[CI] Revise R tests. (#8430)
- Use the standard package check (check on the tarball instead of the source tree). - Run commands in parallel. - Cleanup dependencies installation. - Replace makefile. - Documentation. - Test using the image from rhub.
This commit is contained in:
Jiaming Yuan
GitHub
2
.github/workflows/main.yml
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2
.github/workflows/main.yml
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@@ -146,7 +146,7 @@ jobs:
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python -m pip install wheel setuptools cpplint pylint
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- name: Run lint
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run: |
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LINT_LANG=cpp make lint
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python dmlc-core/scripts/lint.py xgboost cpp R-package/src
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sphinx:
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runs-on: ubuntu-latest
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19
.github/workflows/r_nold.yml
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19
.github/workflows/r_nold.yml
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@@ -1,4 +1,4 @@
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# Run R tests with noLD R. Only triggered by a pull request review
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# Run expensive R tests with the help of rhub. Only triggered by a pull request review
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# See discussion at https://github.com/dmlc/xgboost/pull/6378
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name: XGBoost-R-noLD
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@@ -7,9 +7,6 @@ on:
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pull_request_review_comment:
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types: [created]
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env:
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R_PACKAGES: c('XML', 'igraph', 'data.table', 'ggplot2', 'DiagrammeR', 'Ckmeans.1d.dp', 'vcd', 'testthat', 'lintr', 'knitr', 'rmarkdown', 'e1071', 'cplm', 'devtools', 'float', 'titanic')
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permissions:
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contents: read # to fetch code (actions/checkout)
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@@ -18,26 +15,22 @@ jobs:
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if: github.event.comment.body == '/gha run r-nold-test' && contains('OWNER,MEMBER,COLLABORATOR', github.event.comment.author_association)
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timeout-minutes: 120
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runs-on: ubuntu-latest
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container: rhub/debian-gcc-devel-nold
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container:
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image: rhub/debian-gcc-devel-nold
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steps:
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- name: Install git and system packages
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shell: bash
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run: |
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apt-get update && apt-get install -y git libcurl4-openssl-dev libssl-dev libssh2-1-dev libgit2-dev libxml2-dev
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apt update && apt install libcurl4-openssl-dev libssl-dev libssh2-1-dev libgit2-dev libglpk-dev libxml2-dev libharfbuzz-dev libfribidi-dev git -y
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- uses: actions/checkout@v2
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with:
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submodules: 'true'
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- name: Install dependencies
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shell: bash
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shell: bash -l {0}
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run: |
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cat > install_libs.R <<EOT
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install.packages(${{ env.R_PACKAGES }},
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repos = 'http://cloud.r-project.org',
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dependencies = c('Depends', 'Imports', 'LinkingTo'))
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EOT
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/tmp/R-devel/bin/Rscript install_libs.R
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/tmp/R-devel/bin/Rscript -e "source('./R-package/tests/helper_scripts/install_deps.R')"
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- name: Run R tests
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shell: bash
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129
.github/workflows/r_tests.yml
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129
.github/workflows/r_tests.yml
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@@ -3,9 +3,7 @@ name: XGBoost-R-Tests
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on: [push, pull_request]
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env:
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R_PACKAGES: c('XML', 'data.table', 'ggplot2', 'DiagrammeR', 'Ckmeans.1d.dp', 'vcd', 'testthat', 'lintr', 'knitr', 'rmarkdown', 'e1071', 'cplm', 'devtools', 'float', 'titanic')
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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_R_CHECK_EXAMPLE_TIMING_CPU_TO_ELAPSED_THRESHOLD_: 2.5
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permissions:
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contents: read # to fetch code (actions/checkout)
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@@ -35,29 +33,22 @@ jobs:
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uses: actions/cache@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-r-${{ matrix.config.r }}-5-${{ hashFiles('R-package/DESCRIPTION') }}
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restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-5-${{ hashFiles('R-package/DESCRIPTION') }}
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key: ${{ runner.os }}-r-${{ matrix.config.r }}-6-${{ hashFiles('R-package/DESCRIPTION') }}
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restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-6-${{ hashFiles('R-package/DESCRIPTION') }}
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- name: Install dependencies
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shell: Rscript {0}
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run: |
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install.packages(${{ env.R_PACKAGES }},
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repos = 'http://cloud.r-project.org',
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dependencies = c('Depends', 'Imports', 'LinkingTo'))
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- name: Install igraph on Windows
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shell: Rscript {0}
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if: matrix.config.os == 'windows-latest'
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run: |
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install.packages('igraph', type='binary')
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source("./R-package/tests/helper_scripts/install_deps.R")
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- name: Run lintr
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run: |
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cd R-package
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MAKE="make -j$(nproc)" R CMD INSTALL .
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MAKEFLAGS="-j$(nproc)" R CMD INSTALL .
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# Disable lintr errors for now: https://github.com/dmlc/xgboost/issues/8012
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Rscript tests/helper_scripts/run_lint.R || true
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test-with-R:
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test-R-on-Windows:
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runs-on: ${{ matrix.config.os }}
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name: Test R on OS ${{ matrix.config.os }}, R ${{ matrix.config.r }}, Compiler ${{ matrix.config.compiler }}, Build ${{ matrix.config.build }}
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strategy:
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@@ -66,10 +57,8 @@ jobs:
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config:
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- {os: windows-latest, r: 'release', compiler: 'mingw', build: 'autotools'}
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- {os: windows-latest, r: 'release', compiler: 'msvc', build: 'cmake'}
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- {os: windows-latest, r: 'release', compiler: 'mingw', build: 'cmake'}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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_R_CHECK_EXAMPLE_TIMING_CPU_TO_ELAPSED_THRESHOLD_: 2.5
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RSPM: ${{ matrix.config.rspm }}
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steps:
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@@ -85,80 +74,60 @@ jobs:
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uses: actions/cache@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-r-${{ matrix.config.r }}-5-${{ hashFiles('R-package/DESCRIPTION') }}
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restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-5-${{ hashFiles('R-package/DESCRIPTION') }}
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- name: Install dependencies
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shell: Rscript {0}
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if: matrix.config.os != 'windows-latest'
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run: |
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install.packages(${{ env.R_PACKAGES }},
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repos = 'http://cloud.r-project.org',
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dependencies = c('Depends', 'Imports', 'LinkingTo'))
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- name: Install binary dependencies
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shell: Rscript {0}
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if: matrix.config.os == 'windows-latest'
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run: |
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install.packages(${{ env.R_PACKAGES }},
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type = 'binary',
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repos = 'http://cloud.r-project.org',
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dependencies = c('Depends', 'Imports', 'LinkingTo'))
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key: ${{ runner.os }}-r-${{ matrix.config.r }}-6-${{ hashFiles('R-package/DESCRIPTION') }}
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restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-6-${{ hashFiles('R-package/DESCRIPTION') }}
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- uses: actions/setup-python@v2
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with:
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python-version: "3.8"
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architecture: 'x64'
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- name: Test R
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run: |
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python tests/ci_build/test_r_package.py --compiler='${{ matrix.config.compiler }}' --build-tool='${{ matrix.config.build }}'
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test-R-CRAN:
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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config:
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- {r: 'release'}
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env:
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_R_CHECK_EXAMPLE_TIMING_CPU_TO_ELAPSED_THRESHOLD_: 2.5
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MAKE: "make -j$(nproc)"
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: 'true'
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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- uses: r-lib/actions/setup-tinytex@v2
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- name: Install system packages
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run: |
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sudo apt-get update && sudo apt-get install libcurl4-openssl-dev libssl-dev libssh2-1-dev libgit2-dev pandoc pandoc-citeproc libglpk-dev
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- name: Cache R packages
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uses: actions/cache@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-r-${{ matrix.config.r }}-5-${{ hashFiles('R-package/DESCRIPTION') }}
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restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-5-${{ hashFiles('R-package/DESCRIPTION') }}
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- name: Install dependencies
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shell: Rscript {0}
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run: |
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install.packages(${{ env.R_PACKAGES }},
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repos = 'http://cloud.r-project.org',
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dependencies = c('Depends', 'Imports', 'LinkingTo'))
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install.packages('igraph', repos = 'http://cloud.r-project.org', dependencies = c('Depends', 'Imports', 'LinkingTo'))
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source("./R-package/tests/helper_scripts/install_deps.R")
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- name: Check R Package
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- name: Test R
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run: |
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# Print stacktrace upon success of failure
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make Rcheck || tests/ci_build/print_r_stacktrace.sh fail
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tests/ci_build/print_r_stacktrace.sh success
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python tests/ci_build/test_r_package.py --compiler='${{ matrix.config.compiler }}' --build-tool="${{ matrix.config.build }}" --task=check
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test-R-on-Debian:
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name: Test R package on Debian
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runs-on: ubuntu-latest
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container:
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image: rhub/debian-gcc-devel
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steps:
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- name: Install system dependencies
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run: |
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# Must run before checkout to have the latest git installed.
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# No need to add pandoc, the container has it figured out.
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apt update && apt install libcurl4-openssl-dev libssl-dev libssh2-1-dev libgit2-dev libglpk-dev libxml2-dev libharfbuzz-dev libfribidi-dev git -y
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- uses: actions/checkout@v2
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with:
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submodules: 'true'
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- name: Install dependencies
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shell: bash -l {0}
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run: |
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/tmp/R-devel/bin/Rscript -e "source('./R-package/tests/helper_scripts/install_deps.R')"
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- name: Test R
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shell: bash -l {0}
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run: |
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python3 tests/ci_build/test_r_package.py --r=/tmp/R-devel/bin/R --build-tool=autotools --task=check
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- uses: dorny/paths-filter@v2
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id: changes
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with:
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filters: |
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r_package:
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- 'R-package/**'
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- name: Run document check
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if: steps.changes.outputs.r_package == 'true'
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run: |
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python3 tests/ci_build/test_r_package.py --r=/tmp/R-devel/bin/R --task=doc
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