Static Code Analysis for R
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russHyde and jimhester fixes #322: allows Rmd chunks using {lang} engine format (#350)
Allow Rmd chunks using {lang} engine format

Rmarkdown format allows the use of code blocks in the following format

```{some_engine}
# not necessarily R syntax
foo = bar
```

These blocks should be filtered out before linting the remaining R-code blocks.

A couple of python blocks were added to test.Rmd: one with R-like syntax and one with syntax that can't be parsed as R.

The function `defines_knitr_engine` was extracted from `extract_r_source` and extended. This tests for the presence of {r engine = some_engine} and {some_engine} in the start line of a code chunk. The names of valid engines are obtained from `knitr::knit_engines`

Fixes #322
Latest commit 4ade1fc Sep 19, 2018

README.md

lintr

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Static code analysis for R

lintr is an R package offering static code analysis for R. It checks adherence to a given style, syntax errors and possible semantic issues, see the animation below. In this README find out

lintr

What to do with lintr output?

If you need a bit automatic help for re-styling your code, have a look at the styler package

Available linters

  • Syntax errors: reported by parse.
  • object_usage_linter: check that closures have the proper usage using codetools::checkUsage(). Note this runs base::eval() on the code, so do not use with untrusted code.
  • absolute_path_linter: check that no absolute paths are used (e.g. "/var", "C:\System", "~/docs").
  • nonportable_path_linter: check that file.path() is used to construct safe and portable paths.
  • pipe_continuation_linter: Check that each step in a pipeline is on a new line, or the entire pipe fits on one line.
  • assignment_linter: check that <- is always used for assignment
  • closed_curly_linter: check that closed curly braces should always be on their own line unless they follow an else.
  • commas_linter: check that all commas are followed by spaces, but do not have spaces before them.
  • extraction_operator_linter: check that the [[ operator is used when extracting a single element from an object, not [ (subsetting) nor $ (interactive use).
  • implicit_integer_linter: check that integers are explicitly typed using the form 1L instead of 1.
  • infix_spaces_linter: check that all infix operators have spaces around them.
  • line_length_linter: check the line length of both comments and code is less than length.
  • no_tab_linter: check that only spaces are used, never tabs.
  • object_length_linter: check that function and variable names are not more than length characters.
  • object_name_linter: check that object names conform to a single naming style, e.g. snake_case or lowerCamelCase.
  • open_curly_linter: check that opening curly braces are never on their own line and are always followed by a newline.
  • semicolon_terminator_linter: check that no semicolons terminate statements.
  • single_quotes_linter: check that only single quotes are used to delimit string contestants.
  • spaces_inside_linter: check that parentheses and square brackets do not have spaces directly inside them.
  • spaces_left_parentheses_linter: check that all left parentheses have a space before them unless they are in a function call.
  • todo_comment_linter: check that the source contains no TODO comments (case-insensitive).
  • trailing_blank_lines_linter: check there are no trailing blank lines.
  • trailing_whitespace_linter: check there are no trailing whitespace characters.
  • T_and_F_symbol_linter: avoid the symbols T and F (for TRUE and FALSE).
  • undesirable_function_linter: report the use of undesirable functions, e.g. options or sapply and suggest an alternative.
  • undesirable_operator_linter: report the use of undesirable operators, e.g. ::: or <<- and suggest an alternative.
  • unneeded_concatenation_linter: check that the c function is not used without arguments nor with a single constant.

References

Most of the default linters are based on Hadley Wickham's R Style Guide.

Project Configuration

Lintr supports per-project configuration of the following fields. The config file (default file name: .lintr) is in Debian Control Field Format.

  • linters - see ?with_defaults for example of specifying only a few non-default linters.
  • exclusions - a list of filenames to exclude from linting. You can use a named item to exclude only certain lines from a file.
  • exclude - a regex pattern for lines to exclude from linting. Default is "# nolint"
  • exclude_start - a regex pattern to start exclusion range. Default is "# nolint start"
  • exclude_end - a regex pattern to end exclusion range. Default is "# nolint end"

An example file that uses 120 character line lengths, excludes a couple of files and sets different default exclude regexs follows.

linters: with_defaults(line_length_linter(120))
exclusions: list("inst/doc/creating_linters.R" = 1, "inst/example/bad.R", "tests/testthat/exclusions-test")
exclude: "# Exclude Linting"
exclude_start: "# Begin Exclude Linting"
exclude_end: "# End Exclude Linting"

With the following command, you can create a configuration file for lintr that ignores all linters that show at least one error:

library(magrittr)
library(dplyr)
lintr::lint_package() %>%
  as.data.frame %>%
  group_by(linter) %>%
  tally(sort = TRUE) %$%
  sprintf("linters: with_defaults(\n    %s\n    NULL\n  )\n",
          paste0(linter, " = NULL, # ", n, collapse="\n    ")) %>%
  cat(file = ".lintr")

The resulting configuration will contain each currently failing linter and the corresponding number of hits as a comment. Proceed by successively enabling linters, starting with those with the least number of hits. Note that this requires lintr 0.3.0.9001 or later.

Continuous integration

If you want to run lintr on Travis-CI in order to check that commits and pull requests don't deteriorate code style, you will need to have Travis install the package first. This can be done by adding the following line to your .travis.yml

r_github_packages:
  - jimhester/lintr

There are two strategies for getting lintr results:

In both cases the lintr-bot will add comments to the commit or pull request with the lints found and they will also be printed on Travis-CI. If you want to disable the commenting you can set the environment variable LINTR_COMMENT_BOT=false.

Non-failing Lints

If you do not want to fail the travis build on lints or do not use testthat you can simply add the following to your .travis.yml

after_success:
  - R CMD INSTALL $PKG_TARBALL
  - Rscript -e 'lintr::lint_package()'

Live example of a package using this setup: hibpwned, lintr-bot commenting on a PR.

Testthat

If you are already using testthat for testing simply add the following to your tests to fail if there are any lints in your project. You will have to add Suggests: lintr to your package DESCRIPTION as well.

if (requireNamespace("lintr", quietly = TRUE)) {
  context("lints")
  test_that("Package Style", {
    lintr::expect_lint_free()
  })
}

Installation of development version

To install the latest development version of lintr from GitHub

devtools::install_github("jimhester/lintr")

Editors setup

RStudio

lintr lints are automatically displayed in the RStudio Markers pane, Rstudio versions (> v0.99.206). RStudio Example

Installation

Install lintr, type install.packages("lintr") in the Console.

In order to show the "Markers" pane in RStudio: Menu "Tools" -> "Global Options...", a window with title "Options" will pop up. In that window: Click "Code" on the left; Click "Diagnostics" tab; check "Show diagnostics for R".

To lint a source file test.R type in the Console lintr::lint("test.R") and look at the result in the "Markers" pane.

This package also includes two addins for linting the current source and package. To bind the addin to a keyboard shortcut navigate to Tools > addins > Browse Addins > Keyboard Shortcuts. It's recommended to use Alt+Shift+L for linting the current source code and Ctrl+Shift+Alt+L to code the package. These are easy to remember as you are Alt+Shift+L(int) ;)

Emacs

lintr has built-in integration with flycheck versions greater than 0.23. Emacs Example

Installation

lintr is fully integrated into flycheck when using ESS. See the installalation documentation for those packages for more information.

Configuration

You can also configure what linters are used. e.g. using a different line length cutoff.

  • M-x customize-option -> flycheck-lintr-linters -> with_defaults(line_length_linter(120))

Vim

lintr can be integrated with syntastic for on the fly linting.

Vim Example

Installation

Put the file syntastic/lintr.vim in syntastic/syntax_checkers/r. If you are using pathogen this directory is ~/.vim/bundles/syntastic/syntax_checkers/r.

You will also need to add the following lines to your .vimrc.

let g:syntastic_enable_r_lintr_checker = 1
let g:syntastic_r_checkers = ['lintr']

Configuration

You can also configure what linters are used. e.g. using a different line length cutoff.

let g:syntastic_r_lintr_linters = "with_defaults(line_length_linter(120))"

Sublime Text 3

lintr can be integrated with Sublime Linter for on the fly linting.

Sublime Example

Installation

Simply install sublimeLinter-contrib-lintr using Package Control.

For more information see Sublime Linter Docs

Configuration

You can also configure what linters are used. e.g. disabling the assignment linter and using a different line length cutoff. In the SublimeLinter User Settings

{
  "linters": {
    "lintr": {
      "linters": "with_defaults(assignment_linter = NULL, line_length_linter(120))"
    }
  }
}

Atom

lintr can be integrated with Linter for on the fly linting.

Atom Example

Installation

Simply install linter-lintr from within Atom or on the command line with:

apm install linter-lintr

For more information and bug reports see Atom linter-lintr.