diff --git a/.github/workflows/basic_checks.yaml b/.github/workflows/basic_checks.yaml index 8f1ad55..ad3b372 100644 --- a/.github/workflows/basic_checks.yaml +++ b/.github/workflows/basic_checks.yaml @@ -12,32 +12,35 @@ jobs: env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest + steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Query dependencies and update old packages run: | - BiocManager::install(ask=FALSE) + install.packages('remotes') + dir.create(".github") saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) shell: Rscript {0} - name: Cache R packages if: runner.os != 'Windows' - uses: actions/cache@v1 + uses: actions/cache@v4 with: path: /usr/local/lib/R/site-library key: ${{ env.cache-version }}-${{ runner.os }}-r-${{ hashFiles('.github/depends.Rds') }} restore-keys: ${{ env.cache-version }}-${{ runner.os }}-r- # This lets us augment with additional dependencies - - name: Install system dependencies - if: runner.os == 'Linux' - env: - RHUB_PLATFORM: linux-x86_64-ubuntu-gcc - run: | - Rscript -e "remotes::install_github('r-hub/sysreqs')" - sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") - sudo -s eval "$sysreqs" + # - name: Install system dependencies + # if: runner.os == 'Linux' + # env: + # RHUB_PLATFORM: linux-x86_64-ubuntu-gcc + # run: | + # Rscript -e "remotes::install_github('r-hub/sysreqs')" + # sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") + # sudo -s eval "$sysreqs" - name: Install dependencies run: | diff --git a/.github/workflows/push_docker.yaml b/.github/workflows/push_docker.yaml deleted file mode 100644 index e33d5d7..0000000 --- a/.github/workflows/push_docker.yaml +++ /dev/null @@ -1,28 +0,0 @@ -on: - push: - branches: [master] - pull_request: - branches: [master] -jobs: - build: - runs-on: ubuntu-latest - container: bioconductor/bioconductor_docker:RELEASE_3_18 - steps: - - name: Checkout code - uses: actions/checkout@v1 - - - name: Build pkgdown - run: | - PATH=$PATH:$HOME/bin/ Rscript -e 'BiocManager::install(c("knitr", "rmarkdown", "pkgdown")); pkgdown::build_site(".")' - # deploy needs rsync? Seems so. - - name: Install deploy dependencies - run: | - apt-get update - apt-get -y install rsync - - name: Deploy 🚀 - uses: JamesIves/github-pages-deploy-action@releases/v3 - with: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - BRANCH: gh-pages # The branch the action should deploy to. - FOLDER: docs # The folder the action should deploy. - diff --git a/DESCRIPTION b/DESCRIPTION index ae6b8d9..dc0f76f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,4 +1,4 @@ -Package: basicBioinformaticsDRC2023 +Package: basicBioinformaticsDRC2024 Type: Package Version: 1.0.6 Title: DRC2024 basic bioinformatics diff --git a/LICENSE b/LICENSE index 5878c61..5396cf6 100644 --- a/LICENSE +++ b/LICENSE @@ -1,2 +1,2 @@ -YEAR: 2023 +YEAR: 2024 COPYRIGHT HOLDER: Jianhong Ou diff --git a/inst/images/dockerhub_result.png b/inst/images/dockerhub_result.png deleted file mode 100644 index 7ed812f..0000000 Binary files a/inst/images/dockerhub_result.png and /dev/null differ