Updates from 1.2.0 cran submission (#6077)

* update for 1.2.0 cran submission

* recover cmakelists

* fix unittest from the shap PR

* trigger CI

R-package/tests/helper_scripts/generate_models.R

@@ -0,0 +1,101 @@
+# Script to generate reference models. The reference models are used to test backward compatibility
+# of saved model files from XGBoost version 0.90 and 1.0.x.
+library(xgboost)
+library(Matrix)
+source('./generate_models_params.R')
+
+set.seed(0)
+metadata <- list(
+  kRounds = 2,
+  kRows = 1000,
+  kCols = 4,
+  kForests = 2,
+  kMaxDepth = 2,
+  kClasses = 3
+)
+X <- Matrix(data = rnorm(metadata$kRows * metadata$kCols), nrow = metadata$kRows,
+            ncol = metadata$kCols, sparse = TRUE)
+w <- runif(metadata$kRows)
+
+version <- packageVersion('xgboost')
+target_dir <- 'models'
+
+save_booster <- function (booster, model_name) {
+  booster_bin <- function (model_name) {
+    return (file.path(target_dir, paste('xgboost-', version, '.', model_name, '.bin', sep = '')))
+  }
+  booster_json <- function (model_name) {
+    return (file.path(target_dir, paste('xgboost-', version, '.', model_name, '.json', sep = '')))
+  }
+  booster_rds <- function (model_name) {
+    return (file.path(target_dir, paste('xgboost-', version, '.', model_name, '.rds', sep = '')))
+  }
+  xgb.save(booster, booster_bin(model_name))
+  saveRDS(booster, booster_rds(model_name))
+  if (version >= '1.0.0') {
+    xgb.save(booster, booster_json(model_name))
+  }
+}
+
+generate_regression_model <- function () {
+  print('Regression')
+  y <- rnorm(metadata$kRows)
+
+  data <- xgb.DMatrix(X, label = y)
+  params <- list(tree_method = 'hist', num_parallel_tree = metadata$kForests,
+                 max_depth = metadata$kMaxDepth)
+  booster <- xgb.train(params, data, nrounds = metadata$kRounds)
+  save_booster(booster, 'reg')
+}
+
+generate_logistic_model <- function () {
+  print('Binary classification with logistic loss')
+  y <- sample(0:1, size = metadata$kRows, replace = TRUE)
+  stopifnot(max(y) == 1, min(y) == 0)
+
+  data <- xgb.DMatrix(X, label = y, weight = w)
+  params <- list(tree_method = 'hist', num_parallel_tree = metadata$kForests,
+                 max_depth = metadata$kMaxDepth, objective = 'binary:logistic')
+  booster <- xgb.train(params, data, nrounds = metadata$kRounds)
+  save_booster(booster, 'logit')
+}
+
+generate_classification_model <- function () {
+  print('Multi-class classification')
+  y <- sample(0:(metadata$kClasses - 1), size = metadata$kRows, replace = TRUE)
+  stopifnot(max(y) == metadata$kClasses - 1, min(y) == 0)
+
+  data <- xgb.DMatrix(X, label = y, weight = w)
+  params <- list(num_class = metadata$kClasses, tree_method = 'hist',
+                 num_parallel_tree = metadata$kForests, max_depth = metadata$kMaxDepth,
+                 objective = 'multi:softmax')
+  booster <- xgb.train(params, data, nrounds = metadata$kRounds)
+  save_booster(booster, 'cls')
+}
+
+generate_ranking_model <- function () {
+  print('Learning to rank')
+  y <- sample(0:4, size = metadata$kRows, replace = TRUE)
+  stopifnot(max(y) == 4, min(y) == 0)
+  kGroups <- 20
+  w <- runif(kGroups)
+  g <- rep(50, times = kGroups)
+
+  data <- xgb.DMatrix(X, label = y, group = g)
+  # setinfo(data, 'weight', w)
+  # ^^^ does not work in version <= 1.1.0; see https://github.com/dmlc/xgboost/issues/5942
+  # So call low-level function XGDMatrixSetInfo_R directly. Since this function is not an exported
+  # symbol, use the triple-colon operator.
+  .Call(xgboost:::XGDMatrixSetInfo_R, data, 'weight', as.numeric(w))
+  params <- list(objective = 'rank:ndcg', num_parallel_tree = metadata$kForests,
+                 tree_method = 'hist', max_depth = metadata$kMaxDepth)
+  booster <- xgb.train(params, data, nrounds = metadata$kRounds)
+  save_booster(booster, 'ltr')
+}
+
+dir.create(target_dir)
+
+invisible(generate_regression_model())
+invisible(generate_logistic_model())
+invisible(generate_classification_model())
+invisible(generate_ranking_model())

R-package/tests/helper_scripts/run_lint.R

@@ -0,0 +1,71 @@
+library(lintr)
+library(crayon)
+
+my_linters <- list(
+  absolute_path_linter = lintr::absolute_path_linter,
+  assignment_linter = lintr::assignment_linter,
+  closed_curly_linter = lintr::closed_curly_linter,
+  commas_linter = lintr::commas_linter,
+  equals_na = lintr::equals_na_linter,
+  infix_spaces_linter = lintr::infix_spaces_linter,
+  line_length_linter = lintr::line_length_linter,
+  no_tab_linter = lintr::no_tab_linter,
+  object_usage_linter = lintr::object_usage_linter,
+  object_length_linter = lintr::object_length_linter,
+  open_curly_linter = lintr::open_curly_linter,
+  semicolon = lintr::semicolon_terminator_linter,
+  seq = lintr::seq_linter,
+  spaces_inside_linter = lintr::spaces_inside_linter,
+  spaces_left_parentheses_linter = lintr::spaces_left_parentheses_linter,
+  trailing_blank_lines_linter = lintr::trailing_blank_lines_linter,
+  trailing_whitespace_linter = lintr::trailing_whitespace_linter,
+  true_false = lintr::T_and_F_symbol_linter,
+  unneeded_concatenation = lintr::unneeded_concatenation_linter
+)
+
+results <- lapply(
+  list.files(path = '.', pattern = '\\.[Rr]$', recursive = TRUE),
+  function (r_file) {
+    cat(sprintf("Processing %s ...\n", r_file))
+    list(r_file = r_file,
+         output = lintr::lint(filename = r_file, linters = my_linters))
+  })
+num_issue <- Reduce(sum, lapply(results, function (e) length(e$output)))
+
+lint2str <- function(lint_entry) {
+  color <- function(type) {
+    switch(type,
+      "warning" = crayon::magenta,
+      "error" = crayon::red,
+      "style" = crayon::blue,
+      crayon::bold
+    )
+  }
+
+  paste0(
+    lapply(lint_entry$output,
+      function (lint_line) {
+        paste0(
+          crayon::bold(lint_entry$r_file, ":",
+          as.character(lint_line$line_number), ":",
+          as.character(lint_line$column_number), ": ", sep = ""),
+          color(lint_line$type)(lint_line$type, ": ", sep = ""),
+          crayon::bold(lint_line$message), "\n",
+          lint_line$line, "\n",
+          lintr:::highlight_string(lint_line$message, lint_line$column_number, lint_line$ranges),
+          "\n",
+          collapse = "")
+      }),
+    collapse = "")
+}
+
+if (num_issue > 0) {
+  cat(sprintf('R linters found %d issues:\n', num_issue))
+  for (entry in results) {
+    if (length(entry$output)) {
+      cat(paste0('**** ', crayon::bold(entry$r_file), '\n'))
+      cat(paste0(lint2str(entry), collapse = ''))
+    }
+  }
+  quit(save = 'no', status = 1)  # Signal error to parent shell
+}