From b270f9ef599f86b5475a2487bce8683d319f8da8 Mon Sep 17 00:00:00 2001 From: Hannah Owens Date: Mon, 14 Oct 2024 15:13:29 +0200 Subject: [PATCH 01/19] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 640ce63..8518c67 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -39,7 +39,7 @@ jobs: with: r-version: ${{ matrix.config.r }} - - uses: r-lib/actions/setup-pandoc@v1 + - uses: r-lib/actions/setup-pandoc@v2 - name: Query dependencies run: | From 0e8c314b8d1a566209c498da50e7eb7846880195 Mon Sep 17 00:00:00 2001 From: Hannah Owens Date: Mon, 14 Oct 2024 15:14:50 +0200 Subject: [PATCH 02/19] Update test-coverage.yaml --- .github/workflows/test-coverage.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 4a2f20a..4b01af7 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -21,7 +21,7 @@ jobs: with: use-public-rspm: true - - uses: r-lib/actions/setup-r-dependencies@v1 + - uses: r-lib/actions/setup-r-dependencies@v2 with: extra-packages: covr From 6f89c90c5e8b61737053f3b8ce25357dab0fc1d0 Mon Sep 17 00:00:00 2001 From: Hannah Owens Date: Mon, 14 Oct 2024 15:22:03 +0200 Subject: [PATCH 03/19] Update test-coverage.yaml --- .github/workflows/test-coverage.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 4b01af7..a44e3c3 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -23,7 +23,9 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: covr + extra-packages: + covr + taxize - name: Test coverage run: covr::codecov() From 2e3025292b64e288c671630b3ba60a1203229d26 Mon Sep 17 00:00:00 2001 From: Hannah Owens Date: Mon, 14 Oct 2024 15:31:31 +0200 Subject: [PATCH 04/19] Update test-coverage.yaml --- .github/workflows/test-coverage.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index a44e3c3..da93ede 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -15,7 +15,7 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-r@v2 with: From d10830fbab3bf725209f3e6d0b960e799626a1aa Mon Sep 17 00:00:00 2001 From: Hannah Owens Date: Mon, 14 Oct 2024 15:32:56 +0200 Subject: [PATCH 05/19] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 8518c67..79dcc90 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -33,7 +33,7 @@ jobs: RSPM: ${{ matrix.config.rspm }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-r@v2 with: From 6e80c908ac3202f6df825054d0669403c9c795af Mon Sep 17 00:00:00 2001 From: Hannah Owens Date: Tue, 15 Oct 2024 11:19:32 +0200 Subject: [PATCH 06/19] Update test-coverage.yaml --- .github/workflows/test-coverage.yaml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index da93ede..4a5dcc2 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -22,10 +22,7 @@ jobs: use-public-rspm: true - uses: r-lib/actions/setup-r-dependencies@v2 - with: - extra-packages: - covr - taxize + run: install.packages(c("covr", "taxize"), repos='http://cran.us.r-project.org') - name: Test coverage run: covr::codecov() From c8e3945be10e4420f2c9d5fb94195822eb764b41 Mon Sep 17 00:00:00 2001 From: Hannah Owens Date: Tue, 15 Oct 2024 11:20:46 +0200 Subject: [PATCH 07/19] Update test-coverage.yaml --- .github/workflows/test-coverage.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 4a5dcc2..e91a58a 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -22,7 +22,8 @@ jobs: use-public-rspm: true - uses: r-lib/actions/setup-r-dependencies@v2 - run: install.packages(c("covr", "taxize"), repos='http://cran.us.r-project.org') + + - run: install.packages(c("covr", "taxize"), repos='http://cran.us.r-project.org') - name: Test coverage run: covr::codecov() From 72deb2aee7e6cdb63935f0869d09d5552a552da7 Mon Sep 17 00:00:00 2001 From: Hannah Owens Date: Tue, 15 Oct 2024 11:24:34 +0200 Subject: [PATCH 08/19] Update test-coverage.yaml --- .github/workflows/test-coverage.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index e91a58a..09d5681 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -23,7 +23,8 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 - - run: install.packages(c("covr", "taxize"), repos='http://cran.us.r-project.org') + - run: install.packages(c("covr", "remotes"), repos='http://cran.us.r-project.org') + - run: remotes::install_github("ropensci/taxize") - name: Test coverage run: covr::codecov() From 201d7c645ed387a2d6ebbe541e2f9a4f72d74401 Mon Sep 17 00:00:00 2001 From: Hannah Owens Date: Tue, 15 Oct 2024 11:33:02 +0200 Subject: [PATCH 09/19] Update test-coverage.yaml --- .github/workflows/test-coverage.yaml | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 09d5681..58211b5 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -21,10 +21,17 @@ jobs: with: use-public-rspm: true - - uses: r-lib/actions/setup-r-dependencies@v2 - - - run: install.packages(c("covr", "remotes"), repos='http://cran.us.r-project.org') - - run: remotes::install_github("ropensci/taxize") + - name: Query dependencies + run: | + install.packages("remotes") + saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2) + shell: Rscript {0} + + - name: Install dependencies + run: | + remotes::install_deps(dependencies = TRUE) + remotes::install_cran("rcmdcheck") + shell: Rscript {0} - name: Test coverage run: covr::codecov() From d3845b54c592b8290b6f300935f98c37b4dcc3dc Mon Sep 17 00:00:00 2001 From: Hannah Owens Date: Tue, 15 Oct 2024 11:38:20 +0200 Subject: [PATCH 10/19] Update test-coverage.yaml --- .github/workflows/test-coverage.yaml | 47 +++++++++++++++++++++------- 1 file changed, 35 insertions(+), 12 deletions(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 58211b5..9882260 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -1,4 +1,4 @@ -# Workflow derived from https://github.com/r-lib/actions/tree/master/examples +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: @@ -6,7 +6,9 @@ on: pull_request: branches: [main, master] -name: test-coverage +name: test-coverage.yaml + +permissions: read-all jobs: test-coverage: @@ -21,18 +23,39 @@ jobs: with: use-public-rspm: true - - name: Query dependencies + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::covr, any::xml2 + needs: coverage + + - name: Test coverage run: | - install.packages("remotes") - saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2) + cov <- covr::package_coverage( + quiet = FALSE, + clean = FALSE, + install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") + ) + covr::to_cobertura(cov) shell: Rscript {0} - - name: Install dependencies + - uses: codecov/codecov-action@v4 + with: + fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} + file: ./cobertura.xml + plugin: noop + disable_search: true + token: ${{ secrets.CODECOV_TOKEN }} + + - name: Show testthat output + if: always() run: | - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("rcmdcheck") - shell: Rscript {0} + ## -------------------------------------------------------------------- + find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true + shell: bash - - name: Test coverage - run: covr::codecov() - shell: Rscript {0} + - name: Upload test results + if: failure() + uses: actions/upload-artifact@v4 + with: + name: coverage-test-failures + path: ${{ runner.temp }}/package From f9a94b8070dd7daf5414f8365879a69c68e24e2a Mon Sep 17 00:00:00 2001 From: Hannah Owens Date: Tue, 15 Oct 2024 11:40:16 +0200 Subject: [PATCH 11/19] Update test-coverage.yaml --- .github/workflows/test-coverage.yaml | 64 ++++++++++++---------------- 1 file changed, 28 insertions(+), 36 deletions(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 9882260..55b1622 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -6,56 +6,48 @@ on: pull_request: branches: [main, master] -name: test-coverage.yaml +name: R-CMD-check.yaml permissions: read-all jobs: - test-coverage: - runs-on: ubuntu-latest + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: macos-latest, r: 'release'} + - {os: windows-latest, r: 'release'} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes steps: - uses: actions/checkout@v4 + - uses: r-lib/actions/setup-pandoc@v2 + - uses: r-lib/actions/setup-r@v2 with: + r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} use-public-rspm: true - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::covr, any::xml2 - needs: coverage - - - name: Test coverage - run: | - cov <- covr::package_coverage( - quiet = FALSE, - clean = FALSE, - install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") - ) - covr::to_cobertura(cov) - shell: Rscript {0} - - - uses: codecov/codecov-action@v4 - with: - fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} - file: ./cobertura.xml - plugin: noop - disable_search: true - token: ${{ secrets.CODECOV_TOKEN }} - - - name: Show testthat output - if: always() - run: | - ## -------------------------------------------------------------------- - find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true - shell: bash - - - name: Upload test results - if: failure() - uses: actions/upload-artifact@v4 + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 with: - name: coverage-test-failures - path: ${{ runner.temp }}/package + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' + From 2358f7203547442df938242447daf709bec74496 Mon Sep 17 00:00:00 2001 From: Hannah Owens Date: Tue, 15 Oct 2024 11:46:06 +0200 Subject: [PATCH 12/19] Update test-coverage.yaml --- .github/workflows/test-coverage.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 55b1622..60a44a8 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -43,7 +43,9 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::rcmdcheck + extra-packages: + any::covr + git::https://github.com/ropensci/taxize needs: check - uses: r-lib/actions/check-r-package@v2 From ad6f925924e4cc97a37ca166351216c1d7a3fee1 Mon Sep 17 00:00:00 2001 From: Hannah Owens Date: Tue, 15 Oct 2024 11:54:14 +0200 Subject: [PATCH 13/19] Update test-coverage.yaml --- .github/workflows/test-coverage.yaml | 66 +++++++++++++++------------- 1 file changed, 36 insertions(+), 30 deletions(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 60a44a8..9882260 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -6,50 +6,56 @@ on: pull_request: branches: [main, master] -name: R-CMD-check.yaml +name: test-coverage.yaml permissions: read-all jobs: - R-CMD-check: - runs-on: ${{ matrix.config.os }} - - name: ${{ matrix.config.os }} (${{ matrix.config.r }}) - - strategy: - fail-fast: false - matrix: - config: - - {os: macos-latest, r: 'release'} - - {os: windows-latest, r: 'release'} - - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} - - {os: ubuntu-latest, r: 'release'} - - {os: ubuntu-latest, r: 'oldrel-1'} - + test-coverage: + runs-on: ubuntu-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - R_KEEP_PKG_SOURCE: yes steps: - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-pandoc@v2 - - uses: r-lib/actions/setup-r@v2 with: - r-version: ${{ matrix.config.r }} - http-user-agent: ${{ matrix.config.http-user-agent }} use-public-rspm: true - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: - any::covr - git::https://github.com/ropensci/taxize - needs: check - - - uses: r-lib/actions/check-r-package@v2 + extra-packages: any::covr, any::xml2 + needs: coverage + + - name: Test coverage + run: | + cov <- covr::package_coverage( + quiet = FALSE, + clean = FALSE, + install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") + ) + covr::to_cobertura(cov) + shell: Rscript {0} + + - uses: codecov/codecov-action@v4 + with: + fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} + file: ./cobertura.xml + plugin: noop + disable_search: true + token: ${{ secrets.CODECOV_TOKEN }} + + - name: Show testthat output + if: always() + run: | + ## -------------------------------------------------------------------- + find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true + shell: bash + + - name: Upload test results + if: failure() + uses: actions/upload-artifact@v4 with: - upload-snapshots: true - build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' - + name: coverage-test-failures + path: ${{ runner.temp }}/package From c04859ca058274aa69286b21511a9d29da1ba255 Mon Sep 17 00:00:00 2001 From: Hannah Owens Date: Tue, 15 Oct 2024 13:14:24 +0200 Subject: [PATCH 14/19] Update test-coverage.yaml --- .github/workflows/test-coverage.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 9882260..d10bf26 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -32,9 +32,7 @@ jobs: run: | cov <- covr::package_coverage( quiet = FALSE, - clean = FALSE, - install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") - ) + clean = FALSE) covr::to_cobertura(cov) shell: Rscript {0} From 35ab7e06d419469a4b3a886d72c57be10ded63c9 Mon Sep 17 00:00:00 2001 From: Hannah Owens Date: Tue, 15 Oct 2024 13:23:59 +0200 Subject: [PATCH 15/19] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 79dcc90..9e4b6ef 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -35,11 +35,11 @@ jobs: steps: - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-r@v2 + - uses: r-lib/actions/setup-r@v3 with: r-version: ${{ matrix.config.r }} - - uses: r-lib/actions/setup-pandoc@v2 + - uses: r-lib/actions/setup-pandoc@v3 - name: Query dependencies run: | @@ -50,7 +50,7 @@ jobs: - name: Cache R packages if: runner.os != 'Windows' - uses: actions/cache@v2 + uses: actions/cache@v3 with: path: ${{ env.R_LIBS_USER }} key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} From 8666bd24c009413c676465ad489352c7d287f5c0 Mon Sep 17 00:00:00 2001 From: Hannah Owens Date: Tue, 15 Oct 2024 13:24:41 +0200 Subject: [PATCH 16/19] Update test-coverage.yaml --- .github/workflows/test-coverage.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index d10bf26..237febb 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -19,11 +19,11 @@ jobs: steps: - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-r@v2 + - uses: r-lib/actions/setup-r@v3 with: use-public-rspm: true - - uses: r-lib/actions/setup-r-dependencies@v2 + - uses: r-lib/actions/setup-r-dependencies@v3 with: extra-packages: any::covr, any::xml2 needs: coverage From 81015e22a923be4439b883d0886c6a16bbd4f988 Mon Sep 17 00:00:00 2001 From: Hannah Owens Date: Wed, 16 Oct 2024 11:46:02 +0200 Subject: [PATCH 17/19] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 9e4b6ef..b298dc7 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -35,11 +35,11 @@ jobs: steps: - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-r@v3 + - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} - - uses: r-lib/actions/setup-pandoc@v3 + - uses: r-lib/actions/setup-pandoc@v2 - name: Query dependencies run: | From 70b35c02f3d811be8482454330ef7a64e585e1c3 Mon Sep 17 00:00:00 2001 From: Hannah Owens Date: Wed, 16 Oct 2024 11:57:21 +0200 Subject: [PATCH 18/19] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index b298dc7..54d0100 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -50,7 +50,7 @@ jobs: - name: Cache R packages if: runner.os != 'Windows' - uses: actions/cache@v3 + uses: actions/cache@v4 with: path: ${{ env.R_LIBS_USER }} key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} From 680836e4e97425527edda1c93fedad8abf7c25a0 Mon Sep 17 00:00:00 2001 From: Hannah Owens Date: Wed, 16 Oct 2024 12:03:26 +0200 Subject: [PATCH 19/19] Update test-coverage.yaml --- .github/workflows/test-coverage.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 237febb..d10bf26 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -19,11 +19,11 @@ jobs: steps: - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-r@v3 + - uses: r-lib/actions/setup-r@v2 with: use-public-rspm: true - - uses: r-lib/actions/setup-r-dependencies@v3 + - uses: r-lib/actions/setup-r-dependencies@v2 with: extra-packages: any::covr, any::xml2 needs: coverage