Add: R (.r/.R) language support via bespoke extract_r

[Sirhan1]

Summary

This PR adds initial support for R (.r/.R) source files via a dedicated extract_r extractor, following the same approach used for Julia and Elixir.

The scope is intentionally limited to R source code structure and call relationships. Package metadata (DESCRIPTION, NAMESPACE, exports), package-qualified resolution, .Rmd support, and other R-specific semantics are intentionally deferred to a follow-up PR.

Why a dedicated extractor?

Unlike languages with named function declarations, R functions are typically anonymous functions assigned to variables:

foo <- function(x) {
    ...
}

Tree-sitter represents these as assignments containing anonymous function definitions rather than named declarations, making the generic extractor a poor fit. This follows the existing pattern used for other languages that require bespoke extractors.

What this PR adds

Parser integration

• Adds an optional r extra using tree-sitter-language-pack
• Registers .r, .R, and Rscript
• Integrates with the existing language dispatch system
• Preserves the existing missing-language warning (pip install "graphifyy[r]")

R extraction

The new extractor supports:

• Named functions created using all common assignment operators:
  • <-
  • <<-
  • =
  • ->
  • ->>
• Nested functions with the same ownership model used by other bespoke extractors
• Function calls attributed to the correct enclosing scope
• Cross-file call resolution via the existing shared resolver
• Detection of:
  • package-qualified calls (pkg::fn, pkg:::fn)
  • member-style calls ($, @)
  • pipe expressions (|>, %>%)

Nested function bodies are skipped while traversing an enclosing function to prevent double attribution.

Imports

Supports static detection of:

• library()
• require()
• requireNamespace()
• source("file.R")

source() imports are only created when the referenced file exists locally, matching Graphify's existing behaviour for Bash source.

Tests

Added:

• 4 fixture files
• 22 language tests covering dispatch, parsing, extraction, and optional dependency behaviour
• 2 new extraction tests plus updates to existing warning tests

The optional grammar follows the same testing pattern as the existing optional language parsers:

• Parser-dependent tests are skipped when the grammar isn't installed
• Missing-dependency tests remain network-free
• The test suite never downloads a parser automatically

The implementation was also verified on a synthetic multi-file R project covering common R idioms, including nested functions, pipes, package-qualified calls, cross-file resolution, and ambiguous definitions.

Results

• ✅ R-specific tests: 22/22
• ✅ Updated extraction tests: 13/13
• ✅ Full test suite: 3250 passed, 3 skipped
• ✅ ruff check
• ✅ pyright
• ✅ Local graph regenerated with graphify update .

Out of scope

The following are intentionally deferred to a future PR:

• DESCRIPTION / NAMESPACE parsing
• Exported symbol modelling
• Package-qualified call resolution
• .Rmd extraction
• S3/S4/R6 support
• Non-standard evaluation (NSE)
• renv.lock integration