From 1995db85e81ca6c5655980bcc3fcb13853951aa4 Mon Sep 17 00:00:00 2001 From: Tong He Date: Thu, 25 Jul 2019 00:37:38 -0700 Subject: [PATCH] fix additional files note (#4699) * fix additional files note * Trigger CI * Trigger CI --- R-package/R/xgb.Booster.R | 2 ++ R-package/R/xgb.DMatrix.R | 1 + R-package/R/xgb.DMatrix.save.R | 1 + R-package/R/xgb.load.R | 1 + R-package/R/xgb.save.R | 1 + R-package/man/predict.xgb.Booster.Rd | 4 ++-- R-package/man/xgb.Booster.complete.Rd | 1 + R-package/man/xgb.DMatrix.Rd | 1 + R-package/man/xgb.DMatrix.save.Rd | 1 + R-package/man/xgb.attr.Rd | 1 + R-package/man/xgb.cv.Rd | 11 +++++------ R-package/man/xgb.load.Rd | 1 + R-package/man/xgb.plot.deepness.Rd | 8 ++++---- R-package/man/xgb.plot.importance.Rd | 4 ++-- R-package/man/xgb.plot.shap.Rd | 4 ++-- R-package/man/xgb.save.Rd | 1 + R-package/man/xgb.train.Rd | 10 ++++------ R-package/tests/testthat/test_helpers.R | 3 +++ 18 files changed, 34 insertions(+), 22 deletions(-) diff --git a/R-package/R/xgb.Booster.R b/R-package/R/xgb.Booster.R index 0c412f0f1..6904219b5 100644 --- a/R-package/R/xgb.Booster.R +++ b/R-package/R/xgb.Booster.R @@ -95,6 +95,7 @@ xgb.get.handle <- function(object) { #' saveRDS(bst, "xgb.model.rds") #' #' bst1 <- readRDS("xgb.model.rds") +#' if (file.exists("xgb.model.rds")) file.remove("xgb.model.rds") #' # the handle is invalid: #' print(bst1$handle) #' @@ -418,6 +419,7 @@ predict.xgb.Booster.handle <- function(object, ...) { #' #' xgb.save(bst, 'xgb.model') #' bst1 <- xgb.load('xgb.model') +#' if (file.exists('xgb.model')) file.remove('xgb.model') #' print(xgb.attr(bst1, "my_attribute")) #' print(xgb.attributes(bst1)) #' diff --git a/R-package/R/xgb.DMatrix.R b/R-package/R/xgb.DMatrix.R index 625c320e9..b96aeba08 100644 --- a/R-package/R/xgb.DMatrix.R +++ b/R-package/R/xgb.DMatrix.R @@ -19,6 +19,7 @@ #' dtrain <- xgb.DMatrix(train$data, label=train$label) #' xgb.DMatrix.save(dtrain, 'xgb.DMatrix.data') #' dtrain <- xgb.DMatrix('xgb.DMatrix.data') +#' if (file.exists('xgb.DMatrix.data')) file.remove('xgb.DMatrix.data') #' @export xgb.DMatrix <- function(data, info = list(), missing = NA, silent = FALSE, ...) { cnames <- NULL diff --git a/R-package/R/xgb.DMatrix.save.R b/R-package/R/xgb.DMatrix.save.R index f25d31e5f..1c659e529 100644 --- a/R-package/R/xgb.DMatrix.save.R +++ b/R-package/R/xgb.DMatrix.save.R @@ -11,6 +11,7 @@ #' dtrain <- xgb.DMatrix(train$data, label=train$label) #' xgb.DMatrix.save(dtrain, 'xgb.DMatrix.data') #' dtrain <- xgb.DMatrix('xgb.DMatrix.data') +#' if (file.exists('xgb.DMatrix.data')) file.remove('xgb.DMatrix.data') #' @export xgb.DMatrix.save <- function(dmatrix, fname) { if (typeof(fname) != "character") diff --git a/R-package/R/xgb.load.R b/R-package/R/xgb.load.R index cfe5dc87c..df6a21153 100644 --- a/R-package/R/xgb.load.R +++ b/R-package/R/xgb.load.R @@ -28,6 +28,7 @@ #' eta = 1, nthread = 2, nrounds = 2,objective = "binary:logistic") #' xgb.save(bst, 'xgb.model') #' bst <- xgb.load('xgb.model') +#' if (file.exists('xgb.model')) file.remove('xgb.model') #' pred <- predict(bst, test$data) #' @export xgb.load <- function(modelfile) { diff --git a/R-package/R/xgb.save.R b/R-package/R/xgb.save.R index 426c70d14..d969dae61 100644 --- a/R-package/R/xgb.save.R +++ b/R-package/R/xgb.save.R @@ -27,6 +27,7 @@ #' eta = 1, nthread = 2, nrounds = 2,objective = "binary:logistic") #' xgb.save(bst, 'xgb.model') #' bst <- xgb.load('xgb.model') +#' if (file.exists('xgb.model')) file.remove('xgb.model') #' pred <- predict(bst, test$data) #' @export xgb.save <- function(model, fname) { diff --git a/R-package/man/predict.xgb.Booster.Rd b/R-package/man/predict.xgb.Booster.Rd index e77411b5f..0a9bb4616 100644 --- a/R-package/man/predict.xgb.Booster.Rd +++ b/R-package/man/predict.xgb.Booster.Rd @@ -7,8 +7,8 @@ \usage{ \method{predict}{xgb.Booster}(object, newdata, missing = NA, outputmargin = FALSE, ntreelimit = NULL, predleaf = FALSE, - predcontrib = FALSE, approxcontrib = FALSE, - predinteraction = FALSE, reshape = FALSE, ...) + predcontrib = FALSE, approxcontrib = FALSE, predinteraction = FALSE, + reshape = FALSE, ...) \method{predict}{xgb.Booster.handle}(object, ...) } diff --git a/R-package/man/xgb.Booster.complete.Rd b/R-package/man/xgb.Booster.complete.Rd index fcb7bd94b..2b38b4c04 100644 --- a/R-package/man/xgb.Booster.complete.Rd +++ b/R-package/man/xgb.Booster.complete.Rd @@ -39,6 +39,7 @@ bst <- xgboost(data = agaricus.train$data, label = agaricus.train$label, max_dep saveRDS(bst, "xgb.model.rds") bst1 <- readRDS("xgb.model.rds") +if (file.exists("xgb.model.rds")) file.remove("xgb.model.rds") # the handle is invalid: print(bst1$handle) diff --git a/R-package/man/xgb.DMatrix.Rd b/R-package/man/xgb.DMatrix.Rd index 9a4263003..c3d47a97d 100644 --- a/R-package/man/xgb.DMatrix.Rd +++ b/R-package/man/xgb.DMatrix.Rd @@ -31,4 +31,5 @@ train <- agaricus.train dtrain <- xgb.DMatrix(train$data, label=train$label) xgb.DMatrix.save(dtrain, 'xgb.DMatrix.data') dtrain <- xgb.DMatrix('xgb.DMatrix.data') +if (file.exists('xgb.DMatrix.data')) file.remove('xgb.DMatrix.data') } diff --git a/R-package/man/xgb.DMatrix.save.Rd b/R-package/man/xgb.DMatrix.save.Rd index eb4c95370..7f25c5a45 100644 --- a/R-package/man/xgb.DMatrix.save.Rd +++ b/R-package/man/xgb.DMatrix.save.Rd @@ -20,4 +20,5 @@ train <- agaricus.train dtrain <- xgb.DMatrix(train$data, label=train$label) xgb.DMatrix.save(dtrain, 'xgb.DMatrix.data') dtrain <- xgb.DMatrix('xgb.DMatrix.data') +if (file.exists('xgb.DMatrix.data')) file.remove('xgb.DMatrix.data') } diff --git a/R-package/man/xgb.attr.Rd b/R-package/man/xgb.attr.Rd index 7bbf45b8b..ff55d432f 100644 --- a/R-package/man/xgb.attr.Rd +++ b/R-package/man/xgb.attr.Rd @@ -73,6 +73,7 @@ xgb.attributes(bst) <- list(a = 123, b = "abc") xgb.save(bst, 'xgb.model') bst1 <- xgb.load('xgb.model') +if (file.exists('xgb.model')) file.remove('xgb.model') print(xgb.attr(bst1, "my_attribute")) print(xgb.attributes(bst1)) diff --git a/R-package/man/xgb.cv.Rd b/R-package/man/xgb.cv.Rd index f39f386b7..180c09379 100644 --- a/R-package/man/xgb.cv.Rd +++ b/R-package/man/xgb.cv.Rd @@ -4,12 +4,11 @@ \alias{xgb.cv} \title{Cross Validation} \usage{ -xgb.cv(params = list(), data, nrounds, nfold, label = NULL, - missing = NA, prediction = FALSE, showsd = TRUE, - metrics = list(), obj = NULL, feval = NULL, stratified = TRUE, - folds = NULL, verbose = TRUE, print_every_n = 1L, - early_stopping_rounds = NULL, maximize = NULL, callbacks = list(), - ...) +xgb.cv(params = list(), data, nrounds, nfold, label = NULL, missing = NA, + prediction = FALSE, showsd = TRUE, metrics = list(), obj = NULL, + feval = NULL, stratified = TRUE, folds = NULL, verbose = TRUE, + print_every_n = 1L, early_stopping_rounds = NULL, maximize = NULL, + callbacks = list(), ...) } \arguments{ \item{params}{the list of parameters. Commonly used ones are: diff --git a/R-package/man/xgb.load.Rd b/R-package/man/xgb.load.Rd index 4cfccdd2d..3f743e1f5 100644 --- a/R-package/man/xgb.load.Rd +++ b/R-package/man/xgb.load.Rd @@ -33,6 +33,7 @@ bst <- xgboost(data = train$data, label = train$label, max_depth = 2, eta = 1, nthread = 2, nrounds = 2,objective = "binary:logistic") xgb.save(bst, 'xgb.model') bst <- xgb.load('xgb.model') +if (file.exists('xgb.model')) file.remove('xgb.model') pred <- predict(bst, test$data) } \seealso{ diff --git a/R-package/man/xgb.plot.deepness.Rd b/R-package/man/xgb.plot.deepness.Rd index 7d76f9f0a..fc9351c55 100644 --- a/R-package/man/xgb.plot.deepness.Rd +++ b/R-package/man/xgb.plot.deepness.Rd @@ -5,11 +5,11 @@ \alias{xgb.plot.deepness} \title{Plot model trees deepness} \usage{ -xgb.ggplot.deepness(model = NULL, which = c("2x1", "max.depth", - "med.depth", "med.weight")) +xgb.ggplot.deepness(model = NULL, which = c("2x1", "max.depth", "med.depth", + "med.weight")) -xgb.plot.deepness(model = NULL, which = c("2x1", "max.depth", - "med.depth", "med.weight"), plot = TRUE, ...) +xgb.plot.deepness(model = NULL, which = c("2x1", "max.depth", "med.depth", + "med.weight"), plot = TRUE, ...) } \arguments{ \item{model}{either an \code{xgb.Booster} model generated by the \code{xgb.train} function diff --git a/R-package/man/xgb.plot.importance.Rd b/R-package/man/xgb.plot.importance.Rd index e93d1a9d8..fce29f052 100644 --- a/R-package/man/xgb.plot.importance.Rd +++ b/R-package/man/xgb.plot.importance.Rd @@ -9,8 +9,8 @@ xgb.ggplot.importance(importance_matrix = NULL, top_n = NULL, measure = NULL, rel_to_first = FALSE, n_clusters = c(1:10), ...) xgb.plot.importance(importance_matrix = NULL, top_n = NULL, - measure = NULL, rel_to_first = FALSE, left_margin = 10, - cex = NULL, plot = TRUE, ...) + measure = NULL, rel_to_first = FALSE, left_margin = 10, cex = NULL, + plot = TRUE, ...) } \arguments{ \item{importance_matrix}{a \code{data.table} returned by \code{\link{xgb.importance}}.} diff --git a/R-package/man/xgb.plot.shap.Rd b/R-package/man/xgb.plot.shap.Rd index e972e5c81..79643ecb4 100644 --- a/R-package/man/xgb.plot.shap.Rd +++ b/R-package/man/xgb.plot.shap.Rd @@ -6,8 +6,8 @@ \usage{ xgb.plot.shap(data, shap_contrib = NULL, features = NULL, top_n = 1, model = NULL, trees = NULL, target_class = NULL, - approxcontrib = FALSE, subsample = NULL, n_col = 1, col = rgb(0, - 0, 1, 0.2), pch = ".", discrete_n_uniq = 5, discrete_jitter = 0.01, + approxcontrib = FALSE, subsample = NULL, n_col = 1, col = rgb(0, 0, 1, + 0.2), pch = ".", discrete_n_uniq = 5, discrete_jitter = 0.01, ylab = "SHAP", plot_NA = TRUE, col_NA = rgb(0.7, 0, 1, 0.6), pch_NA = ".", pos_NA = 1.07, plot_loess = TRUE, col_loess = 2, span_loess = 0.5, which = c("1d", "2d"), plot = TRUE, ...) diff --git a/R-package/man/xgb.save.Rd b/R-package/man/xgb.save.Rd index 08126bd87..7d1842d89 100644 --- a/R-package/man/xgb.save.Rd +++ b/R-package/man/xgb.save.Rd @@ -33,6 +33,7 @@ bst <- xgboost(data = train$data, label = train$label, max_depth = 2, eta = 1, nthread = 2, nrounds = 2,objective = "binary:logistic") xgb.save(bst, 'xgb.model') bst <- xgb.load('xgb.model') +if (file.exists('xgb.model')) file.remove('xgb.model') pred <- predict(bst, test$data) } \seealso{ diff --git a/R-package/man/xgb.train.Rd b/R-package/man/xgb.train.Rd index 828451b91..8b2cdc556 100644 --- a/R-package/man/xgb.train.Rd +++ b/R-package/man/xgb.train.Rd @@ -5,17 +5,15 @@ \alias{xgboost} \title{eXtreme Gradient Boosting Training} \usage{ -xgb.train(params = list(), data, nrounds, watchlist = list(), - obj = NULL, feval = NULL, verbose = 1, print_every_n = 1L, +xgb.train(params = list(), data, nrounds, watchlist = list(), obj = NULL, + feval = NULL, verbose = 1, print_every_n = 1L, early_stopping_rounds = NULL, maximize = NULL, save_period = NULL, - save_name = "xgboost.model", xgb_model = NULL, callbacks = list(), - ...) + save_name = "xgboost.model", xgb_model = NULL, callbacks = list(), ...) xgboost(data = NULL, label = NULL, missing = NA, weight = NULL, params = list(), nrounds, verbose = 1, print_every_n = 1L, early_stopping_rounds = NULL, maximize = NULL, save_period = NULL, - save_name = "xgboost.model", xgb_model = NULL, callbacks = list(), - ...) + save_name = "xgboost.model", xgb_model = NULL, callbacks = list(), ...) } \arguments{ \item{params}{the list of parameters. diff --git a/R-package/tests/testthat/test_helpers.R b/R-package/tests/testthat/test_helpers.R index 7a78f55d4..37b79020f 100644 --- a/R-package/tests/testthat/test_helpers.R +++ b/R-package/tests/testthat/test_helpers.R @@ -163,6 +163,7 @@ test_that("xgb-attribute functionality", { # serializing: xgb.save(bst.Tree, 'xgb.model') bst <- xgb.load('xgb.model') + if (file.exists('xgb.model')) file.remove('xgb.model') expect_equal(xgb.attr(bst, "my_attr"), val) expect_equal(xgb.attributes(bst), list.ch) # deletion: @@ -199,10 +200,12 @@ if (grepl('Windows', Sys.info()[['sysname']]) || test_that("xgb.Booster serializing as R object works", { saveRDS(bst.Tree, 'xgb.model.rds') bst <- readRDS('xgb.model.rds') + if (file.exists('xgb.model.rds')) file.remove('xgb.model.rds') dtrain <- xgb.DMatrix(sparse_matrix, label = label) expect_equal(predict(bst.Tree, dtrain), predict(bst, dtrain), tolerance = float_tolerance) expect_equal(xgb.dump(bst.Tree), xgb.dump(bst)) xgb.save(bst, 'xgb.model') + if (file.exists('xgb.model')) file.remove('xgb.model') nil_ptr <- new("externalptr") class(nil_ptr) <- "xgb.Booster.handle" expect_true(identical(bst$handle, nil_ptr))