lintr style code check for Bioconductor

[nturaga]

Implement a BiocLint() function which takes in an .R file(s) and returns lines in the code which need to be improved.

lintr: https://github.com/jimhester/lintr#project-configuration

Goal: Create a new .lintr file (lintr configuration file)

[LiNk-NY]

Here is a starter .lintr configuration file

linters: with_defaults(
    assignment_linter,
    absolute_paths_linter,
    no_tab_linter,
    camel_case_linter = NULL,
    snake_case_linter,
    closed_curly_linter = NULL,
    commented_code_linter = NULL,
    open_curly_linter = NULL,
    line_length_linter(80),
    multiple_dots_linter,
    single_quotes_linter = NULL,
    spaces_left_parentheses_linter,
    trailing_whitespace_linter
  )

[lcolladotor]

Hi,

Sorry, I'm new to lintr (I've seen the name here and there before, haven't dived into it). When I first quickly looked at it, it seemed to me that BiocCheck was already doing something similar.

If so, is the idea to have BiocCheck rely on lintr for all the formatting checks?

If so, it might be good to have an example .R file that fails the formatting checks to test this on as well as see if any auto-formatting tools like in #57 help resolve these issues or most of them.

Best,
Leo

[Bisaloo]

I am one of the current authors of lintr and I would be happy to support an effort to rely on lintr for checks in checkRcoding.R.

This means checks would have more developers working on them and a wider user base.

As a result:

• potential new checks in BiocCheck could also result in new linters, thus benefitting the wider R community outside of Bioconductor as well
• both lintr and new linters from BiocCheck would get more user testing and feedback
• more checks might be added in BiocCheck if desired

A practical example where we would get immediate benefits from here: I get a biocCheck NOTE on the following line:

    stop(paste("Invalid filter", filter, sep = ": "))

But as far as I can tell, the use of paste() is justified here because sep is not the default. The lintr package already filters these cases and doesn't raise a lint.

If it helps, I believe a new bioconductor tag could be added to linters to facilitate setting up lintr for bioconductor users and purposes.

lintr::lint_package(linters = lintr::linters_with_tags("bioconductor"))