Merge pull request #19 from libKriging/fix-debian-clang-devel-Rcpp-co… #171
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: rhub-local_check | |
| on: | |
| push: | |
| pull_request: | |
| schedule: | |
| - cron: '0 2 * * SAT' | |
| env: | |
| DEBUG_CI: true | |
| jobs: | |
| rhub-local_check: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| #rhub::local_check_linux_images() | |
| rhubos: [ 'debian-clang-devel','debian-gcc-devel','debian-gcc-devel-nold','debian-gcc-patched','debian-gcc-release','fedora-clang-devel','fedora-gcc-devel','rocker-gcc-san','ubuntu-gcc-devel','ubuntu-gcc-release' ] | |
| # not suitable for compile: ,'ubuntu-rchk' ] | |
| runs-on: ubuntu-latest | |
| container: | |
| image: rhub/${{ matrix.rhubos }} | |
| options: --user root | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| BRANCH_NAME: ${{ github.head_ref || github.ref_name }} | |
| steps: | |
| - name: Add dependencies | |
| shell: bash | |
| run: | | |
| echo "`cat /etc/*-release | grep ID | cut -d= -f2 | head -1 | tr -d '\t'`"; \ | |
| if [ `cat /etc/*-release | grep ID | cut -d= -f2 | head -1 | tr -d '\t'` = "fedora" ]; \ | |
| then dnf install -y git cmake gfortran libcurl-devel libxml2-devel openssl-devel fontconfig-devel hdf5-devel; \ | |
| else apt-get update; apt-get install -y git cmake gfortran libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev libxml2-dev libssl-dev libfontconfig1-dev libhdf5-dev; \ | |
| fi | |
| - name: Add workaround dependencies | |
| shell: bash | |
| run: | | |
| apt install -y libc++-dev libc++abi-dev | |
| if: matrix.rhubos == 'debian-clang-devel' | |
| - uses: actions/checkout@v3.0.2 | |
| # with: | |
| # submodules: recursive | |
| - name: Checkout submodules | |
| shell: bash | |
| run: | | |
| git config --global --add safe.directory /__w/rlibkriging/rlibkriging | |
| git submodule update --init --recursive | |
| - name: Remove tmp requirements | |
| shell: bash | |
| run: | | |
| if [ `cat /etc/*-release | grep ID | cut -d= -f2 | head -1 | tr -d '\t'` = "fedora" ]; \ | |
| then dnf remove -y git; \ | |
| else apt-get remove -y git; \ | |
| fi | |
| - name: Install devtools | |
| shell: bash | |
| run: | | |
| # Add --insecure to workaround missing certificates on Windows | |
| # --header is not required by an useful example if the repo becomes private | |
| curl --insecure --header 'authorization: Bearer ${{ secrets.GITHUB_TOKEN }}' -LO https://raw.githubusercontent.com/libKriging/rlibkriging/${{ env.BRANCH_NAME }}/tools/install_packages.R | |
| export PATH=$PATH:/opt/R-devel/bin/:/opt/R-patched/bin/:/opt/R/bin | |
| Rscript --no-save ./install_packages.R devtools | |
| - name: BioConductor install Rhdf5lib (Bioconductor deps not suported by devtools::install_github) | |
| shell: bash | |
| run: | | |
| export PATH=$PATH:/opt/R-devel/bin/:/opt/R-patched/bin/:/opt/R/bin | |
| Rscript -e "install.packages('BiocManager',repos='https://cloud.r-project.org'); BiocManager::install('Rhdf5lib'); remove.packages('BiocManager')" | |
| - name: devtools install_deps from ${{ env.BRANCH_NAME }} | |
| shell: bash | |
| run: | | |
| export PATH=$PATH:/opt/R-devel/bin/:/opt/R-patched/bin/:/opt/R/bin | |
| Rscript -e "library(devtools); install_deps('.',dependencies = TRUE)" | |
| # - name: devtools install_github from ${{ env.BRANCH_NAME }} | |
| # shell: bash | |
| # run: | | |
| # export PATH=$PATH:/opt/R-devel/bin/:/opt/R-patched/bin/:/opt/R/bin | |
| # Rscript -e "library(devtools); install_github('libKriging/rlibkriging', ref='${{ env.BRANCH_NAME }}'); if (!library('rlibkriging', character.only=TRUE, logical.return=TRUE)) quit(status=1, save='no')" | |
| - name: setup for CRAN | |
| shell: bash | |
| run: | | |
| export PATH=$PATH:/opt/R-devel/bin/:/opt/R-patched/bin/:/opt/R/bin | |
| Rscript --no-save ./install_packages.R roxygen2 | |
| ./tools/setup.sh | |
| Rscript -e "remove.packages('roxygen2')" | |
| - name: R CMD build | |
| shell: bash | |
| env: # this alias helps to reuse following line as script | |
| OS: ${{ matrix.rhubos }} | |
| run: | | |
| export PATH=$PATH:/opt/R-devel/bin/:/opt/R-patched/bin/:/opt/R/bin | |
| pushd .. | |
| R CMD build rlibkriging | |
| mkdir rlibkriging/CRAN-$OS | |
| mv rlibkriging_*.* rlibkriging/CRAN-$OS/. | |
| popd | |
| - name: R CMD check | |
| shell: bash | |
| env: | |
| OS: ${{ matrix.rhubos }} | |
| run: | | |
| export PATH=$PATH:/opt/R-devel/bin/:/opt/R-patched/bin/:/opt/R/bin | |
| R CMD check --as-cran --no-manual CRAN-$OS/rlibkriging* || ( | |
| test -f rlibkriging.Rcheck/00install.out && cat rlibkriging.Rcheck/00install.out | sed -e 's/^/00install.out| /' && echo "[The error may be shown before 00install.out| listing"; | |
| exit 1 | |
| ) |