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Merge branch 'jg-devel'
* jg-devel: (35 commits) Use latest Pandoc in GHA and update workflow (rstudio#2244) Add class to book cover to size using CSS fix the syntax highlighting of |> in LaTeX/PDF output: rstudio/bookdown#1157 (rstudio#2228) Add an option to opt-out the header-attrs HTML dependency in `html_document_base()` (rstudio#2227) Clean up NEWS.md. Updated autogenerated documentation. Fixed conflicts with rstudio main version. Update documentation for html_document. Add self (JG) as a contributor in DESCRIPTION. Resolve conflicts with new updates to RStudio main branch. Clean up a few things from the merge. Fix problem building with GitHub Actions because of `mathjax: local` in the testthat tests. Revert unnecessary formatting change to code in render.R. Revert an unnecessary formatting change to comments in render.R. Update NEWS.md. revert inadevertent change from accidental merge with jg-tree-fix. Removed unnecessary references to `allow_uptree_lib_dir` in `ioslides_presentation` and `slidy_presentation`. Prepare for PR to RStudio. Updated documentation for new parameter in output_format(). Removed packages.bib from tests/testthat. ...
2 parents 81d52ec + 1a2f70a commit a70fa6c

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‎.Rbuildignore

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^tests/testthat/site/_site/
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^tests/testthat/site/lib/
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^tests/testthat/site/.*_files/
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^tests/testthat/html-uptree-lib_dir/.*\.html$
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^tests/testthat/html-uptree-lib_dir/.*\.gitkeep$
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^tests/manual/
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^\.github$
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^pkgdown$

‎.github/workflows/R-CMD-check.yaml

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matrix:
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config:
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# testing R release with last shipped pandoc version in RStudio IDE and new pandoc
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# TODO: issue on windows with pandoc 2.11.4 - change when fixed
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- {os: windows-latest, pandoc: '2.7.3', r: 'release'}
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- {os: macOS-latest, pandoc: '2.11.4', r: 'release'}
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- {os: ubuntu-18.04, pandoc: '2.11.4', r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
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- {os: ubuntu-18.04, pandoc: 'devel', r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
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- {os: windows-latest, pandoc: '2.16.1', r: 'release'}
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- {os: macOS-latest, pandoc: '2.16.1', r: 'release'}
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- {os: ubuntu-18.04, pandoc: '2.16.1', r: 'release'}
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- {os: ubuntu-18.04, pandoc: 'devel', r: 'release'}
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# testing older pandoc versions
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- {os: ubuntu-18.04, pandoc: '2.7.3', r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
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- {os: ubuntu-18.04, pandoc: '2.5', r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
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- {os: ubuntu-18.04, pandoc: '2.0.0.1', r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
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- {os: ubuntu-18.04, pandoc: '2.14.2', r: 'release'}
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- {os: ubuntu-18.04, pandoc: '2.11.4', r: 'release'}
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- {os: ubuntu-18.04, pandoc: '2.7.3', r: 'release'}
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- {os: ubuntu-18.04, pandoc: '2.5', r: 'release'}
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- {os: ubuntu-18.04, pandoc: '2.0.0.1', r: 'release'}
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# testing other R versions
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- {os: ubuntu-18.04, pandoc: '2.11.4', r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
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- {os: ubuntu-18.04, pandoc: '2.11.4', r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.0.0 (ubuntu-18.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
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- {os: ubuntu-18.04, pandoc: '2.11.4', r: 'oldrel'}
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- {os: ubuntu-18.04, pandoc: '2.11.4', r: 'devel', http-user-agent: 'release'}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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RSPM: ${{ matrix.config.rspm }}
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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: r-lib/actions/setup-r@v1
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id: install-r
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- name: change temp dir
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if: runner.os == 'Windows'
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cat(readLines("~/.Rprofile"), sep = "\n")
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shell: Rscript {0}
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- name: Install pak and query dependencies
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run: |
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install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
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saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
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shell: Rscript {0}
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- name: Restore R package cache
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uses: actions/cache@v2
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- uses: r-lib/actions/setup-r-dependencies@v1
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with:
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path: |
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${{ env.R_LIBS_USER }}/*
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!${{ env.R_LIBS_USER }}/pak
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key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
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restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
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- name: Install system dependencies
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if: runner.os == 'Linux'
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run: |
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pak::local_system_requirements(execute = TRUE)
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pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
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shell: Rscript {0}
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extra-packages: rcmdcheck
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- name: Install dependencies
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- name: Pandoc and Tinytex info
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run: |
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pak::local_install_dev_deps(upgrade = TRUE)
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pak::pkg_install("rcmdcheck")
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shell: Rscript {0}
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- name: Session info
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run: |
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options(width = 100)
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pkgs <- .packages(TRUE)
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sessioninfo::session_info(pkgs, include_base = TRUE)
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rmarkdown::find_pandoc()
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tinytex::tlmgr("--version")
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tinytex::tl_pkgs()
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shell: Rscript {0}
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- name: Check
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env:
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_R_CHECK_CRAN_INCOMING_: false
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_R_CHECK_TESTS_NLINES_: 0
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run: |
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options(crayon.enabled = TRUE)
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rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
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shell: Rscript {0}
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- uses: r-lib/actions/check-r-package@v1
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- name: Show testthat output
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if: always()

‎.github/workflows/check-pandoc-daily.yaml

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config:
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- {os: windows-latest}
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- {os: macOS-latest}
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- {os: ubuntu-18.04, rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
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- {os: ubuntu-18.04}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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RSPM: ${{ matrix.config.rspm }}
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@v1
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id: install-r
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with:
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use-public-rspm: true
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- name: change temp dir
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cat(readLines("~/.Rprofile"), sep = "\n")
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shell: Rscript {0}
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- name: Install pak and query dependencies
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run: |
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install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
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saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
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shell: Rscript {0}
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- name: Restore R package cache
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uses: actions/cache@v2
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- uses: r-lib/actions/setup-r-dependencies@v1
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with:
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path: |
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${{ env.R_LIBS_USER }}/*
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!${{ env.R_LIBS_USER }}/pak
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key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
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restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
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- name: Install system dependencies
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if: runner.os == 'Linux'
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run: |
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pak::local_system_requirements(execute = TRUE)
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pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
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shell: Rscript {0}
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extra-packages: rcmdcheck
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- name: Install dependencies
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- name: Pandoc and Tinytex info
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run: |
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pak::local_install_dev_deps(upgrade = TRUE)
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pak::pkg_install("rcmdcheck")
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shell: Rscript {0}
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- name: Session info
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run: |
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options(width = 100)
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pkgs <- .packages(TRUE)
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sessioninfo::session_info(pkgs, include_base = TRUE)
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rmarkdown::find_pandoc()
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tinytex::tlmgr("--version")
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tinytex::tl_pkgs()
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shell: Rscript {0}
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- name: Check
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env:
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_R_CHECK_CRAN_INCOMING_: false
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_R_CHECK_TESTS_NLINES_: 0
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run: |
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options(crayon.enabled = TRUE)
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rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
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shell: Rscript {0}
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- uses: r-lib/actions/check-r-package@v1
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- name: Show testthat output
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if: always()

‎.github/workflows/pkgdown.yaml

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if: ${{ github.event_name == 'push' || startsWith(github.head_ref, 'pkgdown/') }}
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runs-on: ubuntu-18.04
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env:
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RSPM: https://packagemanager.rstudio.com/cran/__linux__/bionic/latest
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: r-lib/actions/setup-r@v1
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id: install-r
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-pandoc@v1
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- name: Install pak and query dependencies
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run: |
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install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
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saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
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shell: Rscript {0}
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- name: Cache R packages
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uses: actions/cache@v2
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- uses: r-lib/actions/setup-r-dependencies@v1
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
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restore-keys: ${{ runner.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
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- name: Install system dependencies
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if: runner.os == 'Linux'
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run: |
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pak::local_system_requirements(execute = TRUE)
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pak::pkg_system_requirements("pkgdown", execute = TRUE)
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shell: Rscript {0}
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- name: Install package and dependencies
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run: |
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pak::local_install_dev_deps(upgrade = TRUE)
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pak::pkg_install("r-lib/pkgdown")
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pak::pkg_install("rstudio/quillt")
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shell: Rscript {0}
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extra-packages: |
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r-lib/pkgdown
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rstudio/quillt
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needs: website
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- name: Install package
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run: R CMD INSTALL .

‎DESCRIPTION

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Package: rmarkdown
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Type: Package
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Title: Dynamic Documents for R
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Version: 2.11.2
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Version: 2.11.3.9000
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Authors@R: c(
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person("JJ", "Allaire", role = "aut", email = "[email protected]"),
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person("Yihui", "Xie", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0003-0645-5666")),
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person("Devon", "Ryan", role = "ctb", email = "[email protected]", comment = c(ORCID = "0000-0002-8549-0971")),
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person("Frederik", "Aust", role = "ctb", email = "[email protected]", comment = c(ORCID = "0000-0003-4900-788X")),
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person("Jeff", "Allen", role = "ctb", email = "[email protected]"),
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person("Jonathan", "Gilligan", role = "ctb", email = "[email protected]", comment = c(ORCID = "0000-0003-1375-6686")),
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person("JooYoung", "Seo", role="ctb", comment = c(ORCID = "0000-0002-4064-6012")),
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person("Malcolm", "Barrett", role = "ctb"),
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person("Rob", "Hyndman", role = "ctb", email = "[email protected]"),

‎NEWS.md

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rmarkdown 2.12
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================================================================================
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- `html_document` output allows `lib_dir` to point to a parent of the output
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directory if the `allow_uptree_lib_dir` parameter is set to `TRUE`. This used
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to throw an error, "The path <file> does not appear to be a descendant of
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<dir>". This makes it possible to have a directory structure for HTML output
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where there is a shared master library with css, javascript, etc. and separate
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child directories with RMarkdown files. #146 and #1859.
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- Added a global option `rmarkdown.html_dependency.header_attr` (`TRUE` by default). It can be set to `FALSE` to opt-out the HTML dependency `html_dependency_header_attrs()` in documents based on `html_document_base()` (thanks, @salim-b rstudio/bookdown#865, @maelle r-lib/downlit#1538).
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- `draft()` now works with `devtools::load_all()` and **testthat** when used in other packages.
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rmarkdown 2.11
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- The previously unexported function `convert_ipynb()` is exported now (thanks, @acircleda).
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rmarkdown 2.10
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================================================================================
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