From 384f7ee7bd03ce9f1f115882d13685242526b9e4 Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Fri, 31 Jan 2025 20:23:49 +0100 Subject: [PATCH 01/11] Move taxize to 'Imports' --- DESCRIPTION | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index fc3f8f2..b3ff04f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -28,8 +28,8 @@ Imports: readr (>= 1.1.1), dbplyr (>= 1.0.0), magrittr (>= 1.5), - hoardr (>= 0.1.0) -Suggests: - testthat, + hoardr (>= 0.1.0), taxize +Suggests: + testthat RoxygenNote: 7.3.2 From a31d0597c0cd9cb010814339f251399bc6691d03 Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Mon, 26 Aug 2024 20:03:19 +0200 Subject: [PATCH 02/11] Update workflow 'R-check' --- .github/workflows/{R-check.yaml => R-CMD-check.yaml} | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) rename .github/workflows/{R-check.yaml => R-CMD-check.yaml} (87%) diff --git a/.github/workflows/R-check.yaml b/.github/workflows/R-CMD-check.yaml similarity index 87% rename from .github/workflows/R-check.yaml rename to .github/workflows/R-CMD-check.yaml index 2a885f6..21164d8 100644 --- a/.github/workflows/R-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -7,10 +7,12 @@ on: pull_request: branches: [main, master] -name: R-check +name: R-CMD-check.yaml + +permissions: read-all jobs: - R-check: + R-CMD-check: runs-on: ${{ matrix.config.os }} name: ${{ matrix.config.os }} (${{ matrix.config.r }}) @@ -30,7 +32,7 @@ jobs: R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 @@ -48,4 +50,4 @@ jobs: - uses: r-lib/actions/check-r-package@v2 with: upload-snapshots: true - \ No newline at end of file + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' \ No newline at end of file From 373cce648d33c3772bd7f40bbf7d0f97445bfaf5 Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Mon, 26 Aug 2024 20:02:54 +0200 Subject: [PATCH 03/11] Remove workflow 'build_docs' --- .github/workflows/build-docs.yml | 46 -------------------------------- 1 file changed, 46 deletions(-) delete mode 100644 .github/workflows/build-docs.yml diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml deleted file mode 100644 index 8bc9210..0000000 --- a/.github/workflows/build-docs.yml +++ /dev/null @@ -1,46 +0,0 @@ -on: - push: - branches: master - -name: pkgdown - -jobs: - pkgdown: - runs-on: macOS-latest - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - steps: - - uses: actions/checkout@v2 - - - uses: r-lib/actions/setup-r@master - - - uses: r-lib/actions/setup-pandoc@master - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Cache R packages - uses: actions/cache@v1 - with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- - - - name: Install dependencies - run: | - remotes::install_deps(dependencies = TRUE) - install.packages("pkgdown") - shell: Rscript {0} - - - name: Install package - run: R CMD INSTALL . - - - name: Deploy package - run: | - git config --local user.email "actions@github.com" - git config --local user.name "GitHub Actions" - Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)' From 5ea001e0372e311afae6004d0befa911eab82493 Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Fri, 31 Jan 2025 20:25:49 +0100 Subject: [PATCH 04/11] Install `taxize` from GitHub --- DESCRIPTION | 1 + 1 file changed, 1 insertion(+) diff --git a/DESCRIPTION b/DESCRIPTION index b3ff04f..3a5a3f1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -32,4 +32,5 @@ Imports: taxize Suggests: testthat +Remotes: ropensci/taxize@v0.9.99 RoxygenNote: 7.3.2 From 1ff978d667f11aaf5ea8019f0e8c547fb8590696 Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Fri, 31 Jan 2025 20:34:30 +0100 Subject: [PATCH 05/11] Add bold which is a taxize dependency --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3a5a3f1..d138d37 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -32,5 +32,5 @@ Imports: taxize Suggests: testthat -Remotes: ropensci/taxize@v0.9.99 +Remotes: ropensci/bold@v1.3.0, ropensci/taxize@v0.9.99 RoxygenNote: 7.3.2 From 12703478767db35cb57dd9e714ac2c4e1bec0df4 Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Sat, 1 Feb 2025 10:29:21 +0100 Subject: [PATCH 06/11] Use "Additional_repositories" field --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index d138d37..3d52ae2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -32,5 +32,5 @@ Imports: taxize Suggests: testthat -Remotes: ropensci/bold@v1.3.0, ropensci/taxize@v0.9.99 +Additional_repositories: https://github.com/ropensci/bold, https://github.com/ropensci/taxize RoxygenNote: 7.3.2 From 6778dba99a415707acbdb415b5ff4be71d0615b3 Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Sat, 1 Feb 2025 10:48:49 +0100 Subject: [PATCH 07/11] Revert "Use "Additional_repositories" field" This reverts commit 12703478767db35cb57dd9e714ac2c4e1bec0df4. --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3d52ae2..d138d37 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -32,5 +32,5 @@ Imports: taxize Suggests: testthat -Additional_repositories: https://github.com/ropensci/bold, https://github.com/ropensci/taxize +Remotes: ropensci/bold@v1.3.0, ropensci/taxize@v0.9.99 RoxygenNote: 7.3.2 From 68431821fdb5a760aa144bf5feeb3ad1c32c02a9 Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Sat, 1 Feb 2025 12:31:48 +0100 Subject: [PATCH 08/11] Update workflow --- .github/workflows/R-CMD-check.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 21164d8..042d422 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -44,7 +44,11 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::rcmdcheck + r-version: 'release' + extra-packages: | + ropensci/taxize + ropensci/bold + any::rcmdcheck needs: check - uses: r-lib/actions/check-r-package@v2 From 386ec095bd32096f229f3e8b5b6ddfbe0fcaad8d Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Sat, 1 Feb 2025 12:33:59 +0100 Subject: [PATCH 09/11] Simplify Remotes --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index d138d37..80829fd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -32,5 +32,5 @@ Imports: taxize Suggests: testthat -Remotes: ropensci/bold@v1.3.0, ropensci/taxize@v0.9.99 +Remotes: ropensci/bold, ropensci/taxize RoxygenNote: 7.3.2 From 80bfd9e74b21160a6f5721f0fcc7e8fca7a3df22 Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Sat, 1 Feb 2025 20:17:48 +0100 Subject: [PATCH 10/11] Attempt to fix checks for macOS --- .github/workflows/R-CMD-check.yaml | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 042d422..6581220 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -36,6 +36,16 @@ jobs: - uses: r-lib/actions/setup-pandoc@v2 + - name: Increase R memory limit on macOS + if: runner.os == 'macOS' + run: echo "R_MAX_VSIZE=32GB" >> $GITHUB_ENV + + - name: Install macOS system dependencies + if: runner.os == 'macOS' + run: | + brew install pkg-config + brew install --cask xquartz + - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} @@ -44,7 +54,6 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - r-version: 'release' extra-packages: | ropensci/taxize ropensci/bold From f4e1899d1524b0c27d59108744b898be6f4b47b9 Mon Sep 17 00:00:00 2001 From: Tamas Stirling Date: Sun, 2 Feb 2025 21:31:21 +0100 Subject: [PATCH 11/11] Revert "Attempt to fix checks for macOS" This reverts commit 80bfd9e74b21160a6f5721f0fcc7e8fca7a3df22. --- .github/workflows/R-CMD-check.yaml | 11 +---------- 1 file changed, 1 insertion(+), 10 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 6581220..042d422 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -36,16 +36,6 @@ jobs: - uses: r-lib/actions/setup-pandoc@v2 - - name: Increase R memory limit on macOS - if: runner.os == 'macOS' - run: echo "R_MAX_VSIZE=32GB" >> $GITHUB_ENV - - - name: Install macOS system dependencies - if: runner.os == 'macOS' - run: | - brew install pkg-config - brew install --cask xquartz - - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} @@ -54,6 +44,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: + r-version: 'release' extra-packages: | ropensci/taxize ropensci/bold