Update the federated secure branch. (#10589)

* [coll] Allow using local host for testing. (#10526) - Don't try to retrieve the IP address if a host is specified. - Fix compiler deprecation warning. * Fix boolean array for arrow-backed DF. (#10527) * [EM] Move prefetch in reset into the end of the iteration. (#10529) * Enhance the threadpool implementation. (#10531) - Accept an initialization function. - Support void return tasks. * [doc] Update link to release notes. [skip ci] (#10533) * [doc] Fix learning to rank tutorial. [skip ci] (#10539) * Cache GPU histogram kernel configuration. (#10538) * [sycl] Reorder if-else statements to allow using of cpu branches for sycl-devices (#10543) * reoder if-else statements for sycl compatibility * trigger check --------- Co-authored-by: Dmitry Razdoburdin <> * [EM] Basic distributed test for external memory. (#10492) * [sycl] Improve build configuration. (#10548) Co-authored-by: Dmitry Razdoburdin <> * [R] Update roxygen. (#10556) * [doc] Add more detailed explanations for advanced objectives (#10283) --------- Co-authored-by: Jiaming Yuan <[email protected]> * [doc] Add `build_info` to autodoc. [skip ci] (#10551) * [doc] Add notes about RMM and device ordinal. [skip ci] (#10562) - Remove the experimental tag, we have been running it for a long time now. - Add notes about avoiding set CUDA device. - Add link in parameter. * Fix empty partition. (#10559) * Avoid the use of size_t in the partitioner. (#10541) - Avoid the use of size_t in the partitioner. - Use `Span` instead of `Elem` where `node_id` is not needed. - Remove the `const_cast`. - Make sure the constness is not removed in the `Elem` by making it reference only. size_t is implementation-defined, which causes issue when we want to pass pointer or span. * [EM] Handle base idx in GPU histogram. (#10549) * [fed] Split up federated test CMake file. (#10566) - Collect all federated test files into the same directory. - Independently list the files. * Avoid thrust vector initialization. (#10544) * Avoid thrust vector initialization. - Add a wrapper for rmm device uvector. - Split up the `Resize` method for HDV. * Fix column split race condition. (#10572) * Small cleanup for CMake scripts. (#10573) - Remove rabit. * replace channel for sycl dependencies (#10576) Co-authored-by: Dmitry Razdoburdin <> * Bump org.apache.maven.plugins:maven-project-info-reports-plugin (#10497) Bumps [org.apache.maven.plugins:maven-project-info-reports-plugin](https://github.com/apache/maven-project-info-reports-plugin) from 3.5.0 to 3.6.1. - [Commits](apache/maven-project-info-reports-plugin@maven-project-info-reports-plugin-3.5.0...maven-project-info-reports-plugin-3.6.1) --- updated-dependencies: - dependency-name: org.apache.maven.plugins:maven-project-info-reports-plugin dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump org.apache.flink:flink-clients in /jvm-packages (#10517) Bumps [org.apache.flink:flink-clients](https://github.com/apache/flink) from 1.19.0 to 1.19.1. - [Commits](apache/flink@release-1.19.0...release-1.19.1) --- updated-dependencies: - dependency-name: org.apache.flink:flink-clients dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump org.apache.maven.plugins:maven-surefire-plugin (#10429) Bumps [org.apache.maven.plugins:maven-surefire-plugin](https://github.com/apache/maven-surefire) from 3.2.5 to 3.3.0. - [Release notes](https://github.com/apache/maven-surefire/releases) - [Commits](apache/maven-surefire@surefire-3.2.5...surefire-3.3.0) --- updated-dependencies: - dependency-name: org.apache.maven.plugins:maven-surefire-plugin dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump commons-logging:commons-logging in /jvm-packages/xgboost4j-spark (#10547) Bumps commons-logging:commons-logging from 1.3.2 to 1.3.3. --- updated-dependencies: - dependency-name: commons-logging:commons-logging dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Jiaming Yuan <[email protected]> * Bump org.apache.maven.plugins:maven-jar-plugin (#10458) Bumps [org.apache.maven.plugins:maven-jar-plugin](https://github.com/apache/maven-jar-plugin) from 3.4.1 to 3.4.2. - [Release notes](https://github.com/apache/maven-jar-plugin/releases) - [Commits](apache/maven-jar-plugin@maven-jar-plugin-3.4.1...maven-jar-plugin-3.4.2) --- updated-dependencies: - dependency-name: org.apache.maven.plugins:maven-jar-plugin dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump org.apache.maven.plugins:maven-project-info-reports-plugin (#10585) Bumps [org.apache.maven.plugins:maven-project-info-reports-plugin](https://github.com/apache/maven-project-info-reports-plugin) from 3.6.1 to 3.6.2. - [Commits](apache/maven-project-info-reports-plugin@maven-project-info-reports-plugin-3.6.1...maven-project-info-reports-plugin-3.6.2) --- updated-dependencies: - dependency-name: org.apache.maven.plugins:maven-project-info-reports-plugin dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump org.apache.maven.plugins:maven-release-plugin (#10586) Bumps [org.apache.maven.plugins:maven-release-plugin](https://github.com/apache/maven-release) from 3.0.1 to 3.1.1. - [Release notes](https://github.com/apache/maven-release/releases) - [Commits](apache/maven-release@maven-release-3.0.1...maven-release-3.1.1) --- updated-dependencies: - dependency-name: org.apache.maven.plugins:maven-release-plugin dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump net.alchim31.maven:scala-maven-plugin in /jvm-packages/xgboost4j (#10536) Bumps net.alchim31.maven:scala-maven-plugin from 4.9.1 to 4.9.2. --- updated-dependencies: - dependency-name: net.alchim31.maven:scala-maven-plugin dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump org.apache.maven.plugins:maven-checkstyle-plugin in /jvm-packages (#10518) Bumps [org.apache.maven.plugins:maven-checkstyle-plugin](https://github.com/apache/maven-checkstyle-plugin) from 3.3.1 to 3.4.0. - [Commits](apache/maven-checkstyle-plugin@maven-checkstyle-plugin-3.3.1...maven-checkstyle-plugin-3.4.0) --- updated-dependencies: - dependency-name: org.apache.maven.plugins:maven-checkstyle-plugin dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [R] Redesigned `xgboost()` interface skeleton (#10456) --------- Co-authored-by: Michael Mayer <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Dmitry Razdoburdin <[email protected]> Co-authored-by: david-cortes <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michael Mayer <[email protected]>
dmlc · Jul 15, 2024 · ed47ff5 · ed47ff5
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diff --git a/R-package/DESCRIPTION b/R-package/DESCRIPTION
@@ -57,7 +57,8 @@ Suggests:
     igraph (>= 1.0.1),
     float,
     titanic,
-    RhpcBLASctl
+    RhpcBLASctl,
+    survival
 Depends:
     R (>= 4.3.0)
 Imports:

diff --git a/R-package/NAMESPACE b/R-package/NAMESPACE
@@ -13,6 +13,7 @@ S3method(predict,xgb.Booster)
 S3method(print,xgb.Booster)
 S3method(print,xgb.DMatrix)
 S3method(print,xgb.cv.synchronous)
+S3method(print,xgboost)
 S3method(setinfo,xgb.Booster)
 S3method(setinfo,xgb.DMatrix)
 S3method(variable.names,xgb.Booster)

diff --git a/R-package/R/utils.R b/R-package/R/utils.R
@@ -30,6 +30,40 @@ NVL <- function(x, val) {
   return(c('rank:pairwise', 'rank:ndcg', 'rank:map'))
 }
 
+.OBJECTIVES_NON_DEFAULT_MODE <- function() {
+  return(c("reg:logistic", "binary:logitraw", "multi:softmax"))
+}
+
+.BINARY_CLASSIF_OBJECTIVES <- function() {
+  return(c("binary:logistic", "binary:hinge"))
+}
+
+.MULTICLASS_CLASSIF_OBJECTIVES <- function() {
+  return("multi:softprob")
+}
+
+.SURVIVAL_RIGHT_CENSORING_OBJECTIVES <- function() { # nolint
+  return(c("survival:cox", "survival:aft"))
+}
+
+.SURVIVAL_ALL_CENSORING_OBJECTIVES <- function() { # nolint
+  return("survival:aft")
+}
+
+.REGRESSION_OBJECTIVES <- function() {
+  return(c(
+    "reg:squarederror", "reg:squaredlogerror", "reg:logistic", "reg:pseudohubererror",
+    "reg:absoluteerror", "reg:quantileerror", "count:poisson", "reg:gamma", "reg:tweedie"
+  ))
+}
+
+.MULTI_TARGET_OBJECTIVES <- function() {
+  return(c(
+    "reg:squarederror", "reg:squaredlogerror", "reg:logistic", "reg:pseudohubererror",
+    "reg:quantileerror", "reg:gamma"
+  ))
+}
+
 
 #
 # Low-level functions for boosting --------------------------------------------

diff --git a/R-package/R/xgb.Booster.R b/R-package/R/xgb.Booster.R
@@ -663,9 +663,8 @@ validate.features <- function(bst, newdata) {
 #' data(agaricus.train, package = "xgboost")
 #' train <- agaricus.train
 #'
-#' bst <- xgboost(
-#'   data = train$data,
-#'   label = train$label,
+#' bst <- xgb.train(
+#'   data = xgb.DMatrix(train$data, label = train$label),
 #'   max_depth = 2,
 #'   eta = 1,
 #'   nthread = 2,
@@ -767,9 +766,8 @@ xgb.attributes <- function(object) {
 #' data.table::setDTthreads(nthread)
 #' train <- agaricus.train
 #'
-#' bst <- xgboost(
-#'   data = train$data,
-#'   label = train$label,
+#' bst <- xgb.train(
+#'   data = xgb.DMatrix(train$data, label = train$label),
 #'   max_depth = 2,
 #'   eta = 1,
 #'   nthread = nthread,
@@ -817,9 +815,8 @@ xgb.config <- function(object) {
 #' data(agaricus.train, package = "xgboost")
 #' train <- agaricus.train
 #'
-#' bst <- xgboost(
-#'   data = train$data,
-#'   label = train$label,
+#' bst <- xgb.train(
+#'   data = xgb.DMatrix(train$data, label = train$label),
 #'   max_depth = 2,
 #'   eta = 1,
 #'   nthread = 2,
@@ -1230,9 +1227,8 @@ xgb.is.same.Booster <- function(obj1, obj2) {
 #' data(agaricus.train, package = "xgboost")
 #' train <- agaricus.train
 #'
-#' bst <- xgboost(
-#'   data = train$data,
-#'   label = train$label,
+#' bst <- xgb.train(
+#'   data = xgb.DMatrix(train$data, label = train$label),
 #'   max_depth = 2,
 #'   eta = 1,
 #'   nthread = 2,

diff --git a/R-package/R/xgb.DMatrix.R b/R-package/R/xgb.DMatrix.R
@@ -853,36 +853,6 @@ xgb.DMatrix.hasinfo <- function(object, info) {
 }
 
 
-# get dmatrix from data, label
-# internal helper method
-xgb.get.DMatrix <- function(data, label, missing, weight, nthread) {
-  if (inherits(data, "dgCMatrix") || is.matrix(data)) {
-    if (is.null(label)) {
-      stop("label must be provided when data is a matrix")
-    }
-    dtrain <- xgb.DMatrix(data, label = label, missing = missing, nthread = nthread)
-    if (!is.null(weight)) {
-      setinfo(dtrain, "weight", weight)
-    }
-  } else {
-    if (!is.null(label)) {
-      warning("xgboost: label will be ignored.")
-    }
-    if (is.character(data)) {
-      data <- path.expand(data)
-      dtrain <- xgb.DMatrix(data[1])
-    } else if (inherits(data, "xgb.DMatrix")) {
-      dtrain <- data
-    } else if (inherits(data, "data.frame")) {
-      stop("xgboost doesn't support data.frame as input. Convert it to matrix first.")
-    } else {
-      stop("xgboost: invalid input data")
-    }
-  }
-  return(dtrain)
-}
-
-
 #' Dimensions of xgb.DMatrix
 #'
 #' Returns a vector of numbers of rows and of columns in an \code{xgb.DMatrix}.

diff --git a/R-package/R/xgb.dump.R b/R-package/R/xgb.dump.R
@@ -29,8 +29,8 @@
 #' data(agaricus.test, package='xgboost')
 #' train <- agaricus.train
 #' test <- agaricus.test
-#' bst <- xgboost(data = train$data, label = train$label, max_depth = 2,
-#'                eta = 1, nthread = 2, nrounds = 2, objective = "binary:logistic")
+#' bst <- xgb.train(data = xgb.DMatrix(train$data, label = train$label), max_depth = 2,
+#'                  eta = 1, nthread = 2, nrounds = 2, objective = "binary:logistic")
 #' # save the model in file 'xgb.model.dump'
 #' dump_path = file.path(tempdir(), 'model.dump')
 #' xgb.dump(bst, dump_path, with_stats = TRUE)

diff --git a/R-package/R/xgb.importance.R b/R-package/R/xgb.importance.R
@@ -46,9 +46,8 @@
 #' # binomial classification using "gbtree":
 #' data(agaricus.train, package = "xgboost")
 #'
-#' bst <- xgboost(
-#'   data = agaricus.train$data,
-#'   label = agaricus.train$label,
+#' bst <- xgb.train(
+#'   data = xgb.DMatrix(agaricus.train$data, label = agaricus.train$label),
 #'   max_depth = 2,
 #'   eta = 1,
 #'   nthread = 2,
@@ -59,9 +58,8 @@
 #' xgb.importance(model = bst)
 #'
 #' # binomial classification using "gblinear":
-#' bst <- xgboost(
-#'   data = agaricus.train$data,
-#'   label = agaricus.train$label,
+#' bst <- xgb.train(
+#'   data = xgb.DMatrix(agaricus.train$data, label = agaricus.train$label),
 #'   booster = "gblinear",
 #'   eta = 0.3,
 #'   nthread = 1,
@@ -73,9 +71,11 @@
 #' # multiclass classification using "gbtree":
 #' nclass <- 3
 #' nrounds <- 10
-#' mbst <- xgboost(
-#'   data = as.matrix(iris[, -5]),
-#'   label = as.numeric(iris$Species) - 1,
+#' mbst <- xgb.train(
+#'   data = xgb.DMatrix(
+#'     as.matrix(iris[, -5]),
+#'     label = as.numeric(iris$Species) - 1
+#'   ),
 #'   max_depth = 3,
 #'   eta = 0.2,
 #'   nthread = 2,
@@ -99,9 +99,11 @@
 #' )
 #'
 #' # multiclass classification using "gblinear":
-#' mbst <- xgboost(
-#'   data = scale(as.matrix(iris[, -5])),
-#'   label = as.numeric(iris$Species) - 1,
+#' mbst <- xgb.train(
+#'   data = xgb.DMatrix(
+#'     scale(as.matrix(iris[, -5])),
+#'     label = as.numeric(iris$Species) - 1
+#'   ),
 #'   booster = "gblinear",
 #'   eta = 0.2,
 #'   nthread = 1,

diff --git a/R-package/R/xgb.model.dt.tree.R b/R-package/R/xgb.model.dt.tree.R
@@ -43,9 +43,8 @@
 #' nthread <- 1
 #' data.table::setDTthreads(nthread)
 #'
-#' bst <- xgboost(
-#'   data = agaricus.train$data,
-#'   label = agaricus.train$label,
+#' bst <- xgb.train(
+#'   data = xgb.DMatrix(agaricus.train$data, label = agaricus.train$label),
 #'   max_depth = 2,
 #'   eta = 1,
 #'   nthread = nthread,

diff --git a/R-package/R/xgb.plot.deepness.R b/R-package/R/xgb.plot.deepness.R
@@ -48,9 +48,8 @@
 #' data.table::setDTthreads(nthread)
 #'
 #' ## Change max_depth to a higher number to get a more significant result
-#' bst <- xgboost(
-#'   data = agaricus.train$data,
-#'   label = agaricus.train$label,
+#' bst <- xgb.train(
+#'   data = xgb.DMatrix(agaricus.train$data, label = agaricus.train$label),
 #'   max_depth = 6,
 #'   nthread = nthread,
 #'   nrounds = 50,

diff --git a/R-package/R/xgb.plot.importance.R b/R-package/R/xgb.plot.importance.R
@@ -51,9 +51,8 @@
 #' nthread <- 2
 #' data.table::setDTthreads(nthread)
 #'
-#' bst <- xgboost(
-#'   data = agaricus.train$data,
-#'   label = agaricus.train$label,
+#' bst <- xgb.train(
+#'   data = xgb.DMatrix(agaricus.train$data, label = agaricus.train$label),
 #'   max_depth = 3,
 #'   eta = 1,
 #'   nthread = nthread,

diff --git a/R-package/R/xgb.plot.multi.trees.R b/R-package/R/xgb.plot.multi.trees.R
@@ -35,9 +35,8 @@
 #' nthread <- 2
 #' data.table::setDTthreads(nthread)
 #'
-#' bst <- xgboost(
-#'   data = agaricus.train$data,
-#'   label = agaricus.train$label,
+#' bst <- xgb.train(
+#'   data = xgb.DMatrix(agaricus.train$data, label = agaricus.train$label),
 #'   max_depth = 15,
 #'   eta = 1,
 #'   nthread = nthread,

diff --git a/R-package/R/xgb.plot.shap.R b/R-package/R/xgb.plot.shap.R
@@ -82,9 +82,8 @@
 #' data.table::setDTthreads(nthread)
 #' nrounds <- 20
 #'
-#' bst <- xgboost(
-#'   agaricus.train$data,
-#'   agaricus.train$label,
+#' bst <- xgb.train(
+#'   data = xgb.DMatrix(agaricus.train$data, agaricus.train$label),
 #'   nrounds = nrounds,
 #'   eta = 0.1,
 #'   max_depth = 3,
@@ -108,9 +107,8 @@
 #' set.seed(123)
 #' is.na(x[sample(nrow(x) * 4, 30)]) <- TRUE # introduce some missing values
 #'
-#' mbst <- xgboost(
-#'   data = x,
-#'   label = as.numeric(iris$Species) - 1,
+#' mbst <- xgb.train(
+#'   data = xgb.DMatrix(x, label = as.numeric(iris$Species) - 1),
 #'   nrounds = nrounds,
 #'   max_depth = 2,
 #'   eta = 0.3,

diff --git a/R-package/R/xgb.plot.tree.R b/R-package/R/xgb.plot.tree.R
@@ -68,9 +68,8 @@
 #' @examples
 #' data(agaricus.train, package = "xgboost")
 #'
-#' bst <- xgboost(
-#'   data = agaricus.train$data,
-#'   label = agaricus.train$label,
+#' bst <- xgb.train(
+#'   data = xgb.DMatrix(agaricus.train$data, agaricus.train$label),
 #'   max_depth = 3,
 #'   eta = 1,
 #'   nthread = 2,

diff --git a/R-package/R/xgb.train.R b/R-package/R/xgb.train.R
@@ -182,12 +182,6 @@
 #'        as R attributes, and thus do not get saved when using XGBoost's own serializaters like
 #'        \link{xgb.save} (but are kept when using R serializers like \link{saveRDS}).
 #' @param ... other parameters to pass to \code{params}.
-#' @param label vector of response values. Should not be provided when data is
-#'        a local data file name or an \code{xgb.DMatrix}.
-#' @param missing by default is set to NA, which means that NA values should be considered as 'missing'
-#'        by the algorithm. Sometimes, 0 or other extreme value might be used to represent missing values.
-#'        This parameter is only used when input is a dense matrix.
-#' @param weight a vector indicating the weight for each row of the input.
 #'
 #' @return
 #' An object of class \code{xgb.Booster}.
@@ -328,12 +322,10 @@
 #'                  early_stopping_rounds = 3)
 #'
 #' ## An 'xgboost' interface example:
-#' bst <- xgboost(data = agaricus.train$data, label = agaricus.train$label,
-#'                max_depth = 2, eta = 1, nthread = nthread, nrounds = 2,
-#'                objective = "binary:logistic")
+#' bst <- xgboost(x = agaricus.train$data, y = factor(agaricus.train$label),
+#'                params = list(max_depth = 2, eta = 1), nthread = nthread, nrounds = 2)
 #' pred <- predict(bst, agaricus.test$data)
 #'
-#' @rdname xgb.train
 #' @export
 xgb.train <- function(params = list(), data, nrounds, evals = list(),
                       obj = NULL, feval = NULL, verbose = 1, print_every_n = 1L,