Auto-Fix R Code Quality Issues

Automatically fixes common R code quality issues across multiple categories: formatting, trivial transformations, cleanup, simplifications, pipes, namespace usage, dead code detection, and more.

Usage

sonar_fix(
  path = ".",
  include = "\\.[Rr]$",
  exclude = c("renv", ".git", ".Rproj.user", "packrat", "vendor", "node_modules"),
  fixes = "all",
  formatter = c("styler", "air"),
  dry_run = TRUE,
  backup = FALSE,
  parallel = TRUE,
  n_cores = parallel::detectCores(),
  report = TRUE,
  report_file = "sonar-fixes.json",
  verbose = interactive()
)

Arguments

path: Path to the R project or directory. Default ".".
include: Glob pattern for files to include. Default "\\\\.\[Rr\]$".
exclude: Character vector of directories or patterns to exclude. Default c("renv", ".git", ".Rproj.user", "packrat", "vendor", "node_modules").
fixes: Character vector of fix categories to apply, or "all" for all categories. Available categories are: "styler", "spacing", "true_false", "null", "commas", "parens", "cleanup", "simplify", "pipes", "magrittr", "namespace", "library", "dead_code", "return", "assignment", "comments", "unused_vars", "duplicate_libs". See details. Default "all".
formatter: Character vector of formatters to use for code style. Options are "styler" (default, uses tidyverse style) or "air" (Posit's fast formatter). Default c("styler").
dry_run: Logical. If TRUE, only check what would be changed without modifying files. Default TRUE.
backup: Logical. If TRUE, create .bak copies of files before modifying them. Default FALSE.
parallel: Logical. Use parallel processing for multiple files. Default TRUE.
n_cores: Number of cores for parallel processing. Default parallel::detectCores().
report: Logical. Generate a JSON report file. Default TRUE.
report_file: Path to the JSON report. Default "sonar-fixes.json".
verbose: Logical. Show progress and result summary. Default interactive().

Value

An object of class sonar_fix containing:

files_scanned: Total number of R files examined
files_modified: Number of files that were actually modified
fixes_applied: Named list with counts of each fix type applied
fixes_skipped: Named list of fix types that were skipped
elapsed: Duration of the fix run
report: Console-friendly summary text
path: Analyzed project path
timestamp: Execution date/time

Details

Unlike sonar_analyse() which is read-only, sonar_fix() modifies files in the project. Always run with dry_run = TRUE first (default) to preview changes before applying them.

Fix categories

Formatting ("styler" or "air"): Indentation, spacing, parentheses, alignment, line breaks, pipe formatting, braces, blank lines. Equivalent to styler::style_dir() or air format.

Spacing ("spacing"): Fix missing spaces around operators, commas, and assignments. Example: x<-1 → x <- 1.

TRUE/FALSE ("true_false"): Replace T/F with TRUE/FALSE.

NULL ("null"): Replace x=NULL with x <- NULL.

Commas ("commas"): Add spaces after commas. Example: c(1,2,3) → c(1, 2, 3).

Parentheses ("parens"): Remove unnecessary parentheses. Example: return((x)) → return(x).

Cleanup ("cleanup"): Remove double comment lines (#####), empty comment blocks, multiple blank lines, trailing whitespace, ensure single trailing newline.

Simplify ("simplify"): Simplify boolean expressions. Example: if(x==TRUE) → if(x), length(x)==0 → !length(x).

Pipes ("pipes"): Convert %>% to |> (native pipe). Example: x %>% f() → x |> f().

Magrittr ("magrittr"): Convert assignment pipes %<>% to equivalent base R.

Namespace ("namespace"): Convert library(x) + f() to x::f().

Library ("library"): Detect unused library() calls (report only, not applied automatically).

Dead code ("dead_code"): Remove expressions without effect (e.g. 1+1 standalone). Default: report only.

Return ("return"): Fix formatting of return() calls. Example: return(x) without unnecessary line breaks.

Assignment ("assignment"): Convert = to <- outside of function calls.

Comments ("comments"): Standardize long comment separators. Example: ########## → #----------.

Unused Variables ("unused_vars"): Detect and remove variable assignments that are never read within the same file. Example: x <- 1 followed by no usage of x → line removed.

Duplicate Libraries ("duplicate_libs"): Detect and remove duplicate library() calls loading the same package multiple times. Example: library(ggplot2) x2 → second line removed.

Corrections NOT applied automatically

The following are never auto-fixed (remain in sonar_analyse()): business logic changes, renaming, function removal, API changes, type changes, algorithm simplification, cyclomatic complexity.

Examples

if (FALSE) { # \dontrun{
# Preview changes (no files modified)
fix <- sonar_fix(".", dry_run = TRUE)
print(fix)

# Apply all fixes
fix <- sonar_fix(".", dry_run = FALSE)

# Apply only formatting and spacing fixes
fix <- sonar_fix(".", fixes = c("spacing", "styler"))

# Use air formatter instead of styler
fix <- sonar_fix(".", formatter = "air")

# Backup files before modifying
fix <- sonar_fix(".", backup = TRUE, dry_run = FALSE)
} # }