github actions improvements

Author: elgabbas

.Rbuildignore

@@ -16,3 +16,9 @@
 ^src/.*[.](o|so|dll|dSYM|exp)$
 cspell.json
 ^.*\.code-workspace
+
+^vignettes
+^vignettes/.*\.txt$
+^vignettes/.*\.slurm$
+^vignettes/.*\.css$
+^vignettes/.*\.R$

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

@@ -60,18 +60,16 @@ jobs:
         if: runner.os == 'macOS'
         run: |
           brew install pkg-config gdal proj geos
-        shell: bash
-
+        shell: bash        # shell: Rscript {0}
       - name: Install dependencies
         run: |
           install.packages(c("remotes", "rcmdcheck"))
-          remotes::install_version("ggplot2", version = "3.5.2")
-          remotes::install_github("elgabbas/ecokit")
-          remotes::install_github("hmsc-r/HMSC")
-          remotes::install_local(".", dependencies = TRUE, upgrade = "never", Ncpus = parallel::detectCores())
+          remotes::install_deps(dependencies = TRUE, upgrade = "never")
         shell: Rscript {0}
 
       - name: Manual R CMD check
+        env:
+          _R_CHECK_FORCE_SUGGESTS_: false # skip checking for suggested packages
         run: |
           rcmdcheck::rcmdcheck(
             args = c("--no-manual", "--no-vignettes"), # "--as-cran",

.lintr

@@ -1,4 +1,9 @@
 linters: linters_with_defaults(
+	# Set pipe_consistency_linter to NULL in the defaults list
+    defaults = list(
+    pipe_consistency_linter = NULL,
+    commented_code_linter = NULL,
+    indentation_linter = NULL),
 	# absolute_path_linter(),
 	# consecutive_blank_linter = NULL,
 	# cyclocomp_linter = NULL,
@@ -17,7 +22,6 @@ linters: linters_with_defaults(
 	brace_linter(),
 	class_equals_linter(),
 	commas_linter(),
-	commented_code_linter = NULL,
 	comparison_negation_linter(),
 	condition_call_linter(),
 	condition_message_linter(),
@@ -32,7 +36,6 @@ linters: linters_with_defaults(
 	if_switch_linter(),
 	ifelse_censor_linter(),
 	implicit_assignment_linter(),
-	indentation_linter = NULL,
 	infix_spaces_linter(),
 	inner_combine_linter(),
 	is_numeric_linter(),
@@ -58,7 +61,6 @@ linters: linters_with_defaults(
 	paren_body_linter(),
 	paste_linter(),
 	pipe_call_linter(),
-	pipe_consistency_linter(),
 	pipe_continuation_linter(),
 	pipe_return_linter(),
 	print_linter(),

DESCRIPTION

@@ -45,7 +45,7 @@ Suggests:
     colorRamps (>= 2.3.4),
     cowplot (>= 1.1.3),
     crayon (>= 1.5.3),
-    data.table (>= 1.15.4),
+    data.table (>= 1.17),
     devtools (>= 2.4.5),
     doParallel (>= 1.0.17),
     ecospat (>= 4.1.1),
@@ -61,7 +61,7 @@ Suggests:
     ggnewscale (>= 0.5.0),
     ggpubr (>= 0.6.0),
     ggtext (>= 0.1.2),
-    ggtree (>= 3.13.0.1),
+    ggtree (>= 3.99.2),
     grid (>= 4.4.1),
     gridExtra (>= 2.3),
     gridtext (>= 0.1.5),
@@ -82,7 +82,7 @@ Suggests:
     ncdf4 (>= 1.22),
     pak (>= 0.7.2),
     paletteer (>= 1.6.0),
-    parallelly (>= 1.42),
+    parallelly (>= 1.45),
     patchwork (>= 1.2.0),
     pbapply (>= 1.7.2),
     png (>= 0.1.8),

R/mod_ssdm_helpers.R

@@ -2152,7 +2152,7 @@ fit_predict_internal <- function(
                   name_sd <- stringr::str_replace(
                     names(pred_r)[[1]], "_rep\\d+_", "_rep_sd_")
                   pred_r_sd <- stats::setNames(
-                    terra::app(pred_r, "sd"), name_sd) %>%
+                    terra::app(pred_r, stats::sd), name_sd) %>%
                     terra::toMemory()
                   dplyr::bind_rows(
                     pred_sub,