chore: Fix linting after lintr upgrade

.github/workflows/lint-project.yaml

@@ -22,7 +22,7 @@ jobs:
           use-public-rspm: true
 
       - name: Install lintr
-        run: install.packages("lintr")
+        run: install.packages(c("lintr", "cyclocomp"))
         shell: Rscript {0}
 
       - name: Lint root directory

.lintr

@@ -1,6 +1,7 @@
 linters: linters_with_defaults(
     line_length_linter(120),
     commented_code_linter = NULL,
-    object_usage_linter = NULL
+    object_usage_linter = NULL,
+    cyclocomp_linter = cyclocomp_linter()
   )
 

R/eula.R

@@ -86,5 +86,5 @@ auto_accepted_eula <- function() {
   value <- Sys.getenv(AUTO_ACCEPT_ENV_VAR, unset = "false")
   value <- trimws(tolower(value))
 
-  return(value %in% c("t", "true", "y", "yes"))
+  value %in% c("t", "true", "y", "yes")
 }

R/hdf5.R

@@ -67,7 +67,7 @@ write_mat <- function(f, count_mat, feature_ids) {
 
   if (is.null(feature_ids)) {
     feature_ids <- lapply(seq_along(features), function(x) {
-      return(sprintf("feature_%d", x))
+      sprintf("feature_%d", x)
     })
   }
 

R/setup.R

@@ -166,9 +166,9 @@ bundled_executable_path <- function() {
 
 executable_basename <- function() {
   if (get_system_os() == "windows") {
-    return("louper.exe")
+    "louper.exe"
   } else {
-    return("louper")
+    "louper"
   }
 }
 
@@ -195,10 +195,10 @@ get_artifact <- function() {
   os <- get_system_os()
 
   if (os == "windows") {
-    return(artifacts$windows)
+    artifacts$windows
   } else if (os == "mac") {
-    return(artifacts$mac)
+    artifacts$mac
   } else {
-    return(artifacts$linux)
+    artifacts$linux
   }
 }

R/util.R

@@ -81,13 +81,13 @@ select_assay <- function(obj) {
 #' @export
 counts_matrix_from_assay <- function(assay) {
   if (packageVersion("Seurat") >= package_version("5.0.0")) {
-    return(assay$counts)
+    assay$counts
   } else {
     if (is(assay, "Assay5")) {
       stop("Cannot get count matrix: Please upgrade to Seurat > 5 to support dataset")
     }
 
-    return(assay@counts)
+    assay@counts
   }
 }
 

R/validate.R

@@ -180,21 +180,19 @@ validate_clusters <- function(clusters, barcode_count) { # nolint: cyclocomp_lin
 #' @export
 validate_projections <- function(projections, barcode_count) { # nolint: cyclocomp_linter.
   is_projection <- function(p) {
-    return(is.matrix(p))
+    is.matrix(p)
   }
 
   # should have dimensions barcodeCount x 2
   projection_dims_good <- function(p) {
     pdims <- dim(p)
-    return(pdims[[1]] == barcode_count && pdims[[2]] == 2)
+    pdims[[1]] == barcode_count && pdims[[2]] == 2
   }
 
   # no values should be NaN or Infinite
   projection_values_good <- function(p) {
-    return(
-      !any(is.nan(p)) &&
-        !any(is.infinite(p))
-    )
+    !any(is.nan(p)) &&
+      !any(is.infinite(p))
   }
 
   proj_names <- names(projections)

tests/testthat/helper.R

@@ -54,8 +54,8 @@ get_executable_path <- function() {
   wd <- getwd()
   os <- get_system_os()
   if (os == "windows") {
-    return(file.path(wd, "mock_louper.bat"))
+    file.path(wd, "mock_louper.bat")
   } else {
-    return(file.path(wd, "mock_louper"))
+    file.path(wd, "mock_louper")
   }
 }