From 669f01461a39b7f87185a9b248f3b383ddaaffac Mon Sep 17 00:00:00 2001 From: Leonardo Schwarz Date: Thu, 12 Jun 2025 12:58:49 +0200 Subject: [PATCH 1/5] Fix CI --- .github/workflows/r.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/r.yml b/.github/workflows/r.yml index 51afdfc..8ffd9ef 100644 --- a/.github/workflows/r.yml +++ b/.github/workflows/r.yml @@ -33,7 +33,7 @@ jobs: with: r-version: ${{ matrix.r-version }} - name: Install Linux packages - run: sudo apt-get install -y mono-mcs mono-xbuild libcurl4-openssl-dev libicu-dev pandoc pandoc-citeproc texlive texlive-latex-extra texlive-fonts-extra + run: sudo apt-get install -y mono-mcs mono-xbuild libcurl4-openssl-dev libicu-dev pandoc texlive texlive-latex-extra texlive-fonts-extra shell: bash {0} - name: Install dependencies run: | From db917f2b35ee8ed21c17544166f40eed5c9cfda8 Mon Sep 17 00:00:00 2001 From: Leonardo Schwarz Date: Thu, 12 Jun 2025 13:17:03 +0200 Subject: [PATCH 2/5] use pak for ci --- .github/workflows/r.yml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/workflows/r.yml b/.github/workflows/r.yml index 8ffd9ef..01f8f52 100644 --- a/.github/workflows/r.yml +++ b/.github/workflows/r.yml @@ -37,9 +37,10 @@ jobs: shell: bash {0} - name: Install dependencies run: | - install.packages(c("remotes", "covr", "rcmdcheck", "rmarkdown", "protViz", "testthat", "knitr", "BiocManager")) - BiocManager::install(c("BiocStyle", "ExperimentHub", "tartar")) - remotes::install_deps(dependencies = TRUE) + install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch)) + pak::pkg_install(c("covr", "rcmdcheck", "rmarkdown", "protViz", "testthat", "knitr")) + pak::pkg_install(c("bioc::BiocStyle", "bioc::ExperimentHub", "bioc::tartar")) + pak::local_install_deps(dependencies = TRUE) shell: Rscript {0} - name: Check run: rcmdcheck::rcmdcheck(build_args = "", args = "", error_on = "error", check_dir = "/tmp/rawrr.Rcheck") From 5fc601a0db84fdb513878f083a3f976cf3293e2d Mon Sep 17 00:00:00 2001 From: Leonardo Schwarz Date: Thu, 12 Jun 2025 13:20:51 +0200 Subject: [PATCH 3/5] bump R to 4.5 for BioC 3.21 --- .github/workflows/r.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/r.yml b/.github/workflows/r.yml index 01f8f52..f1a1d74 100644 --- a/.github/workflows/r.yml +++ b/.github/workflows/r.yml @@ -25,7 +25,7 @@ jobs: runs-on: ubuntu-24.04 strategy: matrix: - r-version: [4.3] + r-version: [4.5] steps: - uses: actions/checkout@v4 - name: Set up R ${{ matrix.r-version }} From 95fea34316c2476bb48e06eccf7e5e666d77ab34 Mon Sep 17 00:00:00 2001 From: Leonardo Schwarz Date: Thu, 12 Jun 2025 13:34:51 +0200 Subject: [PATCH 4/5] Correctly name the package --- .github/workflows/r.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/r.yml b/.github/workflows/r.yml index f1a1d74..c0629fc 100644 --- a/.github/workflows/r.yml +++ b/.github/workflows/r.yml @@ -33,13 +33,13 @@ jobs: with: r-version: ${{ matrix.r-version }} - name: Install Linux packages - run: sudo apt-get install -y mono-mcs mono-xbuild libcurl4-openssl-dev libicu-dev pandoc texlive texlive-latex-extra texlive-fonts-extra + run: sudo apt-get install -y libcurl4-openssl-dev libicu-dev pandoc texlive texlive-latex-extra texlive-fonts-extra shell: bash {0} - name: Install dependencies run: | install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch)) pak::pkg_install(c("covr", "rcmdcheck", "rmarkdown", "protViz", "testthat", "knitr")) - pak::pkg_install(c("bioc::BiocStyle", "bioc::ExperimentHub", "bioc::tartar")) + pak::pkg_install(c("bioc::BiocStyle", "bioc::ExperimentHub", "bioc::tartare")) pak::local_install_deps(dependencies = TRUE) shell: Rscript {0} - name: Check From 190894b715c68267933fab1902518834a513eca4 Mon Sep 17 00:00:00 2001 From: Leonardo Schwarz Date: Thu, 12 Jun 2025 14:04:39 +0200 Subject: [PATCH 5/5] optimize --- .github/workflows/r.yml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/r.yml b/.github/workflows/r.yml index c0629fc..acedab2 100644 --- a/.github/workflows/r.yml +++ b/.github/workflows/r.yml @@ -32,14 +32,16 @@ jobs: uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.r-version }} + use-public-rspm: true - name: Install Linux packages run: sudo apt-get install -y libcurl4-openssl-dev libicu-dev pandoc texlive texlive-latex-extra texlive-fonts-extra shell: bash {0} - name: Install dependencies run: | install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch)) - pak::pkg_install(c("covr", "rcmdcheck", "rmarkdown", "protViz", "testthat", "knitr")) - pak::pkg_install(c("bioc::BiocStyle", "bioc::ExperimentHub", "bioc::tartare")) + cat("Repository being used:\n") + print(getOption("repos")) + pak::pkg_install(c("covr", "rcmdcheck", "rmarkdown", "protViz", "testthat", "knitr", "bioc::BiocStyle", "bioc::ExperimentHub", "bioc::tartare")) pak::local_install_deps(dependencies = TRUE) shell: Rscript {0} - name: Check @@ -52,4 +54,4 @@ jobs: with: name: rawrr.Rcheck path: /tmp/rawrr.Rcheck - if-no-files-found: warn + if-no-files-found: warn \ No newline at end of file