[R] enforce lintr checks (fixes #8012) (#8613)

.github/workflows/r_tests.yml

@@ -44,8 +44,7 @@ jobs:
     - name: Run lintr
       run: |
         MAKEFLAGS="-j$(nproc)" R CMD INSTALL R-package/
-        # Disable lintr errors for now: https://github.com/dmlc/xgboost/issues/8012
+        Rscript tests/ci_build/lint_r.R $(pwd)
-        Rscript tests/ci_build/lint_r.R $(pwd) || true
 
   test-R-on-Windows:
     runs-on: ${{ matrix.config.os }}

R-package/R/xgb.ggplot.R

@@ -4,7 +4,7 @@
 #' @rdname xgb.plot.importance
 #' @export
 xgb.ggplot.importance <- function(importance_matrix = NULL, top_n = NULL, measure = NULL,
-                                  rel_to_first = FALSE, n_clusters = c(1:10), ...) {
+                                  rel_to_first = FALSE, n_clusters = seq_len(10), ...) {
 
   importance_matrix <- xgb.plot.importance(importance_matrix, top_n = top_n, measure = measure,
                                            rel_to_first = rel_to_first, plot = FALSE, ...)

R-package/R/xgb.plot.multi.trees.R

@@ -97,9 +97,9 @@ xgb.plot.multi.trees <- function(model, feature_names = NULL, features_keep = 5,
         , by = .(abs.node.position, Feature)
       ][, .(Text = paste0(
               paste0(
-                Feature[1:min(length(Feature), features_keep)],
+                Feature[seq_len(min(length(Feature), features_keep))],
                 " (",
-                format(Quality[1:min(length(Quality), features_keep)], digits = 5),
+                format(Quality[seq_len(min(length(Quality), features_keep))], digits = 5),
                 ")"
               ),
               collapse = "\n"

R-package/R/xgb.plot.shap.R

@@ -273,7 +273,7 @@ xgb.shap.data <- function(data, shap_contrib = NULL, features = NULL, top_n = 1,
     }
     top_n <- top_n[1]
     if (top_n < 1 | top_n > 100) stop("top_n: must be an integer within [1, 100]")
-    features <- imp$Feature[1:min(top_n, NROW(imp))]
+    features <- imp$Feature[seq_len(min(top_n, NROW(imp)))]
   }
   if (is.character(features)) {
     features <- match(features, colnames(data))

R-package/R/xgb.train.R

@@ -389,7 +389,7 @@ xgb.train <- function(params = list(), data, nrounds, watchlist = list(),
     xgb.iter.update(bst$handle, dtrain, iteration - 1, obj)
 
     if (length(watchlist) > 0)
-      bst_evaluation <- xgb.iter.eval(bst$handle, watchlist, iteration - 1, feval)
+      bst_evaluation <- xgb.iter.eval(bst$handle, watchlist, iteration - 1, feval)  # nolint: object_usage_linter
 
     xgb.attr(bst$handle, 'niter') <- iteration - 1
 

R-package/demo/interaction_constraints.R

@@ -33,7 +33,7 @@ treeInteractions <- function(input_tree, input_max_depth) {
   }
 
   # Extract nodes with interactions
-  interaction_trees <- trees[!is.na(Split) & !is.na(parent_1),
+  interaction_trees <- trees[!is.na(Split) & !is.na(parent_1),  # nolint: object_usage_linter
                              c('Feature', paste0('parent_feat_', 1:(input_max_depth - 1))),
                              with = FALSE]
   interaction_trees_split <- split(interaction_trees, seq_len(nrow(interaction_trees)))

R-package/man/xgb.plot.importance.Rd

@@ -10,7 +10,7 @@ xgb.ggplot.importance(
   top_n = NULL,
   measure = NULL,
   rel_to_first = FALSE,
-  n_clusters = c(1:10),
+  n_clusters = seq_len(10),
   ...
 )
 

demo/kaggle-higgs/speedtest.R

@@ -26,7 +26,7 @@ print(paste("weight statistics: wpos=", sumwpos, "wneg=", sumwneg, "ratio=", sum
 
 xgboost.time <- list()
 threads <- c(1, 2, 4, 8, 16)
-for (i in 1:length(threads)){
+for (i in seq_along(threads)){
   thread <- threads[i]
   xgboost.time[[i]] <- system.time({
     xgmat <- xgb.DMatrix(data, label = label, weight = weight, missing = -999.0)

demo/kaggle-otto/otto_train_pred.R

@@ -13,7 +13,7 @@ y <- as.integer(y) - 1  # xgboost take features in [0,numOfClass)
 x <- rbind(train[, -ncol(train)], test)
 x <- as.matrix(x)
 x <- matrix(as.numeric(x), nrow(x), ncol(x))
-trind <- 1:length(y)
+trind <- seq_along(y)
 teind <- (nrow(train) + 1):nrow(x)
 
 # Set necessary parameter
@@ -43,6 +43,6 @@ pred <- t(pred)
 
 # Output submission
 pred <- format(pred, digits = 2, scientific = FALSE) # shrink the size of submission
-pred <- data.frame(1:nrow(pred), pred)
+pred <- data.frame(seq_len(nrow(pred)), pred)
 names(pred) <- c('id', paste0('Class_', 1:9))
 write.csv(pred, file = 'submission.csv', quote = FALSE, row.names = FALSE)

demo/kaggle-otto/understandingXGBoostModel.Rmd

@@ -30,7 +30,7 @@ require(xgboost)
 require(methods)
 require(data.table)
 require(magrittr)
-train <- fread('data/train.csv', header = T, stringsAsFactors = FALSE)
+train <- fread('data/train.csv', header = TRUE, stringsAsFactors = FALSE)
 test <- fread('data/test.csv', header = TRUE, stringsAsFactors = FALSE)
 ```
 > `magrittr` and `data.table` are here to make the code cleaner and much more rapid.

tests/ci_build/lint_r.R

@@ -67,6 +67,5 @@ noquote(paste0("Total linting issues found: ", issues_found))
 
 if (issues_found > 0L) {
     print(results)
+    quit(save = "no", status = 1L)
 }
-
-quit(save = "no", status = 1L)