Mark regexes as fixed where possible

Author: Bisaloo

.lintr

@@ -3,5 +3,6 @@ linters: linters_with_defaults(
     any_is_na_linter(),
     outer_negation_linter(),
     nzchar_linter(),
+    fixed_regex_linter(),
     object_name_linter = object_name_linter(styles = c("snake_case", "symbols", "CamelCase", "SNAKE_CASE"))
   )

R/from_Seurat.R

@@ -527,7 +527,7 @@ from_Seurat <- function(
       next
     }
 
-    dest_name <- gsub(paste0(assay_name, "_"), "", graph_name)
+    dest_name <- gsub(paste0(assay_name, "_"), "", graph_name, fixed = TRUE)
 
     obsp_mapping[dest_name] <- graph_name
   }

R/generate_dataset.R

@@ -226,14 +226,14 @@ generate_dataset <- function(
       factor(NA_character_, ordered = TRUE)
     } else if (uns_type == "scalar_logical_with_nas") {
       NA_real_
-    } else if (grepl("scalar_", uns_type)) {
-      generate_vector(1L, gsub("scalar_", "", uns_type))
-    } else if (grepl("vec_", uns_type)) {
-      generate_vector(10L, gsub("vec_", "", uns_type))
-    } else if (grepl("df_", uns_type)) {
-      generate_dataframe(10L, gsub("df_", "", uns_type))
-    } else if (grepl("mat_", uns_type)) {
-      generate_matrix(10L, 10L, gsub("mat_", "", uns_type))
+    } else if (grepl("scalar_", uns_type, fixed = TRUE)) {
+      generate_vector(1L, gsub("scalar_", "", uns_type, fixed = TRUE))
+    } else if (grepl("vec_", uns_type, fixed = TRUE)) {
+      generate_vector(10L, gsub("vec_", "", uns_type, fixed = TRUE))
+    } else if (grepl("df_", uns_type, fixed = TRUE)) {
+      generate_dataframe(10L, gsub("df_", "", uns_type, fixed = TRUE))
+    } else if (grepl("mat_", uns_type, fixed = TRUE)) {
+      generate_matrix(10L, 10L, gsub("mat_", "", uns_type, fixed = TRUE))
     } else {
       cli_abort("Unknown {.field uns} type: {.val {uns_type}}")
     }

vignettes/articles/development_status.Rmd

@@ -28,7 +28,7 @@ source <- list.files(proj_root, pattern = "*.R$", recursive = TRUE)
 # look for trackstatus comments
 status_lines <- map_df(source, function(path) {
   lines <- readLines(paste0(proj_root, "/", path))
-  line_numbers <- grep("# trackstatus:", lines)
+  line_numbers <- grep("# trackstatus:", lines, fixed = TRUE)
 
   map_df(line_numbers, function(line_number) {
     tryCatch(
@@ -200,7 +200,7 @@ for (i in seq_along(data)) {
     " * To investigate: ", data[[i]]$to_investigate, "\n",
     " * To fix: ", data[[i]]$to_fix, "\n\n",
     "### Error message\n\n",
-    paste(paste0("    ", strsplit(data[[i]]$error_message, "\n")[[1]], "\n"), collapse = ""), "\n\n",
+    paste(paste0("    ", strsplit(data[[i]]$error_message, "\n", fixed = TRUE)[[1]], "\n"), collapse = ""), "\n\n",
     "### Proposed solution\n\n",
     data[[i]]$proposed_solution, "\n\n"
   )