[R] [ci] R linters are not being run in CI

[jameslamb]

I tried to pick up part of #5779 tonight, and realized something...I believe that the R linting tests are not being run in CI.

I confirmed this by copying those linters used in test_lint.R into the following script

lintr script (click me)

library(lintr)

args <- commandArgs(
    trailingOnly = TRUE
)
SOURCE_DIR <- args[[1L]]

FILES_TO_LINT <- list.files(
    path = SOURCE_DIR
    , pattern = "\\.r$"
    , all.files = TRUE
    , ignore.case = TRUE
    , full.names = TRUE
    , recursive = TRUE
    , include.dirs = FALSE
)

LINTERS_TO_USE <- list(
    absolute_paths_linter=lintr::absolute_paths_linter
    , assignment_linter=lintr::assignment_linter
    , closed_curly_linter=lintr::closed_curly_linter
    , commas_linter=lintr::commas_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
    , 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
)

cat(sprintf("Found %i R files to lint\n", length(FILES_TO_LINT)))

results <- NULL

for (r_file in FILES_TO_LINT) {

    this_result <- lintr::lint(
        filename = r_file
        , linters = LINTERS_TO_USE
        , cache = FALSE
    )

    print(
        sprintf(
            "Found %i linting errors in %s"
            , length(this_result)
            , r_file
        )
        , quote = FALSE
    )

    results <- c(results, this_result)

}

issues_found <- length(results)

if (issues_found > 0L) {
    print(results)
}

quit(save = "no", status = issues_found)

And then running it like this

Rscript lintr_r_code.R $(pwd)/R-package

I think the issue is that test_lint.R includes a skip_on_cran()

xgboost/R-package/tests/testthat/test_lint.R

Line 3 in b47b5ac

skip_on_cran()

And R tests are run by building a package and using R CMD check --as-cran

xgboost/tests/ci_build/build_test_rpkg.sh

Line 22 in b47b5ac

--as-cran \

xgboost/appveyor.yml

Line 106 in b47b5ac

R.exe CMD check xgboost*.tar.gz --no-manual --no-build-vignettes --as-cran --install-args=--build

When I run the script above, it finds 900+ linting issues.

First 100 R linter issues (click me)

Found 55 R files to lint
[1] Found 30 linting errors in R-package//demo/basic_walkthrough.R
[1] Found 7 linting errors in R-package//demo/boost_from_prediction.R
[1] Found 9 linting errors in R-package//demo/caret_wrapper.R
[1] Found 21 linting errors in R-package//demo/create_sparse_matrix.R
[1] Found 15 linting errors in R-package//demo/cross_validation.R
[1] Found 21 linting errors in R-package//demo/custom_objective.R
[1] Found 9 linting errors in R-package//demo/early_stopping.R
[1] Found 8 linting errors in R-package//demo/generalized_linear_model.R
[1] Found 5 linting errors in R-package//demo/gpu_accelerated.R
[1] Found 73 linting errors in R-package//demo/interaction_constraints.R
[1] Found 15 linting errors in R-package//demo/poisson_regression.R
[1] Found 17 linting errors in R-package//demo/predict_first_ntree.R
[1] Found 13 linting errors in R-package//demo/predict_leaf_indices.R
[1] Found 0 linting errors in R-package//demo/runall.R
[1] Found 7 linting errors in R-package//demo/tweedie_regression.R
[1] Found 0 linting errors in R-package//inst/make-r-def.R
[1] Found 22 linting errors in R-package//R/callbacks.R
[1] Found 14 linting errors in R-package//R/utils.R
[1] Found 23 linting errors in R-package//R/xgb.Booster.R
[1] Found 26 linting errors in R-package//R/xgb.create.features.R
[1] Found 13 linting errors in R-package//R/xgb.cv.R
[1] Found 4 linting errors in R-package//R/xgb.DMatrix.R
[1] Found 4 linting errors in R-package//R/xgb.DMatrix.save.R
[1] Found 14 linting errors in R-package//R/xgb.dump.R
[1] Found 33 linting errors in R-package//R/xgb.ggplot.R
[1] Found 37 linting errors in R-package//R/xgb.importance.R
[1] Found 0 linting errors in R-package//R/xgb.load.R
[1] Found 0 linting errors in R-package//R/xgb.load.raw.R
[1] Found 48 linting errors in R-package//R/xgb.model.dt.tree.R
[1] Found 31 linting errors in R-package//R/xgb.plot.deepness.R
[1] Found 2 linting errors in R-package//R/xgb.plot.importance.R
[1] Found 21 linting errors in R-package//R/xgb.plot.multi.trees.R
[1] Found 9 linting errors in R-package//R/xgb.plot.shap.R
[1] Found 26 linting errors in R-package//R/xgb.plot.tree.R
[1] Found 14 linting errors in R-package//R/xgb.save.R
[1] Found 0 linting errors in R-package//R/xgb.save.raw.R
[1] Found 1 linting errors in R-package//R/xgb.serialize.R
[1] Found 6 linting errors in R-package//R/xgb.train.R
[1] Found 1 linting errors in R-package//R/xgb.unserialize.R
[1] Found 0 linting errors in R-package//R/xgboost.R
[1] Found 0 linting errors in R-package//tests/testthat.R
[1] Found 61 linting errors in R-package//tests/testthat/test_basic.R
[1] Found 44 linting errors in R-package//tests/testthat/test_callbacks.R
[1] Found 13 linting errors in R-package//tests/testthat/test_custom_objective.R
[1] Found 22 linting errors in R-package//tests/testthat/test_dmatrix.R
[1] Found 2 linting errors in R-package//tests/testthat/test_gc_safety.R
[1] Found 4 linting errors in R-package//tests/testthat/test_glm.R
[1] Found 38 linting errors in R-package//tests/testthat/test_helpers.R
[1] Found 29 linting errors in R-package//tests/testthat/test_interaction_constraints.R
[1] Found 57 linting errors in R-package//tests/testthat/test_interactions.R
[1] Found 16 linting errors in R-package//tests/testthat/test_lint.R
[1] Found 13 linting errors in R-package//tests/testthat/test_monotone.R
[1] Found 2 linting errors in R-package//tests/testthat/test_parameter_exposure.R
[1] Found 7 linting errors in R-package//tests/testthat/test_poisson_regression.R
[1] Found 11 linting errors in R-package//tests/testthat/test_update.R
[[1]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:6:29: style: Put spaces around all infix operators.
data(agaricus.train, package='xgboost')
                           ~^~

[[2]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:7:28: style: Put spaces around all infix operators.
data(agaricus.test, package='xgboost')
                          ~^~

[[3]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:29:80: style: Trailing whitespace is superfluous.
bst <- xgboost(data = dtrain, max_depth = 2, eta = 1, nrounds = 2, nthread = 2, 
                                                                               ^

[[4]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:49:54: style: Trailing whitespace is superfluous.
# you can put in Matrix, sparseMatrix, or xgb.DMatrix 
                                                     ^

[[5]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:61:51: style: Put spaces around all infix operators.
print(paste("sum(abs(pred2-pred))=", sum(abs(pred2-pred))))
                                                 ~^~

[[6]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:64:5: style: Use <-, not =, for assignment.
raw = xgb.save.raw(bst)
    ^

[[7]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:69:51: style: Put spaces around all infix operators.
print(paste("sum(abs(pred3-pred))=", sum(abs(pred3-pred))))
                                                 ~^~

[[8]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:73:47: style: Put spaces around all infix operators.
dtrain <- xgb.DMatrix(data = train$data, label=train$label)
                                             ~^~

[[9]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:74:45: style: Put spaces around all infix operators.
dtest <- xgb.DMatrix(data = test$data, label=test$label)
                                           ~^~

[[10]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:77:24: style: Put spaces around all infix operators.
watchlist <- list(train=dtrain, test=dtest)
                      ~^~

[[11]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:77:37: style: Put spaces around all infix operators.
watchlist <- list(train=dtrain, test=dtest)
                                   ~^~

[[12]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:79:79: style: Trailing whitespace is superfluous.
# watchlist allows us to monitor the evaluation result on all data in the list 
                                                                              ^

[[13]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:81:22: style: Put spaces around all infix operators.
bst <- xgb.train(data=dtrain, max_depth=2, eta=1, nrounds=2, watchlist=watchlist,
                    ~^~

[[14]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:81:40: style: Put spaces around all infix operators.
bst <- xgb.train(data=dtrain, max_depth=2, eta=1, nrounds=2, watchlist=watchlist,
                                      ~^~

[[15]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:81:47: style: Put spaces around all infix operators.
bst <- xgb.train(data=dtrain, max_depth=2, eta=1, nrounds=2, watchlist=watchlist,
                                             ~^~

[[16]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:81:58: style: Put spaces around all infix operators.
bst <- xgb.train(data=dtrain, max_depth=2, eta=1, nrounds=2, watchlist=watchlist,
                                                        ~^~

[[17]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:81:71: style: Put spaces around all infix operators.
bst <- xgb.train(data=dtrain, max_depth=2, eta=1, nrounds=2, watchlist=watchlist,
                                                                     ~^~

[[18]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:85:22: style: Put spaces around all infix operators.
bst <- xgb.train(data=dtrain, max_depth=2, eta=1, nrounds=2, watchlist=watchlist,
                    ~^~

[[19]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:85:40: style: Put spaces around all infix operators.
bst <- xgb.train(data=dtrain, max_depth=2, eta=1, nrounds=2, watchlist=watchlist,
                                      ~^~

[[20]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:85:47: style: Put spaces around all infix operators.
bst <- xgb.train(data=dtrain, max_depth=2, eta=1, nrounds=2, watchlist=watchlist,
                                             ~^~

[[21]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:85:58: style: Put spaces around all infix operators.
bst <- xgb.train(data=dtrain, max_depth=2, eta=1, nrounds=2, watchlist=watchlist,
                                                        ~^~

[[22]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:85:71: style: Put spaces around all infix operators.
bst <- xgb.train(data=dtrain, max_depth=2, eta=1, nrounds=2, watchlist=watchlist,
                                                                     ~^~

[[23]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:93:22: style: Put spaces around all infix operators.
bst <- xgb.train(data=dtrain2, max_depth=2, eta=1, nrounds=2, watchlist=watchlist,
                    ~^~

[[24]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:93:41: style: Put spaces around all infix operators.
bst <- xgb.train(data=dtrain2, max_depth=2, eta=1, nrounds=2, watchlist=watchlist,
                                       ~^~

[[25]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:93:48: style: Put spaces around all infix operators.
bst <- xgb.train(data=dtrain2, max_depth=2, eta=1, nrounds=2, watchlist=watchlist,
                                              ~^~

[[26]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:93:59: style: Put spaces around all infix operators.
bst <- xgb.train(data=dtrain2, max_depth=2, eta=1, nrounds=2, watchlist=watchlist,
                                                         ~^~

[[27]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:93:72: style: Put spaces around all infix operators.
bst <- xgb.train(data=dtrain2, max_depth=2, eta=1, nrounds=2, watchlist=watchlist,
                                                                      ~^~

[[28]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:96:7: style: Use <-, not =, for assignment.
label = getinfo(dtest, "label")
      ^

[[29]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:98:56: style: Put spaces around all infix operators.
err <- as.numeric(sum(as.integer(pred > 0.5) != label))/length(label)
                                                      ~^~

[[30]]
/Users/jlamb/repos/xgboost/R-package/demo/basic_walkthrough.R:102:11: style: Use <-, not =, for assignment.
dump_path = file.path(tempdir(), 'dump.raw.txt')
          ^

[[31]]
/Users/jlamb/repos/xgboost/R-package/demo/boost_from_prediction.R:3:29: style: Put spaces around all infix operators.
data(agaricus.train, package='xgboost')
                           ~^~

[[32]]
/Users/jlamb/repos/xgboost/R-package/demo/boost_from_prediction.R:4:28: style: Put spaces around all infix operators.
data(agaricus.test, package='xgboost')
                          ~^~

[[33]]
/Users/jlamb/repos/xgboost/R-package/demo/boost_from_prediction.R:14:24: style: Put spaces around all infix operators.
param <- list(max_depth=2, eta=1, nthread = 2, objective='binary:logistic')
                      ~^~

[[34]]
/Users/jlamb/repos/xgboost/R-package/demo/boost_from_prediction.R:14:31: style: Put spaces around all infix operators.
param <- list(max_depth=2, eta=1, nthread = 2, objective='binary:logistic')
                             ~^~

[[35]]
/Users/jlamb/repos/xgboost/R-package/demo/boost_from_prediction.R:14:57: style: Put spaces around all infix operators.
param <- list(max_depth=2, eta=1, nthread = 2, objective='binary:logistic')
                                                       ~^~

[[36]]
/Users/jlamb/repos/xgboost/R-package/demo/boost_from_prediction.R:18:44: style: Put spaces around all infix operators.
ptrain <- predict(bst, dtrain, outputmargin=TRUE)
                                          ~^~

[[37]]
/Users/jlamb/repos/xgboost/R-package/demo/boost_from_prediction.R:19:43: style: Put spaces around all infix operators.
ptest  <- predict(bst, dtest, outputmargin=TRUE)
                                         ~^~

[[38]]
/Users/jlamb/repos/xgboost/R-package/demo/caret_wrapper.R:2:51: style: Trailing whitespace is superfluous.
devtools::install_github("topepo/caret/pkg/caret") 
                                                  ^

[[39]]
/Users/jlamb/repos/xgboost/R-package/demo/caret_wrapper.R:16:5: style: Commas should always have a space after.
df[,AgeDiscret:= as.factor(round(Age/10,0))]
    ^

[[40]]
/Users/jlamb/repos/xgboost/R-package/demo/caret_wrapper.R:16:15: style: Put spaces around all infix operators.
df[,AgeDiscret:= as.factor(round(Age/10,0))]
             ~^

[[41]]
/Users/jlamb/repos/xgboost/R-package/demo/caret_wrapper.R:16:37: style: Put spaces around all infix operators.
df[,AgeDiscret:= as.factor(round(Age/10,0))]
                                   ~^~

[[42]]
/Users/jlamb/repos/xgboost/R-package/demo/caret_wrapper.R:16:41: style: Commas should always have a space after.
df[,AgeDiscret:= as.factor(round(Age/10,0))]
                                        ^

[[43]]
/Users/jlamb/repos/xgboost/R-package/demo/caret_wrapper.R:19:5: style: Commas should always have a space after.
df[,AgeCat:= as.factor(ifelse(Age > 30, "Old", "Young"))]
    ^

[[44]]
/Users/jlamb/repos/xgboost/R-package/demo/caret_wrapper.R:19:11: style: Put spaces around all infix operators.
df[,AgeCat:= as.factor(ifelse(Age > 30, "Old", "Young"))]
         ~^

[[45]]
/Users/jlamb/repos/xgboost/R-package/demo/caret_wrapper.R:22:5: style: Commas should always have a space after.
df[,ID:=NULL]
    ^

[[46]]
/Users/jlamb/repos/xgboost/R-package/demo/caret_wrapper.R:22:7: style: Put spaces around all infix operators.
df[,ID:=NULL]
     ~^~~

[[47]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:9:66: style: Trailing whitespace is superfluous.
# Sometimes the dataset we have to work on have categorical data. 
                                                                 ^

[[48]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:12:47: style: Trailing whitespace is superfluous.
# In R, categorical variable is called Factor. 
                                              ^

[[49]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:35:5: style: Commas should always have a space after.
df[,AgeDiscret:= as.factor(round(Age/10,0))]
    ^

[[50]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:35:15: style: Put spaces around all infix operators.
df[,AgeDiscret:= as.factor(round(Age/10,0))]
             ~^

[[51]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:35:37: style: Put spaces around all infix operators.
df[,AgeDiscret:= as.factor(round(Age/10,0))]
                                   ~^~

[[52]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:35:41: style: Commas should always have a space after.
df[,AgeDiscret:= as.factor(round(Age/10,0))]
                                        ^

[[53]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:38:5: style: Commas should always have a space after.
df[,AgeCat:= as.factor(ifelse(Age > 30, "Old", "Young"))]
    ^

[[54]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:38:11: style: Put spaces around all infix operators.
df[,AgeCat:= as.factor(ifelse(Age > 30, "Old", "Young"))]
         ~^

[[55]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:41:5: style: Commas should always have a space after.
df[,ID:=NULL]
    ^

[[56]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:41:7: style: Put spaces around all infix operators.
df[,ID:=NULL]
     ~^~~

[[57]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:45:18: style: Commas should always have a space after.
print(levels(df[,Treatment]))
                 ^

[[58]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:55:15: style: Use <-, not =, for assignment.
sparse_matrix = sparse.model.matrix(Improved~.-1, data = df)
              ^

[[59]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:55:47: style: Put spaces around all infix operators.
sparse_matrix = sparse.model.matrix(Improved~.-1, data = df)
                                             ~^~

[[60]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:61:48: style: Trailing whitespace is superfluous.
# 1. Set, for all rows, field in Y column to 0; 
                                               ^

[[61]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:62:41: style: Trailing whitespace is superfluous.
# 2. set Y to 1 when Improved == Marked; 
                                        ^

[[62]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:64:15: style: Use <-, not =, for assignment.
output_vector = df[,Y:=0][Improved == "Marked",Y:=1][,Y]
              ^

[[63]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:64:21: style: Commas should always have a space after.
output_vector = df[,Y:=0][Improved == "Marked",Y:=1][,Y]
                    ^

[[64]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:64:22: style: Put spaces around all infix operators.
output_vector = df[,Y:=0][Improved == "Marked",Y:=1][,Y]
                    ~^~~

[[65]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:64:48: style: Commas should always have a space after.
output_vector = df[,Y:=0][Improved == "Marked",Y:=1][,Y]
                                               ^

[[66]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:64:49: style: Put spaces around all infix operators.
output_vector = df[,Y:=0][Improved == "Marked",Y:=1][,Y]
                                               ~^~~

[[67]]
/Users/jlamb/repos/xgboost/R-package/demo/create_sparse_matrix.R:64:55: style: Commas should always have a space after.
output_vector = df[,Y:=0][Improved == "Marked",Y:=1][,Y]
                                                      ^

[[68]]
/Users/jlamb/repos/xgboost/R-package/demo/cross_validation.R:3:29: style: Put spaces around all infix operators.
data(agaricus.train, package='xgboost')
                           ~^~

[[69]]
/Users/jlamb/repos/xgboost/R-package/demo/cross_validation.R:4:28: style: Put spaces around all infix operators.
data(agaricus.test, package='xgboost')
                          ~^~

[[70]]
/Users/jlamb/repos/xgboost/R-package/demo/cross_validation.R:9:24: style: Put spaces around all infix operators.
param <- list(max_depth=2, eta=1, nthread=2, objective='binary:logistic')
                      ~^~

[[71]]
/Users/jlamb/repos/xgboost/R-package/demo/cross_validation.R:9:31: style: Put spaces around all infix operators.
param <- list(max_depth=2, eta=1, nthread=2, objective='binary:logistic')
                             ~^~

[[72]]
/Users/jlamb/repos/xgboost/R-package/demo/cross_validation.R:9:42: style: Put spaces around all infix operators.
param <- list(max_depth=2, eta=1, nthread=2, objective='binary:logistic')
                                        ~^~

[[73]]
/Users/jlamb/repos/xgboost/R-package/demo/cross_validation.R:9:55: style: Put spaces around all infix operators.
param <- list(max_depth=2, eta=1, nthread=2, objective='binary:logistic')
                                                     ~^~

[[74]]
/Users/jlamb/repos/xgboost/R-package/demo/cross_validation.R:15:37: style: Put spaces around all infix operators.
xgb.cv(param, dtrain, nrounds, nfold=5, metrics={'error'})
                                   ~^~

[[75]]
/Users/jlamb/repos/xgboost/R-package/demo/cross_validation.R:15:48: style: Put spaces around all infix operators.
xgb.cv(param, dtrain, nrounds, nfold=5, metrics={'error'})
                                              ~^~

[[76]]
/Users/jlamb/repos/xgboost/R-package/demo/cross_validation.R:21:37: style: Put spaces around all infix operators.
xgb.cv(param, dtrain, nrounds, nfold=5,
                                   ~^~

[[77]]
/Users/jlamb/repos/xgboost/R-package/demo/cross_validation.R:22:15: style: Put spaces around all infix operators.
       metrics='error', showsd = FALSE)
             ~^~

[[78]]
/Users/jlamb/repos/xgboost/R-package/demo/cross_validation.R:32:13: style: Put spaces around all infix operators.
  preds <- 1/(1 + exp(-preds))
           ~^~

[[79]]
/Users/jlamb/repos/xgboost/R-package/demo/cross_validation.R:32:14: style: Place a space before left parenthesis, except in a function call.
  preds <- 1/(1 + exp(-preds))
             ^

[[80]]
/Users/jlamb/repos/xgboost/R-package/demo/cross_validation.R:39:48: style: Put spaces around all infix operators.
  err <- as.numeric(sum(labels != (preds > 0)))/length(labels)
                                              ~^~

[[81]]
/Users/jlamb/repos/xgboost/R-package/demo/cross_validation.R:43:24: style: Put spaces around all infix operators.
param <- list(max_depth=2, eta=1,
                      ~^~

[[82]]
/Users/jlamb/repos/xgboost/R-package/demo/cross_validation.R:43:31: style: Put spaces around all infix operators.
param <- list(max_depth=2, eta=1,
                             ~^~

[[83]]
/Users/jlamb/repos/xgboost/R-package/demo/custom_objective.R:3:29: style: Put spaces around all infix operators.
data(agaricus.train, package='xgboost')
                           ~^~

[[84]]
/Users/jlamb/repos/xgboost/R-package/demo/custom_objective.R:4:28: style: Put spaces around all infix operators.
data(agaricus.test, package='xgboost')
                          ~^~

[[85]]
/Users/jlamb/repos/xgboost/R-package/demo/custom_objective.R:18:13: style: Put spaces around all infix operators.
  preds <- 1/(1 + exp(-preds))
           ~^~

[[86]]
/Users/jlamb/repos/xgboost/R-package/demo/custom_objective.R:18:14: style: Place a space before left parenthesis, except in a function call.
  preds <- 1/(1 + exp(-preds))
             ^

[[87]]
/Users/jlamb/repos/xgboost/R-package/demo/custom_objective.R:32:48: style: Put spaces around all infix operators.
  err <- as.numeric(sum(labels != (preds > 0)))/length(labels)
                                              ~^~

[[88]]
/Users/jlamb/repos/xgboost/R-package/demo/custom_objective.R:36:24: style: Put spaces around all infix operators.
param <- list(max_depth=2, eta=1, nthread = 2, verbosity=0, 
                      ~^~

[[89]]
/Users/jlamb/repos/xgboost/R-package/demo/custom_objective.R:36:31: style: Put spaces around all infix operators.
param <- list(max_depth=2, eta=1, nthread = 2, verbosity=0, 
                             ~^~

[[90]]
/Users/jlamb/repos/xgboost/R-package/demo/custom_objective.R:36:57: style: Put spaces around all infix operators.
param <- list(max_depth=2, eta=1, nthread = 2, verbosity=0, 
                                                       ~^~

[[91]]
/Users/jlamb/repos/xgboost/R-package/demo/custom_objective.R:36:60: style: Trailing whitespace is superfluous.
param <- list(max_depth=2, eta=1, nthread = 2, verbosity=0, 
                                                           ^

[[92]]
/Users/jlamb/repos/xgboost/R-package/demo/custom_objective.R:37:24: style: Put spaces around all infix operators.
              objective=logregobj, eval_metric=evalerror)
                      ~^~

[[93]]
/Users/jlamb/repos/xgboost/R-package/demo/custom_objective.R:37:47: style: Put spaces around all infix operators.
              objective=logregobj, eval_metric=evalerror)
                                             ~^~

[[94]]
/Users/jlamb/repos/xgboost/R-package/demo/custom_objective.R:44:59: style: Trailing whitespace is superfluous.
# there can be cases where you want additional information 
                                                          ^

[[95]]
/Users/jlamb/repos/xgboost/R-package/demo/custom_objective.R:48:92: style: Trailing whitespace is superfluous.
# set label attribute of dtrain to be label, we use label as an example, it can be anything 
                                                                                           ^

[[96]]
/Users/jlamb/repos/xgboost/R-package/demo/custom_objective.R:55:13: style: Put spaces around all infix operators.
  preds <- 1/(1 + exp(-preds))
           ~^~

[[97]]
/Users/jlamb/repos/xgboost/R-package/demo/custom_objective.R:55:14: style: Place a space before left parenthesis, except in a function call.
  preds <- 1/(1 + exp(-preds))
             ^

[[98]]
/Users/jlamb/repos/xgboost/R-package/demo/custom_objective.R:60:24: style: Put spaces around all infix operators.
param <- list(max_depth=2, eta=1, nthread = 2, verbosity=0, 
                      ~^~

[[99]]
/Users/jlamb/repos/xgboost/R-package/demo/custom_objective.R:60:31: style: Put spaces around all infix operators.
param <- list(max_depth=2, eta=1, nthread = 2, verbosity=0, 
                             ~^~

[[100]]
/Users/jlamb/repos/xgboost/R-package/demo/custom_objective.R:60:57: style: Put spaces around all infix operators.
param <- list(max_depth=2, eta=1, nthread = 2, verbosity=0, 
                                                       ~^~

Proposal for fixing this issue

I think it would be beneficial to move linting out of the R unit tests into a standalone script, like the approach we use in LightGBM

https://github.com/microsoft/LightGBM/blob/4d43e96bbc10de2937aa70a5829977d46bdb1852/.ci/test.sh#L57

If you do that, all skip_* logic can be removed, and it will be really obvious if the tests are not passing.

[jameslamb]

@hcho3 would you be open to me submitting a PR that does what I've described (moving linting out of the R unit tests into a standalone script)?

I think it would make sense for me to do that and only include the linters that can impact code correctness (like T_and_F_symbol_linter), and leave it to maintainers to do the ones that will touch a lot more lines for style things like commas, whitespace, etc.

[trivialfis]

@jameslamb Thanks! That would be great. You don't have to address linting error on the PR, we can follow up by pushing to your branch or open another PR.

[trivialfis]

I opened a PR for fixing existing linting rules: #5911

[jameslamb]

oh nice!

[hcho3]

#5911 added lintr in CI.

[trivialfis]

A better script is still needed. Currently I think on github action it shows only you have errors, but not line number.

[hcho3]

@trivialfis I actually noticed this too. I wonder if running lintr in Ubuntu would fix the issue.

[trivialfis]

I think we need to call lint package explicitly.

[hcho3]

Sure, let me prepare a pull request. I'd like to see clear lintr warnings without having to run it manually.

[jameslamb]

it seems that the R linters are not running in CI right now. This is from the most recent build on master (https://github.com/dmlc/xgboost/runs/948472542):

I wanted to try fixing some issues found by other linters tonight. Without adding any new linters, I ran this

cd R-package
Rscript tests/run_lint.R

A lot of linting issues were found, and echo $? returns 1

[hcho3]

@jameslamb It looks like GitHub Actions job timed out. I restarted the test. As for the issues, make sure to install XGBoost R package first by running R CMD INSTALL .. Otherwise you will see some bogus issue because R linter won't recognize symbols from XGBoost.

This is from the previous commit of the master branch: https://github.com/dmlc/xgboost/runs/948386277?check_suite_focus=true, where the linter check passed.

[jameslamb]

ohhhhh I see! I should have looked at the GitHub Actions config, I see that now. Thank you