# ==================================================================== # # TITLE: # # AMR: An R Package for Working with Antimicrobial Resistance Data # # # # SOURCE CODE: # # https://github.com/msberends/AMR # # # # PLEASE CITE THIS SOFTWARE AS: # # Berends MS, Luz CF, Friedrich AW, et al. (2022). # # AMR: An R Package for Working with Antimicrobial Resistance Data. # # Journal of Statistical Software, 104(3), 1-31. # # https://doi.org/10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # # colleagues from around the world, see our website. # # # # This R package is free software; you can freely use and distribute # # it for both personal and commercial purposes under the terms of the # # GNU General Public License version 2.0 (GNU GPL-2), as published by # # the Free Software Foundation. # We created this package for both routine data analysis and academic # # research and it was publicly released in the hope that it will be # # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # # # # Visit our website for the full manual and a complete tutorial about # # how to conduct AMR data analysis: https://amr-for-r.org # # ==================================================================== # on: push: branches: '**' pull_request: branches: '**' name: lintr jobs: lintr: runs-on: ubuntu-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 - uses: r-lib/actions/setup-r@v2 with: r-version: release # use RStudio Package Manager to quickly install packages use-public-rspm: true - uses: r-lib/actions/setup-r-dependencies@v2 with: extra-packages: | any::lintr any::cyclocomp any::roxygen2 any::devtools any::usethis - name: Remove unneeded folders run: | # do not check these folders rm -rf data-raw rm -rf tests rm -rf vignettes - name: Lint run: | # old: lintr::lint_package(linters = lintr::with_defaults(line_length_linter = NULL, trailing_whitespace_linter = NULL, object_name_linter = NULL, cyclocomp_linter = NULL, object_length_linter = lintr::object_length_linter(length = 50L)), exclusions = list("R/aa_helper_pm_functions.R")) # now get ALL linters, not just default ones linters <- getNamespaceExports(asNamespace("lintr")) linters <- sort(linters[grepl("_linter$", linters)]) # lose deprecated linters <- linters[!grepl("^(closed_curly|open_curly|paren_brace|semicolon_terminator|consecutive_stopifnot|no_tab|single_quotes|unnecessary_nested_if|unneeded_concatenation)_linter$", linters)] linters <- linters[linters != "linter"] # and the ones we find unnnecessary linters <- linters[!grepl("^(commented_code|extraction_operator|implicit_integer|indentation|line_length|namespace|nonportable_path|object_length|object_name|object_usage|is)_linter$", linters)] # put the functions in a list linters_list <- lapply(linters, function(l) eval(parse(text = paste0("lintr::", l, "()")), envir = asNamespace("lintr"))) names(linters_list) <- linters # run them all! lintr::lint_package(linters = linters_list, exclusions = list("R/aa_helper_pm_functions.R")) shell: Rscript {0}