Fix all NOTEs and ERRORS in check()

.github/workflows/R-CMD-check.yaml

@@ -62,7 +62,7 @@ jobs:
           while read -r cmd
           do
             eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "22.04"))')
 
       - name: Install dependencies
         run: |

R/cpue-index-tweedie.R

@@ -25,6 +25,7 @@ fit_cpue_index_glmmtmb <- function(dat, formula = cpue ~ year_factor, ...) {
 #' @export
 #' @rdname fit_cpue_index_glmmtmb
 predict_cpue_index_tweedie <- function(object, center = FALSE) {
+  # Following causes NOTE in check()
   if (class(object) != "glmmTMB") stop("Class of `object` must be glmmTMB.")
     sdr <- object$sdr
     yrs <- sort(unique(object$frame$year_factor))

R/gfplot.R

@@ -46,6 +46,36 @@ if (getRversion() >= "2.15.1") {
     "landed_pcs", "species_common_name", "species_desc", "species_science_name",
     "trip_start_date", "year",
 
+    # binomial_perc:
+    "uniroot",
+
+    # extract_maturity_perc, extract_maturity_perc_re, fit_mat_ogive,
+    # mat_par_delta_method, plot_mat_annual_ogives
+    "family",
+
+    # plot_growth:
+    "geom_jitter",
+
+    # plot_lengths:
+    "survey_abbrev2",
+
+    # plot_mat_ogive:
+    "age_or_length",
+
+    # plot_survey_index:
+    "geomean",
+
+    # plot_survey_index:
+    "biomass_scaled",
+
+    # split_catch_by_sex:
+    "new_weight", "group_name", "group_weight", "est_sample_weight",
+    "n_fish_sampled", "mean_weight_kg", "group_n", "weighted.mean",
+    "median_prop_ann", "n_events_sampled", "n_fish_by_surv_yr",
+    "mean_prop_ann", "mean_ann_weight_kg", "median_prop", "total_ann_samples",
+    "total_ann_fish", "mean_prop", "total_survey_samples",
+    "total_survey_fish", "split_catch_type",
+
     # weighting:
     "month", "freq", "trip_id", "sample_id", "survey_id", "value", "prop",
     "annual_prop", "quarter", "sum_freq",

R/growth.R

@@ -149,6 +149,8 @@ fit_vb <- function(dat,
     }
 
     vb_mod_gfplot <- rstan::stan_model(.f)
+
+    # Following causes a NOTE in check()
     assign("vb_mod_gfplot", vb_mod_gfplot, envir = globalenv())
   }
 

R/plot-lengths.R

@@ -21,6 +21,8 @@
 #' `"F"` and `"M"` for female and male.
 #' @param survey_cols An optional named character vector of colors for the
 #'   various surveys.
+#' @param survey_facets A vector of names to use in the survey formula labels
+#' used in the facets. If `NULL`, the survey abbreviations will be used.
 #' @param alpha Transparency for the fill color in the histograms.
 #' @param bin_size Bin size. Should match the bin size used with the `tidy_*()`
 #'   function.

R/tidy-cpue-index.R

@@ -35,6 +35,8 @@
 #' @param lat_bin_quantiles Quantiles for the latitude bands. Values above and
 #'   below these quantiles will be discarded.
 #' @param gear One or more gear types as a character vector.
+#' @param return_raw_data If `TRUE`, return a data.frame containing the raw
+#' data
 #'
 #' @export
 #'
@@ -61,7 +63,8 @@ tidy_cpue_index <- function(dat, species_common,
                             depth_bin_quantiles = c(0.001, 0.999),
                             min_bin_prop = 0.001,
                             lat_bin_quantiles = c(0, 1),
-                            gear = "bottom trawl", return_raw_data = FALSE) {
+                            gear = "bottom trawl",
+                            return_raw_data = FALSE) {
   pbs_areas <- gfplot::pbs_areas[grep(
     area_grep_pattern,
     gfplot::pbs_areas$major_stat_area_description