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Fix checks: "R code for possible problems", "Rd files"/"metadata"/"cross-references"/"code/documentation mismatches"; kml_to_csv bug/tests #228

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merged 57 commits into from
Aug 14, 2024

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@mhpob mhpob commented May 11, 2024

This PR is an attempt to start clearing up some of the "ignorable" output of R CMD check. Commits are small to aid in cherry-picking.

  • Declares all of the variables used in dplyr, data.table, or base (subset) NSE (Closes dplyr programming throws R CMD check warnings #190)
    • This was done using the data.table suggestion rather than the tidyverse rlang ".data" way as it seems a universal fix for all programming styles and didn't add a dependency.
    • Necessary to pass R CMD check: "checking R code for possible problems"
  • Explicitly calls dplyr::across, stats::setNames, utils::head, and utils:tails
    • Necessary to pass R CMD check: "checking R code for possible problems"
  • Fixes bug in kml_to_csv (Closes kml_to_csv doesn't check file extension as expected #227) and adds a few unit tests for kml_to_csv
    • Former is necessary to pass R CMD check: "checking R code for possible problems"
  • Adjust target to "_PACKAGE" (introduced in d5d5759) and remove LATeX escapes in package-glatos.R
    • Necessary to pass R CMD check: "checking Rd files"
  • Fixes misc. mis-specified itemized list in documentation
    • Necessary to pass R CMD check: "checking Rd files"
  • Puts backticks around anything with [...] that isn't supposed to be a link
    • Passes "checking Rd cross-references"
  • Switch @usage roxygen tag to @example in testdata.R and extdata.R to get around the need to document system.file
    • Necessary to pass R CMD check: "checking for code/documentation mismatches"
  • Slight adjustment of convert_otn_erddap_to_att test from expect_identical to expect_equal to avoid failure related to floating point issues on macOS

mhpob and others added 30 commits May 11, 2024 09:35
@mhpob mhpob changed the title Fix "no visible binding for global variable" warnings; kml_to_csv bug; add tests Fix checks: "R code for possible problems", "Rd files"/"metadata"/"cross-references"/"code/documentation mismatches"; kml_to_csv bug/tests May 13, 2024
@chrisholbrook chrisholbrook merged commit f9a65ca into ocean-tracking-network:dev Aug 14, 2024
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3 participants