flir: Find and Fix Lints in R Code

Description

Lints are code patterns that are not optimal because they are inefficient, forget corner cases, or are less readable. 'flir' provides a small set of functions to detect those lints and automatically fix them. It builds on 'astgrepr', which itself uses the 'Rust' crate 'ast-grep' to parse and navigate R code.

Author(s)

Maintainer: Etienne Bacher etienne.bacher@protonmail.com [copyright holder]

See Also

Useful links:

• https://flir.etiennebacher.com

• https://github.com/etiennebacher/flir

• Report bugs at https://github.com/etiennebacher/flir/issues

T and F symbol linter

Description

See https://lintr.r-lib.org/reference/T_and_F_symbol_linter.

Usage

T_and_F_symbol_linter

Value

The name of the linter

Create a custom rule for internal use

Description

This function creates a YAML file with the placeholder text to define a new rule. The file is stored in flir/rules/custom. You need to create the flir folder with setup_flir() if it doesn't exist.

If you want to create a rule that users of your package will be able to access, use export_new_rule() instead.

Usage

add_new_rule(name, path)

Arguments

Value

Create new file(s) but doesn't return anything

Require usage of anyDuplicated(x) > 0 over any(duplicated(x))

Description

See https://lintr.r-lib.org/reference/any_duplicated_linter.

Usage

any_duplicated_linter

Value

The name of the linter

Require usage of anyNA(x) over any(is.na(x))

Description

See https://lintr.r-lib.org/reference/any_is_na_linter.

Usage

any_is_na_linter

Value

The name of the linter

Block comparison of class with ==

Description

See https://lintr.r-lib.org/reference/class_equals_linter.

Usage

class_equals_linter

Value

The name of the linter

Block usage of paste() and paste0() with messaging functions using ...

Description

See https://lintr.r-lib.org/reference/condition_message_linter.

Usage

condition_message_linter

Value

The name of the linter

double_assignment

Description

double_assignment

Usage

double_assignment_linter

Value

The name of the linter

Duplicate argument linter

Description

See https://lintr.r-lib.org/reference/duplicate_argument_linter.

Usage

duplicate_argument_linter

Value

The name of the linter

empty_assignment

Description

empty_assignment

Usage

empty_assignment_linter

Value

The name of the linter

equal_assignment

Description

equal_assignment

Usage

equal_assignment_linter

Value

The name of the linter

Equality check with NA linter

Description

See https://lintr.r-lib.org/reference/equals_na_linter.

Usage

equals_na_linter

Value

The name of the linter

Require usage of expect_gt(x, y) over expect_true(x > y) (and similar)

Description

See https://lintr.r-lib.org/reference/expect_comparison_linter.

Usage

expect_comparison_linter

Value

The name of the linter

Require usage of expect_identical(x, y) where appropriate

Description

See https://lintr.r-lib.org/reference/expect_identical_linter.

Usage

expect_identical_linter

Value

The name of the linter

Require usage of expect_length(x, n) over expect_equal(length(x), n)

Description

See https://lintr.r-lib.org/reference/expect_length_linter.

Usage

expect_length_linter

Value

The name of the linter

Require usage of expect_named(x, n) over expect_equal(names(x), n)

Description

See https://lintr.r-lib.org/reference/expect_named_linter.

Usage

expect_named_linter

Value

The name of the linter

Require usage of expect_false(x) over expect_true(!x)

Description

See https://lintr.r-lib.org/reference/expect_not_linter.

Usage

expect_not_linter

Value

The name of the linter

Require usage of expect_null for checking NULL

Description

See https://lintr.r-lib.org/reference/expect_null_linter.

Usage

expect_null_linter

Value

The name of the linter

Require usage of expect_true(x) over expect_equal(x, TRUE)

Description

See https://lintr.r-lib.org/reference/expect_true_false_linter.

Usage

expect_true_false_linter

Value

The name of the linter

Require usage of expect_type(x, type) over expect_equal(typeof(x), type)

Description

See https://lintr.r-lib.org/reference/expect_type_linter.

Usage

expect_type_linter

Value

The name of the linter

Create a custom rule for external use

Description

This function creates a YAML file with the placeholder text to define a new rule. The file is stored in inst/flir/rules and will be available to users of your package if they use flir.

To create a new rule that you can use in the current project only, use add_new_rule() instead.

Usage

export_new_rule(name, path)

Arguments

Value

Create new file(s) but doesn't return anything

Automatically replace lints

Description

fix(), fix_package(), and fix_dir() all replace lints in files. The only difference is in the input they take:

• fix() takes path to files or directories

• fix_dir() takes a path to one directory

• fix_package() takes a path to the root of a package and looks at the following list of folders: R, tests, inst, vignettes, data-raw, demo, exec.

fix_text() takes some text input. Its main interest is to be able to quickly experiment with some lints and fixes.

Usage

fix(
  path,
  linters = NULL,
  exclude_path = NULL,
  exclude_linters = NULL,
  force = FALSE,
  verbose = TRUE,
  rerun = TRUE,
  interactive = FALSE
)

fix_dir(
  path,
  linters = NULL,
  exclude_path = NULL,
  exclude_linters = NULL,
  force = FALSE,
  verbose = TRUE,
  rerun = TRUE,
  interactive = FALSE
)

fix_package(
  path,
  linters = NULL,
  exclude_path = NULL,
  exclude_linters = NULL,
  force = FALSE,
  verbose = TRUE,
  rerun = TRUE,
  interactive = FALSE
)

fix_text(text, linters = NULL, exclude_linters = NULL, rerun = TRUE)

Arguments

Value

A list with as many elements as there are files to fix (in fix_text(), the text is written to a temporary file).

Each element of the list contains the fixed text, where all fixes available have been applied.

Ignoring lines

flir supports ignoring single lines of code with ⁠# flir-ignore⁠. For example, this will not warn:

# flir-ignore
any(duplicated(x))

However, this will warn for the second any(duplicated()):

# flir-ignore
any(duplicated(x))
any(duplicated(y))

To ignore more than one line of code, use ⁠# flir-ignore-start⁠ and ⁠# flir-ignore-end⁠:

# flir-ignore-start
any(duplicated(x))
any(duplicated(y))
# flir-ignore-end

Examples

# `fix_text()` is convenient to explore with a small example
fix_text("any(duplicated(rnorm(5)))")

fix_text("any(duplicated(rnorm(5)))
any(is.na(x))
")

# Setup for the example with `fix()`
destfile <- tempfile()
cat("
x = c(1, 2, 3)
any(duplicated(x), na.rm = TRUE)

any(duplicated(x))

if (any(is.na(x))) {
  TRUE
}

any(
  duplicated(x)
)", file = destfile)

fix(destfile)
cat(paste(readLines(destfile), collapse = "\n"))

Block usage of for loops directly overwriting the indexing variable

Description

See https://lintr.r-lib.org/reference/for_loop_index_linter.

Usage

for_loop_index_linter

Value

The name of the linter

Lint common mistakes/style issues cropping up from return statements

Description

See https://lintr.r-lib.org/reference/function_return_linter.

Usage

function_return_linter

Value

The name of the linter

implicit_assignment

Description

implicit_assignment

Usage

implicit_assignment_linter

Value

The name of the linter

Redirect is.numeric(x) || is.integer(x) to just use is.numeric(x)

Description

See https://lintr.r-lib.org/reference/is_numeric_linter.

Usage

is_numeric_linter

Value

The name of the linter

Require usage of nlevels over length(levels(.))

Description

See https://lintr.r-lib.org/reference/length_levels_linter.

Usage

length_levels_linter

Value

The name of the linter

Check for a common mistake where length is applied in the wrong place

Description

See https://lintr.r-lib.org/reference/length_test_linter.

Usage

length_test_linter

Value

The name of the linter

Require usage of lengths() where possible

Description

See https://lintr.r-lib.org/reference/lengths_linter.

Usage

lengths_linter

Value

The name of the linter

Library call linter

Description

See https://lintr.r-lib.org/reference/library_call_linter.

Usage

library_call_linter

Value

The name of the linter

List all lints in a file or a directory

Description

lint(), lint_text(), lint_package(), and lint_dir() all produce a data.frame containing the lints, their location, and potential fixes. The only difference is in the input they take:

• lint() takes path to files or directories

• lint_text() takes some text input

• lint_dir() takes a path to one directory

• lint_package() takes a path to the root of a package and looks at the following list of folders: R, tests, inst, vignettes, data-raw, demo, exec.

Usage

lint(
  path = ".",
  linters = NULL,
  exclude_path = NULL,
  exclude_linters = NULL,
  open = TRUE,
  use_cache = TRUE,
  verbose = TRUE
)

lint_dir(
  path = ".",
  linters = NULL,
  open = TRUE,
  exclude_path = NULL,
  exclude_linters = NULL,
  use_cache = TRUE,
  verbose = TRUE
)

lint_package(
  path = ".",
  linters = NULL,
  open = TRUE,
  exclude_path = NULL,
  exclude_linters = NULL,
  use_cache = TRUE,
  verbose = TRUE
)

lint_text(text, linters = NULL, exclude_linters = NULL)

Arguments

Value

A dataframe where each row is a lint. The columns show the text, its location (both the position in the text and the file in which it was found) and the severity.

Ignoring lines

flir supports ignoring single lines of code with ⁠# flir-ignore⁠. For example, this will not warn:

# flir-ignore
any(duplicated(x))

However, this will warn for the second any(duplicated()):

# flir-ignore
any(duplicated(x))
any(duplicated(y))

To ignore more than one line of code, use ⁠# flir-ignore-start⁠ and ⁠# flir-ignore-end⁠:

# flir-ignore-start
any(duplicated(x))
any(duplicated(y))
# flir-ignore-end

Examples

# `lint_text()` is convenient to explore with a small example
lint_text("any(duplicated(rnorm(5)))")

lint_text("any(duplicated(rnorm(5)))
any(is.na(x))
")

# Setup for the example with `lint()`
destfile <- tempfile()
cat("
x = c(1, 2, 3)
any(duplicated(x), na.rm = TRUE)

any(duplicated(x))

if (any(is.na(x))) {
  TRUE
}

any(
  duplicated(x)
)", file = destfile)

lint(destfile)

Block usage of comparison operators with known-list() functions like lapply

Description

See https://lintr.r-lib.org/reference/list_comparison_linter.

Usage

list_comparison_linter

Value

The name of the linter

Get the list of linters in flir

Description

Get the list of linters in flir

Usage

list_linters(path)

Arguments

Value

A character vector

Examples

list_linters(".")

Require usage of correctly-typed literals over literal coercions

Description

See https://lintr.r-lib.org/reference/literal_coercion_linter.

Usage

literal_coercion_linter

Value

The name of the linter

Require usage of colSums(x) or rowSums(x) over apply(x, ., sum)

Description

See https://lintr.r-lib.org/reference/matrix_apply_linter.

Usage

matrix_apply_linter

Value

The name of the linter

Missing argument linter

Description

See https://lintr.r-lib.org/reference/missing_argument_linter.

Usage

missing_argument_linter

Value

The name of the linter

Block usage of nested ifelse() calls

Description

See https://lintr.r-lib.org/reference/nested_ifelse_linter.

Usage

nested_ifelse_linter

Value

The name of the linter

Require usage of a leading zero in all fractional numerics

Description

See https://lintr.r-lib.org/reference/numeric_leading_zero_linter.

Usage

numeric_leading_zero_linter

Value

The name of the linter

Require usage of !any(x) over all(!x), !all(x) over any(!x)

Description

See https://lintr.r-lib.org/reference/outer_negation_linter.

Usage

outer_negation_linter

Value

The name of the linter

Package hooks linter

Description

See https://lintr.r-lib.org/reference/package_hooks_linter.

Usage

package_hooks_linter

Value

The name of the linter

Raise lints for several common poor usages of paste()

Description

See https://lintr.r-lib.org/reference/paste_linter.

Usage

paste_linter

Value

The name of the linter

Block usage of ==, != on logical vectors

Description

See https://lintr.r-lib.org/reference/redundant_equals_linter.

Usage

redundant_equals_linter

Value

The name of the linter

Prevent ifelse() from being used to produce TRUE/FALSE or 1/0

Description

See https://lintr.r-lib.org/reference/redundant_ifelse_linter.

Usage

redundant_ifelse_linter

Value

The name of the linter

Require usage of rep_len(x, n) over rep(x, length.out = n)

Description

See https://lintr.r-lib.org/reference/rep_len_linter.

Usage

rep_len_linter

Value

The name of the linter

right_assignment

Description

right_assignment

Usage

right_assignment_linter

Value

The name of the linter

Require usage of sample.int(n, m, ...) over sample(1:n, m, ...)

Description

See https://lintr.r-lib.org/reference/sample_int_linter.

Usage

sample_int_linter

Value

The name of the linter

Sequence linter

Description

See https://lintr.r-lib.org/reference/seq_linter.

Usage

seq_linter

Value

The name of the linter

Setup flir

Description

This creates a flir folder that has multiple purposes. It contains:

• the file config.yml where you can define rules to keep or exclude, as well as rules defined in other packages. More on this below;

• the file cache_file_state.rds, which is used when ⁠lint_*()⁠ or ⁠fix_*()⁠ have cache = TRUE;

• an optional folder rules/custom where you can store your own rules.

This folder must live at the root of the project and cannot be renamed.

Usage

setup_flir(path)

Arguments

Details

The file flir/config.yml can contain three fields: keep, exclude, and from-package.

keep and exclude are used to define the rules to keep or to exclude when running ⁠lint_*()⁠ or ⁠fix_*()⁠.

It is possible for other packages to create their own list of rules, for instance to detect or replace deprecated functions. In from-package, you can list package names where flir should look for additional rules. By default, if you list package foobar, then all rules defined in the package foobar will be used. To ignore some of those rules, you can list ⁠from-foobar-<rulename>⁠ in the exclude field.

See the vignette Sharing rules across packages for more information.

Value

Imports files necessary for flir to work but doesn't return any value in R.

Create a Github Actions workflow for flir

Description

Create a Github Actions workflow for flir

Usage

setup_flir_gha(path, overwrite = FALSE)

Arguments

Value

Creates .github/workflows/flir.yaml but doesn't return any value.

Check for common mistakes around sorting vectors

Description

See https://lintr.r-lib.org/reference/sort_linter.

Usage

sort_linter

Value

The name of the linter

Block usage of all() within stopifnot()

Description

See https://lintr.r-lib.org/reference/stopifnot_all_linter.

Usage

stopifnot_all_linter

Value

The name of the linter

TODO comment linter

Description

See https://lintr.r-lib.org/reference/todo_comment_linter.

Usage

todo_comment_linter

Value

The name of the linter

Undesirable function linter

Description

See https://lintr.r-lib.org/reference/undesirable_function_linter.

Usage

undesirable_function_linter

Value

The name of the linter

Undesirable operator linter

Description

See https://lintr.r-lib.org/reference/undesirable_operator_linter.

Usage

undesirable_operator_linter

Value

The name of the linter

Block instances of unnecessary nesting

Description

See https://lintr.r-lib.org/reference/unnecessary_nesting_linter.

Usage

unnecessary_nesting_linter

Value

The name of the linter

Require usage of grep over which(grepl(.))

Description

See https://lintr.r-lib.org/reference/which_grepl_linter.

Usage

which_grepl_linter

Value

The name of the linter