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updating workflow flies (#243)
* updating workflow flies * Update R-CMD-check.yaml
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Lines changed: 67 additions & 32 deletions

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‎.github/workflows/R-CMD-check.yaml‎

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push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
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name: R-CMD-check
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name: R-CMD-check.yaml
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permissions: read-all
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jobs:
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R-CMD-check:
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fail-fast: false
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matrix:
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config:
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- {os: macOS-latest, r: 'release'}
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- {os: macos-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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# Use older ubuntu to maximise backward compatibility
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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- {os: ubuntu-latest, r: 'oldrel-2'}
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# - {os: ubuntu-latest, r: 'oldrel-3'}
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# - {os: ubuntu-latest, r: 'oldrel-4'}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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- {os: ubuntu-latest, r: 'oldrel-2'}
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- {os: ubuntu-latest, r: 'oldrel-3'}
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# - {os: ubuntu-latest, r: 'oldrel-4'}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/check-r-package@v2
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with:
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upload-snapshots: true
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build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

‎.github/workflows/pkgdown.yaml‎

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push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
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release:
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types: [published]
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workflow_dispatch:
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name: pkgdown
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name: pkgdown.yaml
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permissions: read-all
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jobs:
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pkgdown:
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runs-on: ubuntu-20.04
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runs-on: ubuntu-latest
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# Only restrict concurrency for non-PR jobs
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concurrency:
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group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
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shell: Rscript {0}
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# the pkgdown site is rendered via github.com/ddsjoberg/ggsurvfit
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# we keep this action to check for pkgdown errors
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# - name: Deploy to GitHub pages 🚀
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# if: github.event_name != 'pull_request'
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# uses: JamesIves/github-pages-deploy-action@4.1.4
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# uses: JamesIves/github-pages-deploy-action@v4.5.0
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# with:
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# clean: false
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# branch: gh-pages

‎.github/workflows/pr-commands.yaml‎

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issue_comment:
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types: [created]
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name: Commands
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name: pr-commands.yaml
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permissions: read-all
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jobs:
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document:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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- uses: r-lib/actions/pr-fetch@v2
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with:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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- uses: r-lib/actions/pr-fetch@v2
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with:

‎.github/workflows/test-coverage.yaml‎

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push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
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name: test-coverage
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name: test-coverage.yaml
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permissions: read-all
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jobs:
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test-coverage:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::covr
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extra-packages: any::covr, any::xml2
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needs: coverage
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- name: Test coverage
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run: covr::codecov(quiet = FALSE)
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run: |
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cov <- covr::package_coverage(
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quiet = FALSE,
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clean = FALSE,
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install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
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)
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print(cov)
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covr::to_cobertura(cov)
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shell: Rscript {0}
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- uses: codecov/codecov-action@v5
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with:
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# Fail if error if not on PR, or if on PR and token is given
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fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
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files: ./cobertura.xml
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plugins: noop
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disable_search: true
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token: ${{ secrets.CODECOV_TOKEN }}
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- name: Show testthat output
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if: always()
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run: |
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## --------------------------------------------------------------------
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find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload test results
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if: failure()
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uses: actions/upload-artifact@v4
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with:
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name: coverage-test-failures
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path: ${{ runner.temp }}/package

‎README.Rmd‎

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<!-- badges: start -->
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[![R-CMD-check](https://github.com/pharmaverse/ggsurvfit/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/pharmaverse/ggsurvfit/actions/workflows/R-CMD-check.yaml)
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[![Codecov test coverage](https://codecov.io/gh/pharmaverse/ggsurvfit/branch/main/graph/badge.svg)](https://app.codecov.io/gh/pharmaverse/ggsurvfit?branch=main)
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[![Codecov test coverage](https://codecov.io/gh/pharmaverse/ggsurvfit/graph/badge.svg)](https://app.codecov.io/gh/pharmaverse/ggsurvfit)
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[![CRAN status](https://www.r-pkg.org/badges/version/ggsurvfit)](https://CRAN.R-project.org/package=ggsurvfit)
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[![](https://cranlogs.r-pkg.org/badges/ggsurvfit)](https://cran.r-project.org/package=ggsurvfit)
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[<img src="http://pharmaverse.org/shields/ggsurvfit.svg">](https://pharmaverse.org)

‎README.md‎

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[![R-CMD-check](https://github.com/pharmaverse/ggsurvfit/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/pharmaverse/ggsurvfit/actions/workflows/R-CMD-check.yaml)
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[![Codecov test
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coverage](https://codecov.io/gh/pharmaverse/ggsurvfit/branch/main/graph/badge.svg)](https://app.codecov.io/gh/pharmaverse/ggsurvfit?branch=main)
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coverage](https://codecov.io/gh/pharmaverse/ggsurvfit/graph/badge.svg)](https://app.codecov.io/gh/pharmaverse/ggsurvfit)
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[![CRAN
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status](https://www.r-pkg.org/badges/version/ggsurvfit)](https://CRAN.R-project.org/package=ggsurvfit)
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[![](https://cranlogs.r-pkg.org/badges/ggsurvfit)](https://cran.r-project.org/package=ggsurvfit)

‎codecov.yml‎

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comment: false
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coverage:
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range: 0..100
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round: up
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precision: 0
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status:
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project:
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default:

‎man/figures/README-gt-related-pkgs.png‎

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