gz")
+#' compute_odds_ratios(path)
 compute_odds_ratios <- function(mod_calls_path, refs = NULL, min_reads = 10) {
   mc <- readr::read_tsv(mod_calls_path, show_col_types = FALSE) |>
     dplyr::filter(.data$within_alignment == TRUE)

R/plot-chord.R

@@ -40,9 +40,11 @@
 #'
 #' @examples
 #' \donttest{
-#' path <- clover_example(
-#'   "ecoli/summary/tables/wt-15-ctl-01/wt-15-ctl-01.odds_ratios_filtered.tsv.gz"
+#' or_file <- paste0(
+#'   "ecoli/summary/tables/wt-15-ctl-01/",
+#'   "wt-15-ctl-01.odds_ratios_filtered.tsv.gz"
 #' )
+#' path <- clover_example(or_file)
 #' or_data <- read_odds_ratios(path)
 #' or_data <- dplyr::filter(or_data, ref == "host-tRNA-Glu-TTC-1-1")
 #' plot_chord_or(or_data)
@@ -353,10 +355,12 @@ setup_chord_sectors <- function(chord_df, sprinzl_coords = NULL) {
   } else {
     all_positions <- unique(c(chord_df$from, chord_df$to))
     # Sort positions numerically where possible
-    sector_order <- all_positions[order(
-      suppressWarnings(as.numeric(all_positions)),
-      all_positions
-    )]
+    numeric_pos <- ifelse(
+      grepl("^-?[0-9.]+$", all_positions),
+      as.numeric(all_positions),
+      NA_real_
+    )
+    sector_order <- all_positions[order(numeric_pos, all_positions)]
     grid_col <- rep("grey70", length(sector_order))
     names(grid_col) <- sector_order
     regions <- NULL

R/plot-network.R

@@ -86,13 +86,15 @@ build_or_network <- function(data, value_col = "ror", min_weight = 0) {
 #'
 #' @examples
 #' \donttest{
-#' df <- tibble::tibble(
-#'   pos1 = c("20", "34", "20"),
-#'   pos2 = c("34", "58", "58"),
-#'   ror = c(1.5, -0.8, 0.3)
-#' )
-#' graph <- build_or_network(df)
-#' plot_arc_diagram(graph)
+#' if (requireNamespace("ggraph", quietly = TRUE)) {
+#'   df <- tibble::tibble(
+#'     pos1 = c("20", "34", "20"),
+#'     pos2 = c("34", "58", "58"),
+#'     ror = c(1.5, -0.8, 0.3)
+#'   )
+#'   graph <- build_or_network(df)
+#'   plot_arc_diagram(graph)
+#' }
 #' }
 plot_arc_diagram <- function(
   graph,

R/plot-structure.R

@@ -233,8 +233,10 @@ plot_tRNA_structure <- function(
 #'
 #' @examples
 #' \donttest{
-#' svg <- plot_tRNA_structure("tRNA-Glu-TTC", "Escherichia coli")
-#' structure_to_png(svg)
+#' if (requireNamespace("rsvg", quietly = TRUE)) {
+#'   svg <- plot_tRNA_structure("tRNA-Glu-TTC", "Escherichia coli")
+#'   structure_to_png(svg)
+#' }
 #' }
 structure_to_png <- function(
   svg_path,

R/read-bcerror.R

@@ -9,9 +9,7 @@
 #' @export
 #'
 #' @examples
-#' \dontrun{
-#' read_counts("sample1.counts.tsv.gz")
-#' }
+#' read_counts(clover_example("ecoli/counts.tsv"))
 read_counts <- function(path) {
   readr::read_tsv(path, show_col_types = FALSE)
 }

R/read-charging.R

@@ -104,13 +104,17 @@ read_charging_multi <- function(paths) {
 #' @export
 #'
 #' @examples
+#' or_file1 <- paste0(
+#'   "ecoli/summary/tables/wt-15-ctl-01/",
+#'   "wt-15-ctl-01.odds_ratios_filtered.tsv.gz"
+#' )
+#' or_file2 <- paste0(
+#'   "ecoli/summary/tables/wt-15-ctl-02/",
+#'   "wt-15-ctl-02.odds_ratios_filtered.tsv.gz"
+#' )
 #' paths <- c(
-#'   "wt-15-ctl-01" = clover_example(
-#'     "ecoli/summary/tables/wt-15-ctl-01/wt-15-ctl-01.odds_ratios_filtered.tsv.gz"
-#'   ),
-#'   "wt-15-ctl-02" = clover_example(
-#'     "ecoli/summary/tables/wt-15-ctl-02/wt-15-ctl-02.odds_ratios_filtered.tsv.gz"
-#'   )
+#'   "wt-15-ctl-01" = clover_example(or_file1),
+#'   "wt-15-ctl-02" = clover_example(or_file2)
 #' )
 #' read_odds_ratios_multi(paths)
 read_odds_ratios_multi <- function(paths) {

inst/extdata/ecoli/README.md

@@ -52,6 +52,14 @@ demonstrate the data-loading workflow.
   | host-tRNA-Arg-CCT-1-1 | Least abundant |
   | host-tRNA-Ser-CGA-1-1 | Least abundant |
 
+### Minimal example files
+
+Small example files used in roxygen `@examples`:
+
+- `counts.tsv` -- 3-row counts file for `read_counts()`
+- `mod_annotations.tsv` -- 3-row modification annotations for `read_mod_annotations()`
+- `mod_calls.tsv.gz` -- synthetic mod calls (15 reads, 1 tRNA) for `compute_odds_ratios()`
+
 ### Other files
 
 - `config.yaml` -- pipeline configuration file (used by `create_clover()`)