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MichaelChiricoMichaelChirico
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Merge branch 'master' into regex-based-linter-issue-441
2 parents 83acd5c + b4e3f72 commit 5e16e3b

21 files changed

+435
-110
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‎.github/.gitignore

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*.html

‎.github/workflows/R-CMD-check.yaml

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on:
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push:
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branches:
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- main
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- master
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pull_request:
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branches:
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- main
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- master
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name: R-CMD-check
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jobs:
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R-CMD-check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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strategy:
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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: windows-latest, r: 'release'}
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- {os: windows-latest, r: '3.6'}
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- {os: ubuntu-16.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest", http-user-agent: "R/4.0.0 (ubuntu-16.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
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- {os: ubuntu-16.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.5', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.4', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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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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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@v1
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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- uses: r-lib/actions/setup-pandoc@v1
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- name: Cache R packages
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if: runner.os != 'Windows'
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uses: actions/cache@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/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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while read -r cmd
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do
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eval sudo $cmd
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done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "16.04"))')
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- name: Install dependencies
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run: |
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran("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 <- installed.packages()[, "Package"]
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sessioninfo::session_info(pkgs, include_base = TRUE)
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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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run: 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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- name: Show testthat output
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if: always()
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run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload check results
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if: failure()
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uses: actions/upload-artifact@main
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with:
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name: ${{ runner.os }}-r${{ matrix.config.r }}-results
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path: check

‎.github/workflows/lint.yaml

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on:
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push:
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branches:
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- main
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- master
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- "**"
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pull_request:
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branches:
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- main
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- master
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name: lint
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jobs:
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lint:
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runs-on: macOS-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@v1
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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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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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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- name: Install dependencies
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run: |
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install.packages(c("remotes"))
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remotes::install_deps(dependencies = TRUE)
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remotes::install_github("jimhester/lintr")
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shell: Rscript {0}
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- name: Lint
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run: lintr::lint_package()
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shell: Rscript {0}

‎.github/workflows/test-coverage.yaml

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on:
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push:
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branches:
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- main
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- master
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- '**'
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pull_request:
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branches:
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- main
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- master
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name: test-coverage
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jobs:
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test-coverage:
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runs-on: macOS-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@v1
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- uses: r-lib/actions/setup-pandoc@v1
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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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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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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- name: Install dependencies
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run: |
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install.packages(c("remotes"))
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran("covr")
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shell: Rscript {0}
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- name: Test coverage
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run: covr::codecov()
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shell: Rscript {0}

‎.gitignore

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.Rhistory
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.RData
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.Ruserdata
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.idea
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bad.R
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script.R

‎.lintr

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linters: with_defaults( # The following TODOs are part of an effort to have {lintr} lint-free (#584)
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line_length_linter = line_length_linter(120),
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infix_spaces_linter = NULL, # TODO enable (#594)
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commented_code_linter = NULL, # TODO enable (#595)
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cyclocomp_linter = cyclocomp_linter(29), # TODO reduce to 15
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object_name_linter = NULL, # TODO enable (#597)
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spaces_inside_linter = NULL, # TODO enable (#598)

‎.travis.yml

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This file was deleted.

‎NEWS.md

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# lintr (development version)
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* Switched CI from Travis to GitHub Actions, using the full tidyverse recommended R CMD check. Code coverage and linting are implemented using separate GitHub Actions workflows (#572, @dragosmg)
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* `save_cache` will now recursively create the cache directory; this avoids errors that could arise if any parent directories do not exist (#60, @dankessler).
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* `extract_r_source` handles Rmd containing unevaluated code blocks with named
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format specifiers (#472, @russHyde)
@@ -17,6 +18,7 @@
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and support excluding entire directories (#158, #438, @AshesITR)
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* `object_name_linter()` now excludes special R hook functions such as `.onLoad` (#500, #614, @AshesITR)
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* `equals_na_linter()` now lints `x != NA` and `NA == x`, and skips usages in comments (#545, @michaelchirico)
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* Malformed Rmd files now cause a lint instead of an error (#571, #575, @AshesITR)
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* `paren_brace_linter` and `no_tab_linter` also use more reliable matching (e.g.,
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excluding matches found in comments; #441 and #545, @russHyde)
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‎R/actions.R

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)
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}
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}
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rstudio_source_markers <- function(lints) {
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# package path will be NULL unless it is a relative path
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package_path <- attr(lints, "path")
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# generate the markers
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markers <- lapply(lints, function(x) {
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filename <- if (!is.null(package_path)) {
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file.path(package_path, x$filename)
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} else {
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x$filename
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}
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marker <- list()
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marker$type <- x$type
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marker$file <- filename
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marker$line <- x$line_number
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marker$column <- x$column_number
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marker$message <- x$message
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marker
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})
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# request source markers
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rstudioapi::callFun("sourceMarkers",
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name = "lintr",
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markers = markers,
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basePath = package_path,
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autoSelect = "first")
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}

‎R/extract.R

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# content is the file content from readLines
2-
extract_r_source <- function(filename, lines) {
2+
extract_r_source <- function(filename, lines, error = identity) {
33
pattern <- get_knitr_pattern(filename, lines)
44
if (is.null(pattern$chunk.begin) || is.null(pattern$chunk.end)) {
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return(lines)
66
}
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8-
chunks <- get_chunk_positions(pattern = pattern, lines = lines)
8+
chunks <- tryCatch(get_chunk_positions(pattern = pattern, lines = lines), error = error)
9+
if (inherits(chunks, "error") || inherits(chunks, "lint")) {
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assign("e", chunks, envir = parent.frame())
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# error, so return empty code
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return(character())
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}
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1015
# no chunks found, so just return the lines
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if (length(chunks[["starts"]]) == 0 || length(chunks[["ends"]]) == 0) {
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6772
if (length_difference == 0 && all(ends > starts)) {
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return(ends)
6974
}
70-
if (length_difference < 0) {
71-
stop("Malformed file!", call. = FALSE)
72-
}
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positions <- sort(c(starts = starts, ends = ends))
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code_start_indexes <- grep("starts", names(positions))
76-
code_ends <- positions[1 + code_start_indexes]
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78-
stopifnot(all(grepl("ends", names(code_ends))))
79+
code_ends <- positions[pmin(1 + code_start_indexes, length(positions))]
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81+
bad_end_indexes <- grep("starts", names(code_ends), fixed = TRUE)
82+
if (length(bad_end_indexes)) {
83+
bad_start_positions <- positions[code_start_indexes[bad_end_indexes]]
84+
# This error message is formatted like a parse error
85+
stop(sprintf(
86+
"<rmd>:%1$d:1: Missing chunk end for chunk (maybe starting at line %1$d).\n",
87+
bad_start_positions[1L]
88+
), call. = FALSE)
89+
}
90+
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code_ends
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}
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