diff --git a/.Rbuildignore b/.Rbuildignore index e3ee3b7..ffc78e7 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -11,4 +11,6 @@ ^archive$ ^data\-raw$ ^scratch\.R$ -^demos$ \ No newline at end of file +^demos$ +^cran_comments\.md$ +^NEWS\.md$ \ No newline at end of file diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..e67cd75 --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,59 @@ +# 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 + - dev + pull_request: + branches: + - main + - master + - dev + +name: R-CMD-check.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: windows-latest, r: 'release'} + - {os: macOS-latest, r: 'release'} + - {os: ubuntu-22.04, r: 'release', rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest"} + - {os: ubuntu-22.04, r: 'devel', rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest"} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + + 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: ${{ matrix.config.http-user-agent }} + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' \ No newline at end of file diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml new file mode 100644 index 0000000..74ec7b0 --- /dev/null +++ b/.github/workflows/rhub.yaml @@ -0,0 +1,95 @@ +# R-hub's generic GitHub Actions workflow file. It's canonical location is at +# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml +# You can update this file to a newer version using the rhub2 package: +# +# rhub::rhub_setup() +# +# It is unlikely that you need to modify this file manually. + +name: R-hub +run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}" + +on: + workflow_dispatch: + inputs: + config: + description: 'A comma separated list of R-hub platforms to use.' + type: string + default: 'linux,windows,macos' + name: + description: 'Run name. You can leave this empty now.' + type: string + id: + description: 'Unique ID. You can leave this empty now.' + type: string + +jobs: + + setup: + runs-on: ubuntu-latest + outputs: + containers: ${{ steps.rhub-setup.outputs.containers }} + platforms: ${{ steps.rhub-setup.outputs.platforms }} + + steps: + # NO NEED TO CHECKOUT HERE + - uses: r-hub/actions/setup@v1 + with: + config: ${{ github.event.inputs.config }} + id: rhub-setup + + linux-containers: + needs: setup + if: ${{ needs.setup.outputs.containers != '[]' }} + runs-on: ubuntu-latest + name: ${{ matrix.config.label }} + strategy: + fail-fast: false + matrix: + config: ${{ fromJson(needs.setup.outputs.containers) }} + container: + image: ${{ matrix.config.container }} + + steps: + - uses: r-hub/actions/checkout@v1 + - uses: r-hub/actions/platform-info@v1 + with: + token: ${{ secrets.RHUB_TOKEN }} + job-config: ${{ matrix.config.job-config }} + - uses: r-hub/actions/setup-deps@v1 + with: + token: ${{ secrets.RHUB_TOKEN }} + job-config: ${{ matrix.config.job-config }} + - uses: r-hub/actions/run-check@v1 + with: + token: ${{ secrets.RHUB_TOKEN }} + job-config: ${{ matrix.config.job-config }} + + other-platforms: + needs: setup + if: ${{ needs.setup.outputs.platforms != '[]' }} + runs-on: ${{ matrix.config.os }} + name: ${{ matrix.config.label }} + strategy: + fail-fast: false + matrix: + config: ${{ fromJson(needs.setup.outputs.platforms) }} + + steps: + - uses: r-hub/actions/checkout@v1 + - uses: r-hub/actions/setup-r@v1 + with: + job-config: ${{ matrix.config.job-config }} + token: ${{ secrets.RHUB_TOKEN }} + - uses: r-hub/actions/platform-info@v1 + with: + token: ${{ secrets.RHUB_TOKEN }} + job-config: ${{ matrix.config.job-config }} + - uses: r-hub/actions/setup-deps@v1 + with: + job-config: ${{ matrix.config.job-config }} + token: ${{ secrets.RHUB_TOKEN }} + - uses: r-hub/actions/run-check@v1 + with: + job-config: ${{ matrix.config.job-config }} + token: ${{ secrets.RHUB_TOKEN }} diff --git a/DESCRIPTION b/DESCRIPTION index b48173c..84a675f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: clinify Type: Package -Title: flextable and officer extensions for clinical outputs +Title: Clinical Table Styling Tools and Utilities Version: 0.1.0 Authors@R: c( person(given = "Mike", @@ -11,7 +11,10 @@ Authors@R: c( person("Ross", "Didenko", email = "rostyslav.didenko@atorusresearch.com", role = c("aut")), person("Yevhenii", "Boiko", email = "yevhenii.boiko@atorusresearch.com", role = c("aut")), person("Marat", "Zakirov", email = "marat.zakirov@atorusresearch.com", role = "ctb"), - person("Roman", "Rogoza", email = "roman.rogoza@atorusresearch.com", role = "ctb")) + person("Roman", "Rogoza", email = "roman.rogoza@atorusresearch.com", role = "ctb"), + person(given = "Atorus Research, Inc.", + role = "cph"), + person(given = "Incyte Corporation", role="cph")) Depends: R (>= 4.2) Imports: diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..1870d47 --- /dev/null +++ b/NEWS.md @@ -0,0 +1,3 @@ +# clinify 0.1.0 + +* Initial CRAN submission. diff --git a/README.Rmd b/README.Rmd index 7daef91..485c358 100644 --- a/README.Rmd +++ b/README.Rmd @@ -27,6 +27,8 @@ knitr::opts_chunk$set( You can install the development version of **{clinify}** like so: ```{r, eval=FALSE} +install.packages("clinify") + # Install the development version: devtools::install_github("https://github.com/atorus-research/clinify.git", ref="development") ``` diff --git a/README.md b/README.md index b98a5dd..dbef6a0 100644 --- a/README.md +++ b/README.md @@ -20,6 +20,8 @@ the creation of clinical tables, listings and figures. You can install the development version of **{clinify}** like so: ``` r +install.packages("clinify") + # Install the development version: devtools::install_github("https://github.com/atorus-research/clinify.git", ref="development") ``` diff --git a/cran_comments.md b/cran_comments.md new file mode 100644 index 0000000..c43b25a --- /dev/null +++ b/cran_comments.md @@ -0,0 +1,3 @@ +# clinify 0.1.0 + +Initial CRAN submission \ No newline at end of file