From 7d8c7686a74b978742a91b1b0f3ce1d482102fca Mon Sep 17 00:00:00 2001 From: Florian Hartig Date: Wed, 12 Jan 2022 14:24:39 +0100 Subject: [PATCH 1/8] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 642b8bd9..1dca5385 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -24,11 +24,9 @@ jobs: fail-fast: false matrix: config: - - {os: windows-latest, r: 'release'} - - {os: macOS-latest, r: 'release'} - - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - + - {os: ubuntu-20.04, r: 'devel'} + - {os: ubuntu-20.04, r: 'release'} + - {os: ubuntu-20.04, r: 'oldrel'} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true RSPM: ${{ matrix.config.rspm }} From 027ce8951f60dec1540fb555a2f58817adbb5593 Mon Sep 17 00:00:00 2001 From: Florian Hartig Date: Wed, 12 Jan 2022 15:37:48 +0100 Subject: [PATCH 2/8] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 1dca5385..dd93c122 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -24,6 +24,11 @@ jobs: fail-fast: false matrix: config: + - {os: macOS-latest, r: 'devel'} + - {os: macOS-latest, r: 'release'} + - {os: windows-latest, r: 'devel'} + - {os: windows-latest, r: 'release'} + - {os: windows-latest, r: 'oldrel'} - {os: ubuntu-20.04, r: 'devel'} - {os: ubuntu-20.04, r: 'release'} - {os: ubuntu-20.04, r: 'oldrel'} From b043bfcd537e91454b677cc545eb5fd296027586 Mon Sep 17 00:00:00 2001 From: Florian Hartig Date: Wed, 12 Jan 2022 15:42:01 +0100 Subject: [PATCH 3/8] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index dd93c122..ce23e217 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -62,6 +62,12 @@ jobs: key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- + - name: Install curl for r-devel version + if: runner.os == 'Linux' + run: | + sudo apt-get install -y curl + sudo apt-get install -y texlive texlive-fonts-extra + - name: Install system dependencies if: runner.os == 'Linux' run: | From e80fa0ac52e6685cc429731096e40ae9eeec6fbb Mon Sep 17 00:00:00 2001 From: Florian Hartig Date: Thu, 13 Jan 2022 10:46:06 +0100 Subject: [PATCH 4/8] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index ce23e217..2e7e8002 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -24,14 +24,9 @@ jobs: fail-fast: false matrix: config: - - {os: macOS-latest, r: 'devel'} - - {os: macOS-latest, r: 'release'} - - {os: windows-latest, r: 'devel'} - - {os: windows-latest, r: 'release'} - - {os: windows-latest, r: 'oldrel'} - - {os: ubuntu-20.04, r: 'devel'} - - {os: ubuntu-20.04, r: 'release'} - - {os: ubuntu-20.04, r: 'oldrel'} + - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: ubuntu-20.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true RSPM: ${{ matrix.config.rspm }} From a03fe1148f436f1d19d74b45d406c44cc38ee369 Mon Sep 17 00:00:00 2001 From: Florian Hartig Date: Thu, 13 Jan 2022 12:08:31 +0100 Subject: [PATCH 5/8] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 61 +++++++++++++++++++----------- 1 file changed, 38 insertions(+), 23 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 2e7e8002..c1a0cfe9 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -6,12 +6,12 @@ on: - main - master - GitAction - + pull_request: branches: - main - master - + name: R-CMD-check jobs: @@ -24,14 +24,18 @@ jobs: fail-fast: false matrix: config: + - {os: macOS-latest, r: 'release'} + - {os: windows-latest, r: 'release'} - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true RSPM: ${{ matrix.config.rspm }} GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - + KMP_DUPLICATE_LIB_OK: TRUE + steps: - uses: actions/checkout@v2 @@ -41,6 +45,11 @@ jobs: - uses: r-lib/actions/setup-pandoc@v1 + - uses: r-lib/actions/setup-tinytex@master + + - name: Install makeindex + run: tlmgr install makeindex + - name: Query dependencies run: | setwd("DHARMa") @@ -49,55 +58,61 @@ jobs: writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), "../.github/R-version") shell: Rscript {0} - - name: Cache R packages + - name: Cache R packages if: runner.os != 'Windows' uses: actions/cache@v2 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- + key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }} + restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1- - name: Install curl for r-devel version if: runner.os == 'Linux' run: | sudo apt-get install -y curl sudo apt-get install -y texlive texlive-fonts-extra - + - name: Install system dependencies if: runner.os == 'Linux' run: | - cd DHARMa - while read -r cmd - do - eval sudo $cmd - done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') - + setwd("DHARMa") + pak::local_system_requirements(execute = TRUE) + pak::pkg_system_requirements("rcmdcheck", execute = TRUE) + shell: Rscript {0} + - name: Install dependencies run: | setwd("DHARMa") - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("rcmdcheck") + pak::local_install_dev_deps(upgrade = TRUE) + pak::pkg_install("rcmdcheck") shell: Rscript {0} - - - name: Check_II + + - name: Check I env: _R_CHECK_CRAN_INCOMING_REMOTE_: false CI: true run: | - rcmdcheck::rcmdcheck("DHARMa", args = c("--no-multiarch", "--no-manual"), error_on = "warning", check_dir = "check") + options(crayon.enabled = TRUE) + rcmdcheck::rcmdcheck("DHARMa", args = c("--no-multiarch", "--no-manual"), error_on = "error", check_dir = "check") shell: Rscript {0} - - name: Check + - name: testthat output + if: always() + run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true + shell: bash + + - name: Check II env: _R_CHECK_CRAN_INCOMING_REMOTE_: false CI: true run: | - rcmdcheck::rcmdcheck("DHARMa", args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") + options(crayon.enabled = TRUE) + rcmdcheck::rcmdcheck("DHARMa", args = c("--no-manual", "--as-cran"), error_on = "note", check_dir = "check") shell: Rscript {0} - + - name: Upload check results if: failure() uses: actions/upload-artifact@main with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check + name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results + path: check \ No newline at end of file From 4b484b8c42c5596c59b65c90f9f6baea3fa15063 Mon Sep 17 00:00:00 2001 From: Florian Hartig Date: Thu, 13 Jan 2022 14:18:09 +0100 Subject: [PATCH 6/8] revert to old --- .github/workflows/R-CMD-check.yaml | 69 +++++++++++------------------- 1 file changed, 25 insertions(+), 44 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index c1a0cfe9..7e0c734e 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -6,12 +6,12 @@ on: - main - master - GitAction - + pull_request: branches: - main - master - + name: R-CMD-check jobs: @@ -24,18 +24,16 @@ jobs: fail-fast: false matrix: config: - - {os: macOS-latest, r: 'release'} - - {os: windows-latest, r: 'release'} - - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + # - {os: windows-latest, r: 'release'} + # - {os: macOS-latest, r: 'release'} + # - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: ubuntu-20.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true RSPM: ${{ matrix.config.rspm }} GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - KMP_DUPLICATE_LIB_OK: TRUE - + steps: - uses: actions/checkout@v2 @@ -45,11 +43,6 @@ jobs: - uses: r-lib/actions/setup-pandoc@v1 - - uses: r-lib/actions/setup-tinytex@master - - - name: Install makeindex - run: tlmgr install makeindex - - name: Query dependencies run: | setwd("DHARMa") @@ -58,61 +51,49 @@ jobs: writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), "../.github/R-version") shell: Rscript {0} - - name: Cache R packages + - name: Cache R packages if: runner.os != 'Windows' uses: actions/cache@v2 with: path: ${{ env.R_LIBS_USER }} - key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }} - restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1- + key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} + restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- - - name: Install curl for r-devel version - if: runner.os == 'Linux' - run: | - sudo apt-get install -y curl - sudo apt-get install -y texlive texlive-fonts-extra - - name: Install system dependencies if: runner.os == 'Linux' run: | - setwd("DHARMa") - pak::local_system_requirements(execute = TRUE) - pak::pkg_system_requirements("rcmdcheck", execute = TRUE) - shell: Rscript {0} - + cd DHARMa + while read -r cmd + do + eval sudo $cmd + done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') + - name: Install dependencies run: | setwd("DHARMa") - pak::local_install_dev_deps(upgrade = TRUE) - pak::pkg_install("rcmdcheck") + remotes::install_deps(dependencies = TRUE) + remotes::install_cran("rcmdcheck") shell: Rscript {0} - - - name: Check I + + - name: Check_II env: _R_CHECK_CRAN_INCOMING_REMOTE_: false CI: true run: | - options(crayon.enabled = TRUE) - rcmdcheck::rcmdcheck("DHARMa", args = c("--no-multiarch", "--no-manual"), error_on = "error", check_dir = "check") + rcmdcheck::rcmdcheck("DHARMa", args = c("--no-multiarch", "--no-manual"), error_on = "warning", check_dir = "check") shell: Rscript {0} - - name: testthat output - if: always() - run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true - shell: bash - - - name: Check II + - name: Check env: _R_CHECK_CRAN_INCOMING_REMOTE_: false CI: true run: | - options(crayon.enabled = TRUE) - rcmdcheck::rcmdcheck("DHARMa", args = c("--no-manual", "--as-cran"), error_on = "note", check_dir = "check") + rcmdcheck::rcmdcheck("DHARMa", args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") shell: Rscript {0} - + - name: Upload check results if: failure() uses: actions/upload-artifact@main with: - name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results - path: check \ No newline at end of file + name: ${{ runner.os }}-r${{ matrix.config.r }}-results + path: check From 9e88569cb5cd99c6c773f862bd92d8bd0f768dc1 Mon Sep 17 00:00:00 2001 From: Florian Hartig Date: Thu, 13 Jan 2022 14:27:15 +0100 Subject: [PATCH 7/8] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 7e0c734e..85cfac43 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -58,6 +58,11 @@ jobs: 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 curl for r-devel version + if: runner.os == 'Linux' + run: | + sudo apt-get install -y curl - name: Install system dependencies if: runner.os == 'Linux' @@ -74,7 +79,7 @@ jobs: remotes::install_deps(dependencies = TRUE) remotes::install_cran("rcmdcheck") shell: Rscript {0} - + - name: Check_II env: _R_CHECK_CRAN_INCOMING_REMOTE_: false From 0b607a4e32994fd471c1f5d532134684170214e2 Mon Sep 17 00:00:00 2001 From: Florian Hartig Date: Sat, 15 Jan 2022 19:12:30 +0100 Subject: [PATCH 8/8] Update R-CMD-check.yaml --- .github/workflows/R-CMD-check.yaml | 75 ++++++++++++++++++------------ 1 file changed, 45 insertions(+), 30 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 62e47c0f..f790c74e 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -5,8 +5,6 @@ on: branches: - main - master - - GitAction - pull_request: branches: - main @@ -24,21 +22,17 @@ jobs: fail-fast: false matrix: config: + - {os: macOS-latest, r: 'release'} - {os: windows-latest, r: 'release'} - - {os: windows-latest, r: 'release'} - - {os: windows-latest, r: 'oldrel'} - - #- {os: macOS-latest, r: 'devel'} - - {os: macOS-latest, r: 'release'} - - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - # - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: ubuntu-20.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true RSPM: ${{ matrix.config.rspm }} GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - + KMP_DUPLICATE_LIB_OK: TRUE steps: - uses: actions/checkout@v2 @@ -48,57 +42,78 @@ jobs: - uses: r-lib/actions/setup-pandoc@v1 + - uses: r-lib/actions/setup-tinytex@master + + - name: Install makeindex + run: tlmgr install makeindex + - name: Query dependencies run: | setwd("DHARMa") - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), "../.github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), "../.github/R-version") + install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/") + saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), "../.github/r-depends.rds") shell: Rscript {0} - - name: Cache R packages + - name: Cache R packages if: runner.os != 'Windows' uses: actions/cache@v2 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- + key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }} + restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1- + + - name: Install curl for r-devel version + if: runner.os == 'Linux' + run: | + sudo apt-get install -y curl + sudo apt-get install -y texlive texlive-fonts-extra - name: Install system dependencies if: runner.os == 'Linux' run: | - cd DHARMa - while read -r cmd - do - eval sudo $cmd - done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') + setwd("DHARMa") + pak::local_system_requirements(execute = TRUE) + pak::pkg_system_requirements("rcmdcheck", execute = TRUE) + shell: Rscript {0} - name: Install dependencies run: | setwd("DHARMa") - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("rcmdcheck") + pak::local_install_dev_deps(upgrade = TRUE) + pak::pkg_install("rcmdcheck") shell: Rscript {0} - - name: Check_II + - name: Install Pkg + run: | + cd DHARMa + Rscript -e "pak::local_install()" + + - name: Check I env: _R_CHECK_CRAN_INCOMING_REMOTE_: false CI: true run: | - rcmdcheck::rcmdcheck("DHARMa", args = c("--no-multiarch", "--no-manual"), error_on = "warning", check_dir = "check") + options(crayon.enabled = TRUE) + rcmdcheck::rcmdcheck("DHARMa", args = c("--no-multiarch", "--no-manual"), error_on = "error", check_dir = "check") shell: Rscript {0} - - name: Check + - name: testthat output + if: always() + run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true + shell: bash + + - name: Check II env: _R_CHECK_CRAN_INCOMING_REMOTE_: false CI: true run: | - rcmdcheck::rcmdcheck("DHARMa", args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") + options(crayon.enabled = TRUE) + rcmdcheck::rcmdcheck("DHARMa", args = c("--no-manual", "--as-cran"), error_on = "note", check_dir = "check") shell: Rscript {0} - + - name: Upload check results if: failure() uses: actions/upload-artifact@main with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check + name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results + path: check \ No newline at end of file