[R] release 1.5.0.2 (#7452)

* [R] release 1.5.0.2

* Add cmake list to r build ignore.

.github/workflows/r_tests.yml

@@ -3,7 +3,7 @@ name: XGBoost-R-Tests
 on: [push, pull_request]
 
 env:
-  R_PACKAGES: c('XML', 'igraph', 'data.table', 'ggplot2', 'DiagrammeR', 'Ckmeans.1d.dp', 'vcd', 'testthat', 'lintr', 'knitr', 'rmarkdown', 'e1071', 'cplm', 'devtools', 'float', 'titanic')
+  R_PACKAGES: c('XML', 'data.table', 'ggplot2', 'DiagrammeR', 'Ckmeans.1d.dp', 'vcd', 'testthat', 'lintr', 'knitr', 'rmarkdown', 'e1071', 'cplm', 'devtools', 'float', 'titanic')
   GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
@@ -40,6 +40,11 @@ jobs:
         install.packages(${{ env.R_PACKAGES }},
                          repos = 'http://cloud.r-project.org',
                          dependencies = c('Depends', 'Imports', 'LinkingTo'))
+    - name: Install igraph on Windows
+      shell: Rscript {0}
+      if: matrix.config.os == 'windows-latest'
+      run: |
+        install.packages('igraph', type='binary')
 
     - name: Run lintr
       run: |
@@ -83,6 +88,11 @@ jobs:
         install.packages(${{ env.R_PACKAGES }},
                          repos = 'http://cloud.r-project.org',
                          dependencies = c('Depends', 'Imports', 'LinkingTo'))
+    - name: Install igraph on Windows
+      shell: Rscript {0}
+      if: matrix.config.os == 'windows-2016'
+      run: |
+        install.packages('igraph', type='binary', dependencies = c('Depends', 'Imports', 'LinkingTo'))
 
     - uses: actions/setup-python@v2
       with:
@@ -91,7 +101,7 @@ jobs:
 
     - name: Test R
       run: |
-        python tests/ci_build/test_r_package.py --compiler="${{ matrix.config.compiler }}" --build-tool="${{ matrix.config.build }}"
+        python tests/ci_build/test_r_package.py --compiler='${{ matrix.config.compiler }}' --build-tool='${{ matrix.config.build }}'
 
   test-R-CRAN:
     runs-on: ubuntu-latest
@@ -115,7 +125,7 @@ jobs:
 
     - name: Install system packages
       run: |
-        sudo apt-get update && sudo apt-get install libcurl4-openssl-dev libssl-dev libssh2-1-dev libgit2-dev pandoc pandoc-citeproc
+        sudo apt-get update && sudo apt-get install libcurl4-openssl-dev libssl-dev libssh2-1-dev libgit2-dev pandoc pandoc-citeproc libglpk-dev
 
     - name: Cache R packages
       uses: actions/cache@v2
@@ -130,6 +140,7 @@ jobs:
         install.packages(${{ env.R_PACKAGES }},
                          repos = 'http://cloud.r-project.org',
                          dependencies = c('Depends', 'Imports', 'LinkingTo'))
+        install.packages('igraph', repos = 'http://cloud.r-project.org', dependencies = c('Depends', 'Imports', 'LinkingTo'))
 
     - name: Check R Package
       run: |

R-package/.Rbuildignore

@@ -4,3 +4,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 README.md
+CMakeLists.txt

R-package/DESCRIPTION

@@ -1,8 +1,8 @@
 Package: xgboost
 Type: Package
 Title: Extreme Gradient Boosting
-Version: 1.5.0.1
-Date: 2021-10-13
+Version: 1.5.0.2
+Date: 2021-11-19
 Authors@R: c(
   person("Tianqi", "Chen", role = c("aut"),
          email = "tianqi.tchen@gmail.com"),

R-package/tests/testthat/test_helpers.R

@@ -228,7 +228,7 @@ if (grepl('Windows', Sys.info()[['sysname']]) ||
       X <- 10^runif(100, -20, 20)
       if (capabilities('long.double')) {
           X2X <- as.numeric(format(X, digits = 17))
-          expect_identical(X, X2X)
+          expect_equal(X, X2X, tolerance = float_tolerance)
       }
       # retrieved attributes to be the same as written
       for (x in X) {

include/xgboost/data.h

@@ -211,7 +211,7 @@ struct Entry {
  */
 struct BatchParam {
   /*! \brief The GPU device to use. */
-  int gpu_id;
+  int gpu_id {-1};
   /*! \brief Maximum number of bins per feature for histograms. */
   int max_bin{0};
   /*! \brief Hessian, used for sketching with future approx implementation. */

src/data/simple_dmatrix.h

@@ -49,10 +49,10 @@ class SimpleDMatrix : public DMatrix {
   MetaInfo info_;
   // Primary storage type
   std::shared_ptr<SparsePage> sparse_page_ = std::make_shared<SparsePage>();
-  std::shared_ptr<CSCPage> column_page_;
-  std::shared_ptr<SortedCSCPage> sorted_column_page_;
-  std::shared_ptr<EllpackPage> ellpack_page_;
-  std::shared_ptr<GHistIndexMatrix> gradient_index_;
+  std::shared_ptr<CSCPage> column_page_{nullptr};
+  std::shared_ptr<SortedCSCPage> sorted_column_page_{nullptr};
+  std::shared_ptr<EllpackPage> ellpack_page_{nullptr};
+  std::shared_ptr<GHistIndexMatrix> gradient_index_{nullptr};
   BatchParam batch_param_;
 
   bool EllpackExists() const override {

src/tree/updater_colmaker.cc

@@ -109,10 +109,9 @@ class ColMaker: public TreeUpdater {
     interaction_constraints_.Configure(param_, dmat->Info().num_row_);
     // build tree
     for (auto tree : trees) {
-      Builder builder(
-        param_,
-        colmaker_param_,
-        interaction_constraints_, column_densities_);
+      CHECK(tparam_);
+      Builder builder(param_, colmaker_param_, interaction_constraints_, tparam_,
+                      column_densities_);
       builder.Update(gpair->ConstHostVector(), dmat, tree);
     }
     param_.learning_rate = lr;
@@ -154,12 +153,12 @@ class ColMaker: public TreeUpdater {
   class Builder {
    public:
     // constructor
-    explicit Builder(const TrainParam& param,
-                     const ColMakerTrainParam& colmaker_train_param,
+    explicit Builder(const TrainParam &param, const ColMakerTrainParam &colmaker_train_param,
                      FeatureInteractionConstraintHost _interaction_constraints,
-                     const std::vector<float> &column_densities)
-        : param_(param), colmaker_train_param_{colmaker_train_param},
-          nthread_(omp_get_max_threads()),
+                     GenericParameter const *ctx, const std::vector<float> &column_densities)
+        : param_(param),
+          colmaker_train_param_{colmaker_train_param},
+          ctx_{ctx},
           tree_evaluator_(param_, column_densities.size(), GenericParameter::kCpuId),
           interaction_constraints_{std::move(_interaction_constraints)},
           column_densities_(column_densities) {}
@@ -238,7 +237,7 @@ class ColMaker: public TreeUpdater {
         // setup temp space for each thread
         // reserve a small space
         stemp_.clear();
-        stemp_.resize(this->nthread_, std::vector<ThreadEntry>());
+        stemp_.resize(this->ctx_->Threads(), std::vector<ThreadEntry>());
         for (auto& i : stemp_) {
           i.clear(); i.reserve(256);
         }
@@ -451,8 +450,9 @@ class ColMaker: public TreeUpdater {
       // start enumeration
       const auto num_features = static_cast<bst_omp_uint>(feat_set.size());
 #if defined(_OPENMP)
+      CHECK(this->ctx_);
       const int batch_size =  // NOLINT
-          std::max(static_cast<int>(num_features / this->nthread_ / 32), 1);
+          std::max(static_cast<int>(num_features / this->ctx_->Threads() / 32), 1);
 #endif  // defined(_OPENMP)
       {
         auto page = batch.GetView();
@@ -553,7 +553,8 @@ class ColMaker: public TreeUpdater {
     virtual void SyncBestSolution(const std::vector<int> &qexpand) {
       for (int nid : qexpand) {
         NodeEntry &e = snode_[nid];
-        for (int tid = 0; tid < this->nthread_; ++tid) {
+        CHECK(this->ctx_);
+        for (int tid = 0; tid < this->ctx_->Threads(); ++tid) {
           e.best.Update(stemp_[tid][nid].best);
         }
       }
@@ -609,7 +610,7 @@ class ColMaker: public TreeUpdater {
     const TrainParam& param_;
     const ColMakerTrainParam& colmaker_train_param_;
     // number of omp thread used during training
-    const int nthread_;
+    GenericParameter const* ctx_;
     common::ColumnSampler column_sampler_;
     // Instance Data: current node position in the tree of each instance
     std::vector<int> position_;

src/tree/updater_quantile_hist.cc

@@ -115,9 +115,6 @@ bool QuantileHistMaker::UpdatePredictionCache(
   }
 }
 
-template <typename GradientSumT>
-QuantileHistMaker::Builder<GradientSumT>::~Builder() = default;
-
 
 template <typename GradientSumT>
 template <bool any_missing>

src/tree/updater_quantile_hist.h

@@ -204,7 +204,6 @@ class QuantileHistMaker: public TreeUpdater {
               new HistogramBuilder<GradientSumT, CPUExpandEntry>} {
       builder_monitor_.Init("Quantile::Builder");
     }
-    ~Builder();
     // update one tree, growing
     virtual void Update(const GHistIndexMatrix& gmat,
                         const ColumnMatrix& column_matrix,