From d02d6481a8df643428d397a39f2d76e569bf5eaa Mon Sep 17 00:00:00 2001 From: Alan Haynes Date: Mon, 27 Nov 2023 16:07:54 +0100 Subject: [PATCH 1/9] remove appveyor and travis --- .travis.yml | 22 ------------------- README.Rmd | 2 +- appveyor.yml | 60 ---------------------------------------------------- 3 files changed, 1 insertion(+), 83 deletions(-) delete mode 100644 .travis.yml delete mode 100644 appveyor.yml diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 864539af..00000000 --- a/.travis.yml +++ /dev/null @@ -1,22 +0,0 @@ -services: - - xvfb - -language: r - -r: - - oldrel - - release - - devel - -warnings_are_errors: true - -apt_packages: - - tcl8.5-dev - - tk8.5-dev - - ghostscript - -r_packages: - - covr - -after_success: - - Rscript -e 'library(covr); codecov()' diff --git a/README.Rmd b/README.Rmd index 2c1fd9f8..cf855425 100644 --- a/README.Rmd +++ b/README.Rmd @@ -12,7 +12,7 @@ output: # secuTrialR -`r badger::badge_custom("dev version", as.character(packageVersion("secuTrialR")), "blue", "https://github.com/SwissClinicalTrialOrganisation/secuTrialR")` [![](https://www.r-pkg.org/badges/version/secuTrialR?color=green)](https://cran.r-project.org/package=secuTrialR) [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/SwissClinicalTrialOrganisation/secuTrialR?branch=master&svg=true)](https://ci.appveyor.com/project/SwissClinicalTrialOrganisation/secuTrialR) [![travis](https://api.travis-ci.com/SwissClinicalTrialOrganisation/secuTrialR.svg?branch=master)](https://travis-ci.com/github/SwissClinicalTrialOrganisation/secuTrialR) [![Actions Status](https://github.com/SwissClinicalTrialOrganisation/secuTrialR/workflows/R-CMD-check/badge.svg)](https://github.com/SwissClinicalTrialOrganisation/secuTrialR/actions) +`r badger::badge_custom("dev version", as.character(packageVersion("secuTrialR")), "blue", "https://github.com/SwissClinicalTrialOrganisation/secuTrialR")` [![](https://www.r-pkg.org/badges/version/secuTrialR?color=green)](https://cran.r-project.org/package=secuTrialR) [![Actions Status](https://github.com/SwissClinicalTrialOrganisation/secuTrialR/workflows/R-CMD-check/badge.svg)](https://github.com/SwissClinicalTrialOrganisation/secuTrialR/actions) An R package to handle data from the clinical data management system (CDMS) [secuTrial](https://www.secutrial.com/en/). diff --git a/appveyor.yml b/appveyor.yml deleted file mode 100644 index b74e252a..00000000 --- a/appveyor.yml +++ /dev/null @@ -1,60 +0,0 @@ -# DO NOT CHANGE the "init" and "install" sections below - -# Download script file from GitHub -init: - ps: | - $ErrorActionPreference = "Stop" - Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1" - Import-Module '..\appveyor-tool.ps1' - -environment: - global: - USE_RTOOLS: true - R_CHECK_INSTALL_ARGS: "--install-args=--build --no-multiarch " - _R_CHECK_DONTTEST_EXAMPLES_: false - WARNINGS_ARE_ERRORS: 1 - PYTHON_VERSION: 3.6 - MINICONDA: C:\Miniconda3-x64 - R_ARCH: x64 - matrix: - - R_VERSION: release - - - R_VERSION: oldrel - CRAN: http://cran.rstudio.com - -install: - ps: Bootstrap - -cache: - - C:\RLibrary - -# Adapt as necessary starting from here - -build_script: - - travis-tool.sh install_deps - -test_script: - - travis-tool.sh run_tests - -on_failure: - - 7z a failure.zip *.Rcheck\* - - appveyor PushArtifact failure.zip - -artifacts: - - path: '*.Rcheck\**\*.log' - name: Logs - - - path: '*.Rcheck\**\*.out' - name: Logs - - - path: '*.Rcheck\**\*.fail' - name: Logs - - - path: '*.Rcheck\**\*.Rout' - name: Logs - - - path: '\*_*.tar.gz' - name: Bits - - - path: '\*_*.zip' - name: Bits From 618b3adfb39436a52f45648fe536c4fa75f8e8fd Mon Sep 17 00:00:00 2001 From: Alan Haynes Date: Tue, 28 Nov 2023 09:14:51 +0100 Subject: [PATCH 2/9] r-lib/actions based action --- .github/workflows/R-CMD-full2.yaml | 49 ++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 .github/workflows/R-CMD-full2.yaml diff --git a/.github/workflows/R-CMD-full2.yaml b/.github/workflows/R-CMD-full2.yaml new file mode 100644 index 00000000..1443020c --- /dev/null +++ b/.github/workflows/R-CMD-full2.yaml @@ -0,0 +1,49 @@ +# 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: + branches: [main, master] + pull_request: + branches: [main, master] + +name: R-CMD-check2 + +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'} + + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes + + steps: + - uses: actions/checkout@v3 + + - 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::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true From 0f988064a93572a60075d0a3c74c8d909cb34547 Mon Sep 17 00:00:00 2001 From: Render action Date: Tue, 28 Nov 2023 12:35:00 +0000 Subject: [PATCH 3/9] Re-build README.md --- README.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/README.md b/README.md index 4a88a46a..ca8cf477 100644 --- a/README.md +++ b/README.md @@ -4,9 +4,6 @@ [![](https://img.shields.io/badge/dev%20version-1.2.0-blue.svg)](https://github.com/SwissClinicalTrialOrganisation/secuTrialR) [![](https://www.r-pkg.org/badges/version/secuTrialR?color=green)](https://cran.r-project.org/package=secuTrialR) -[![AppVeyor Build -Status](https://ci.appveyor.com/api/projects/status/github/SwissClinicalTrialOrganisation/secuTrialR?branch=master&svg=true)](https://ci.appveyor.com/project/SwissClinicalTrialOrganisation/secuTrialR) -[![travis](https://api.travis-ci.com/SwissClinicalTrialOrganisation/secuTrialR.svg?branch=master)](https://travis-ci.com/github/SwissClinicalTrialOrganisation/secuTrialR) [![Actions Status](https://github.com/SwissClinicalTrialOrganisation/secuTrialR/workflows/R-CMD-check/badge.svg)](https://github.com/SwissClinicalTrialOrganisation/secuTrialR/actions) From 7146d4a0016c4fd3cdc960e94983e3f6588e1783 Mon Sep 17 00:00:00 2001 From: Alan Haynes Date: Tue, 28 Nov 2023 14:18:02 +0100 Subject: [PATCH 4/9] explicit reference to rcmdcheck --- .github/workflows/R-CMD-full.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/R-CMD-full.yaml b/.github/workflows/R-CMD-full.yaml index 84163ff7..d601704c 100644 --- a/.github/workflows/R-CMD-full.yaml +++ b/.github/workflows/R-CMD-full.yaml @@ -42,6 +42,10 @@ jobs: - uses: r-lib/actions/setup-pandoc@v2 - uses: r-lib/actions/setup-tinytex@v2 + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check - name: Install XQuartz on macOS if: runner.os == 'macOS' From fdca0e0f3dab0521c59917a402bb1de7c3170825 Mon Sep 17 00:00:00 2001 From: Alan Haynes Date: Tue, 28 Nov 2023 14:19:11 +0100 Subject: [PATCH 5/9] remove newer workflow --- .github/workflows/R-CMD-full2.yaml | 49 ------------------------------ 1 file changed, 49 deletions(-) delete mode 100644 .github/workflows/R-CMD-full2.yaml diff --git a/.github/workflows/R-CMD-full2.yaml b/.github/workflows/R-CMD-full2.yaml deleted file mode 100644 index 1443020c..00000000 --- a/.github/workflows/R-CMD-full2.yaml +++ /dev/null @@ -1,49 +0,0 @@ -# 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: - branches: [main, master] - pull_request: - branches: [main, master] - -name: R-CMD-check2 - -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'} - - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - R_KEEP_PKG_SOURCE: yes - - steps: - - uses: actions/checkout@v3 - - - 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::rcmdcheck - needs: check - - - uses: r-lib/actions/check-r-package@v2 - with: - upload-snapshots: true From c4a9ce5552fd8567fdd72ccfbd3762423a89db80 Mon Sep 17 00:00:00 2001 From: Alan Haynes Date: Wed, 29 Nov 2023 08:34:42 +0100 Subject: [PATCH 6/9] change ubuntu systems, remove rcmdcheck install action --- .github/workflows/R-CMD-full.yaml | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/.github/workflows/R-CMD-full.yaml b/.github/workflows/R-CMD-full.yaml index d601704c..93b96c54 100644 --- a/.github/workflows/R-CMD-full.yaml +++ b/.github/workflows/R-CMD-full.yaml @@ -25,8 +25,7 @@ jobs: - {os: windows-latest, r: 'release'} - {os: macOS-latest, r: 'oldrel'} - {os: windows-latest, 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-latest, r: 'release'} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true @@ -42,10 +41,6 @@ jobs: - uses: r-lib/actions/setup-pandoc@v2 - uses: r-lib/actions/setup-tinytex@v2 - - uses: r-lib/actions/setup-r-dependencies@v2 - with: - extra-packages: any::rcmdcheck - needs: check - name: Install XQuartz on macOS if: runner.os == 'macOS' From f3160a70fe40729fe3f53e5da6c8e89a96e15a02 Mon Sep 17 00:00:00 2001 From: Alan Haynes Date: Wed, 29 Nov 2023 09:04:57 +0100 Subject: [PATCH 7/9] go back to 20.04 --- .github/workflows/R-CMD-full.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-full.yaml b/.github/workflows/R-CMD-full.yaml index 93b96c54..1b22bbb5 100644 --- a/.github/workflows/R-CMD-full.yaml +++ b/.github/workflows/R-CMD-full.yaml @@ -25,7 +25,7 @@ jobs: - {os: windows-latest, r: 'release'} - {os: macOS-latest, r: 'oldrel'} - {os: windows-latest, r: 'oldrel'} - - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true From 785934791a3bb43b143dad5d6435c0b4bd39920b Mon Sep 17 00:00:00 2001 From: Alan Haynes Date: Wed, 29 Nov 2023 09:16:26 +0100 Subject: [PATCH 8/9] add oldrel-1 --- .github/workflows/R-CMD-full.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/R-CMD-full.yaml b/.github/workflows/R-CMD-full.yaml index 1b22bbb5..2e76f73d 100644 --- a/.github/workflows/R-CMD-full.yaml +++ b/.github/workflows/R-CMD-full.yaml @@ -25,6 +25,8 @@ jobs: - {os: windows-latest, r: 'release'} - {os: macOS-latest, r: 'oldrel'} - {os: windows-latest, r: 'oldrel'} + - {os: macOS-latest, r: 'oldrel-1'} + - {os: windows-latest, r: 'oldrel-1'} - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} env: From a300fbaa452cb880c3d1990e090bccb9245f164e Mon Sep 17 00:00:00 2001 From: Alan Haynes Date: Wed, 29 Nov 2023 10:00:02 +0100 Subject: [PATCH 9/9] macos not macOS --- .github/workflows/R-CMD-full.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/R-CMD-full.yaml b/.github/workflows/R-CMD-full.yaml index 2e76f73d..f791f74e 100644 --- a/.github/workflows/R-CMD-full.yaml +++ b/.github/workflows/R-CMD-full.yaml @@ -19,13 +19,13 @@ jobs: fail-fast: false matrix: config: - - {os: macOS-latest, r: 'devel'} + - {os: macos-latest, r: 'devel'} - {os: windows-latest, r: 'devel'} - - {os: macOS-latest, r: 'release'} + - {os: macos-latest, r: 'release'} - {os: windows-latest, r: 'release'} - - {os: macOS-latest, r: 'oldrel'} + - {os: macos-latest, r: 'oldrel'} - {os: windows-latest, r: 'oldrel'} - - {os: macOS-latest, r: 'oldrel-1'} + - {os: macos-latest, r: 'oldrel-1'} - {os: windows-latest, r: 'oldrel-1'} - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}