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Auto-Fix with sonar_fix()

Source: vignettes/auto-fix.Rmd
auto-fix.Rmd

Overview

sonar_fix() is the complement to sonar_analyse(). While sonar_analyse() inspects your code and reports issues, sonar_fix() automatically corrects many of them — similar to SonarQube AutoFix, OpenRewrite recipes, or IDE quick-fixes.

⚠️ Unlike sonar_analyse() which is read-only, sonar_fix() modifies files. Always preview with dry_run = TRUE (the default) first.

Quick start 

library(rsonar)

# Preview what would be changed (no files modified)
fix <- sonar_fix(".", dry_run = TRUE)
print(fix)

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

Fix categories

sonar_fix() groups corrections into 18 categories. Use the fixes parameter to select which ones to apply.

Formatting ("styler" or "air")

Uses styler::style_dir() or Posit’s air formatter to apply the tidyverse style guide:

# Use styler (default)
fix <- sonar_fix(".", fixes = "styler")

# Use air (faster, needs to be installed first)
install_air()
fix <- sonar_fix(".", fixes = "styler", formatter = "air")

Corrections include: indentation, spacing, parentheses alignment, line breaks, pipe formatting, braces, blank lines.

Spacing ("spacing")

Fixes missing spaces around operators and assignments:

x<-1               # Before: no spaces
x <- 1             # After:  proper spacing

y = 2              # Before: space only before =
y <- 2             # After:  <- with spaces

TRUE/FALSE ("true_false")

Replaces T/F with TRUE/FALSE:

if(T)              # Before
if(TRUE)           # After

x <- F             # Before
x <- FALSE         # After

NULL ("null")

Converts x=NULL to x <- NULL (outside function arguments):

x = NULL           # Before
x <- NULL          # After

Commas ("commas")

Adds a space after each comma:

c(1,2,3)           # Before
c(1, 2, 3)         # After

Parentheses ("parens")

Removes unnecessary nested parentheses:

return((x))        # Before
return(x)          # After

Cleanup ("cleanup")

Multiple cleanup operations:

# Remove double comment separator lines
##########          # (removed if duplicated)

# Remove trailing whitespace
"hello "            # trailing space removed

# Remove multiple consecutive blank lines
                    # line 1
                    # line 2 (removed, only one blank line)

# Ensure single trailing newline at EOF

Simplify ("simplify")

Simplifies boolean expressions:

if(x == TRUE)       # Before:  if(x == TRUE)
if(x)               # After:   if(x)

if(x == FALSE)      # Before
if(!x)              # After

length(x) == 0      # Before
!length(x)          # After

length(x) > 0       # Before
isTRUE(x) == TRUE   # Before
isTRUE(x)           # After

Pipes ("pipes")

Converts %>% (magrittr pipe) to |> (base R native pipe):

x %>% f()           # Before
x |> f()            # After

Return ("return")

Fixes multi-line return() calls:

return(             # Before: multi-line
  x
)
return(x)           # After: one line

Assignment ("assignment")

Converts = to <- for assignment (outside function calls):

x = 5               # Before
x <- 5              # After

Comments ("comments")

Standardizes long comment separators:

##########          # Before
#----------         # After

Unused Variables ("unused_vars")

Detects and removes variable assignments that are never read within the same file:

unused_value <- 42  # Before: variable never used elsewhere
                     # After:  line removed

Uses conservative heuristics to avoid false positives: - Skips variables shorter than 3 characters - Skips common names (i, j, tmp, etc.) - Skips assignments from function calls (may have side effects) - Skips <<- super-assignments (visible elsewhere)

⚠️ Enabled in fixes = "all" — use with dry_run = TRUE first to review what would be removed.

Duplicate Libraries ("duplicate_libs")

Detects and removes duplicate library() calls loading the same package multiple times:

library(ggplot2)    # Before: first call (kept)
library(ggplot2)    # Before: duplicate (removed)
library(arrow)      # Before: different package (kept)

library(ggplot2)    # After:  only one call remains
library(arrow)

Report-only categories

These categories detect issues but do not modify files:

  • "library" — Detects library(x) calls that may be unused (also counts duplicates)
  • "namespace" — Suggests converting library(x) + f() to x::f()
  • "dead_code" — Detects expressions without effect (e.g. 1+1 standalone)

Selecting specific fixes 

# Only formatting + spacing
fix <- sonar_fix(".", fixes = c("styler", "spacing"))

# Only TRUE/FALSE + NULL + assignment
fix <- sonar_fix(".", fixes = c("true_false", "null", "assignment"))

Safety features

Dry-run mode (default)

dry_run = TRUE previews changes without modifying anything. The result shows which files would change and how many fixes of each type:

fix <- sonar_fix(".", dry_run = TRUE)
print(fix)

Backup

Use backup = TRUE to create .bak copies before modifying:

fix <- sonar_fix(".", backup = TRUE, dry_run = FALSE)

Parallel processing

Files are processed in parallel by default, using all available cores:

# Custom number of cores
fix <- sonar_fix(".", parallel = TRUE, n_cores = 4)

JSON report

A JSON report is generated by default:

sonar_fix(".", dry_run = TRUE, report = TRUE, report_file = "sonar-fixes.json")

Example output:

{
  "files": {
    "scanned": 42,
    "modified": 18
  },
  "fixes": {
    "styler": 205,
    "spacing": 81,
    "true_false": 9,
    "pipes": 5,
    "duplicate_libs": 1,
    "unused_vars": 3
  }
}

Integration with CI/CD

GitLab CI: auto-fix + Merge Request

In your .gitlab-ci.yml, after running sonar_analyse(), trigger sonar_fix() to auto-correct issues and open a Merge Request:

rsonar-fix:
  stage: fix
  when: manual
  script:
    - |
      R -q -e "
      library(rsonar)
      fix <- sonar_fix('.', dry_run = FALSE)
      
      # If there are changes, create a branch and merge request
      if (fix$files_modified > 0) {
        system2('git', c('checkout', '-b', 'auto/style'))
        system2('git', c('add', '.'))
        system2('git', c('commit', '-m', 'style: auto-fix R code'))
        system2('git', c('push', '-o', 'merge_request.create',
                         'origin', 'auto/style'))
      }
      "

GitHub Actions: auto-fix + Pull Request

Using the rsonar/fix action:

- uses: rsonar/fix@v1

Corrections NOT applied

The following are never auto-fixed and remain in sonar_analyse() for developer review:

  • Business logic changes
  • Renaming
  • Function removal
  • API changes
  • Type changes
  • Algorithm simplification
  • Cyclomatic complexity

Comparison: sonar_analyse() vs sonar_fix()

Aspect sonar_analyse() sonar_fix()
Read-only ✅ Yes ❌ Modifies files
Reported issues All Only safe auto-fixes
Default mode Analysis Dry-run preview
Pre-commit usage Check quality Auto-format code
CI usage Gate + Reports Auto-correct + MR/PR
Categories ~20 rule types 18 fix families

See also