[CI] Revise R tests.

.github/workflows/main.yml

@@ -146,7 +146,7 @@ jobs:
         python -m pip install wheel setuptools cpplint pylint
     - name: Run lint
       run: |
-        LINT_LANG=cpp make lint
+        python dmlc-core/scripts/lint.py xgboost cpp R-package/src
 
   sphinx:
     runs-on: ubuntu-latest

.github/workflows/r_nold.yml

@@ -1,4 +1,4 @@
-# Run R tests with noLD R. Only triggered by a pull request review
+# Run expensive R tests with the help of rhub. Only triggered by a pull request review
 # See discussion at https://github.com/dmlc/xgboost/pull/6378
 
 name: XGBoost-R-noLD
@@ -7,9 +7,6 @@ on:
   pull_request_review_comment:
     types: [created]
 
-env:
-  R_PACKAGES: c('XML', 'igraph', 'data.table', 'ggplot2', 'DiagrammeR', 'Ckmeans.1d.dp', 'vcd', 'testthat', 'lintr', 'knitr', 'rmarkdown', 'e1071', 'cplm', 'devtools', 'float', 'titanic')
-
 permissions:
   contents: read # to fetch code (actions/checkout)
 
@@ -18,26 +15,22 @@ jobs:
     if: github.event.comment.body == '/gha run r-nold-test' && contains('OWNER,MEMBER,COLLABORATOR', github.event.comment.author_association)
     timeout-minutes: 120
     runs-on: ubuntu-latest
-    container: rhub/debian-gcc-devel-nold
+    container:
+      image: rhub/debian-gcc-devel-nold
     steps:
     - name: Install git and system packages
       shell: bash
       run: |
-        apt-get update && apt-get install -y git libcurl4-openssl-dev libssl-dev libssh2-1-dev libgit2-dev libxml2-dev
+        apt update && apt install libcurl4-openssl-dev libssl-dev libssh2-1-dev libgit2-dev libglpk-dev libxml2-dev libharfbuzz-dev libfribidi-dev git -y
 
     - uses: actions/checkout@v2
       with:
         submodules: 'true'
 
     - name: Install dependencies
-      shell: bash
+      shell: bash -l {0}
       run: |
-        cat > install_libs.R <<EOT
-          install.packages(${{ env.R_PACKAGES }},
-                           repos = 'http://cloud.r-project.org',
-                           dependencies = c('Depends', 'Imports', 'LinkingTo'))
-        EOT
-        /tmp/R-devel/bin/Rscript install_libs.R
+        /tmp/R-devel/bin/Rscript -e "source('./R-package/tests/helper_scripts/install_deps.R')"
 
     - name: Run R tests
       shell: bash

.github/workflows/r_tests.yml

@@ -3,9 +3,7 @@ name: XGBoost-R-Tests
 on: [push, pull_request]
 
 env:
-  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 }}
-  _R_CHECK_EXAMPLE_TIMING_CPU_TO_ELAPSED_THRESHOLD_: 2.5
 
 permissions:
   contents: read # to fetch code (actions/checkout)
@@ -35,29 +33,22 @@ jobs:
       uses: actions/cache@v2
       with:
         path: ${{ env.R_LIBS_USER }}
-        key: ${{ runner.os }}-r-${{ matrix.config.r }}-5-${{ hashFiles('R-package/DESCRIPTION') }}
-        restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-5-${{ hashFiles('R-package/DESCRIPTION') }}
+        key: ${{ runner.os }}-r-${{ matrix.config.r }}-6-${{ hashFiles('R-package/DESCRIPTION') }}
+        restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-6-${{ hashFiles('R-package/DESCRIPTION') }}
 
     - name: Install dependencies
       shell: Rscript {0}
       run: |
-        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')
+        source("./R-package/tests/helper_scripts/install_deps.R")
 
     - name: Run lintr
       run: |
         cd R-package
-        MAKE="make -j$(nproc)" R CMD INSTALL .
+        MAKEFLAGS="-j$(nproc)" R CMD INSTALL .
         # Disable lintr errors for now: https://github.com/dmlc/xgboost/issues/8012
         Rscript tests/helper_scripts/run_lint.R || true
 
-  test-with-R:
+  test-R-on-Windows:
     runs-on: ${{ matrix.config.os }}
     name: Test R on OS ${{ matrix.config.os }}, R ${{ matrix.config.r }}, Compiler ${{ matrix.config.compiler }}, Build ${{ matrix.config.build }}
     strategy:
@@ -66,10 +57,8 @@ jobs:
         config:
           - {os: windows-latest, r: 'release', compiler: 'mingw', build: 'autotools'}
           - {os: windows-latest, r: 'release', compiler: 'msvc', build: 'cmake'}
-          - {os: windows-latest, r: 'release', compiler: 'mingw', build: 'cmake'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      _R_CHECK_EXAMPLE_TIMING_CPU_TO_ELAPSED_THRESHOLD_: 2.5
       RSPM: ${{ matrix.config.rspm }}
 
     steps:
@@ -85,80 +74,60 @@ jobs:
       uses: actions/cache@v2
       with:
         path: ${{ env.R_LIBS_USER }}
-        key: ${{ runner.os }}-r-${{ matrix.config.r }}-5-${{ hashFiles('R-package/DESCRIPTION') }}
-        restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-5-${{ hashFiles('R-package/DESCRIPTION') }}
-
-    - name: Install dependencies
-      shell: Rscript {0}
-      if: matrix.config.os != 'windows-latest'
-      run: |
-        install.packages(${{ env.R_PACKAGES }},
-                         repos = 'http://cloud.r-project.org',
-                         dependencies = c('Depends', 'Imports', 'LinkingTo'))
-
-    - name: Install binary dependencies
-      shell: Rscript {0}
-      if: matrix.config.os == 'windows-latest'
-      run: |
-        install.packages(${{ env.R_PACKAGES }},
-                         type = 'binary',
-                         repos = 'http://cloud.r-project.org',
-                         dependencies = c('Depends', 'Imports', 'LinkingTo'))
+        key: ${{ runner.os }}-r-${{ matrix.config.r }}-6-${{ hashFiles('R-package/DESCRIPTION') }}
+        restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-6-${{ hashFiles('R-package/DESCRIPTION') }}
 
     - uses: actions/setup-python@v2
       with:
         python-version: "3.8"
         architecture: 'x64'
 
+    - uses: r-lib/actions/setup-tinytex@v2
+
+    - name: Install dependencies
+      shell: Rscript {0}
+      run: |
+        source("./R-package/tests/helper_scripts/install_deps.R")
+
     - 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 }}" --task=check
 
-  test-R-CRAN:
+  test-R-on-Debian:
+    name: Test R package on Debian
     runs-on: ubuntu-latest
-
-    strategy:
-      fail-fast: false
-      matrix:
-        config:
-          - {r: 'release'}
-
-    env:
-      _R_CHECK_EXAMPLE_TIMING_CPU_TO_ELAPSED_THRESHOLD_: 2.5
-      MAKE: "make -j$(nproc)"
+    container:
+      image: rhub/debian-gcc-devel
 
     steps:
+    - name: Install system dependencies
+      run: |
+        # Must run before checkout to have the latest git installed.
+        # No need to add pandoc, the container has it figured out.
+        apt update && apt install libcurl4-openssl-dev libssl-dev libssh2-1-dev libgit2-dev libglpk-dev libxml2-dev libharfbuzz-dev libfribidi-dev git -y
+
     - uses: actions/checkout@v2
       with:
         submodules: 'true'
 
-    - uses: r-lib/actions/setup-r@v2
-      with:
-        r-version: ${{ matrix.config.r }}
-
-    - uses: r-lib/actions/setup-tinytex@v2
+    - name: Install dependencies
+      shell: bash -l {0}
+      run: |
+        /tmp/R-devel/bin/Rscript -e "source('./R-package/tests/helper_scripts/install_deps.R')"
 
-    - name: Install system packages
+    - name: Test R
+      shell: bash -l {0}
       run: |
-        sudo apt-get update && sudo apt-get install libcurl4-openssl-dev libssl-dev libssh2-1-dev libgit2-dev pandoc pandoc-citeproc libglpk-dev
+        python3 tests/ci_build/test_r_package.py --r=/tmp/R-devel/bin/R --build-tool=autotools --task=check
 
-    - name: Cache R packages
-      uses: actions/cache@v2
+    - uses: dorny/paths-filter@v2
+      id: changes
       with:
-        path: ${{ env.R_LIBS_USER }}
-        key: ${{ runner.os }}-r-${{ matrix.config.r }}-5-${{ hashFiles('R-package/DESCRIPTION') }}
-        restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-5-${{ hashFiles('R-package/DESCRIPTION') }}
-
-    - name: Install dependencies
-      shell: Rscript {0}
-      run: |
-        install.packages(${{ 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'))
+        filters: |
+          r_package:
+            - 'R-package/**'
 
-    - name: Check R Package
+    - name: Run document check
+      if: steps.changes.outputs.r_package == 'true'
       run: |
-        # Print stacktrace upon success of failure
-        make Rcheck || tests/ci_build/print_r_stacktrace.sh fail
-        tests/ci_build/print_r_stacktrace.sh success
+        python3 tests/ci_build/test_r_package.py --r=/tmp/R-devel/bin/R --task=doc

R-package/demo/runall.R

@@ -1,4 +1,4 @@
-# running all scripts in demo folder
+# running all scripts in demo folder, removed during packaging.
 demo(basic_walkthrough, package = 'xgboost')
 demo(custom_objective, package = 'xgboost')
 demo(boost_from_prediction, package = 'xgboost')