LSP: implementing goto defitnition/reference/implementation #482

PMassicotte · 2026-01-06T14:47:16Z

This is a first draft of a goto definition/reference based on the LSP internal framework developed in 9f21d6c.

Features

Goto Definition (textDocument/definition)

Scope-aware symbol resolution (respects R's lexical scoping rules)
Workspace-wide search across all R files (.R, .Rmd, .qmd)
Package source lookup via nvimcom (jumps to source files or deparsed functions)
Qualified name support (pkg::fn and pkg:::fn)
Handles both standard (<-, =) and super-assignment (<<-) operators

Find References (textDocument/references)

Scope-aware reference finding (only finds usages that resolve to the same definition)
Distinguishes between public (file-level) and private (function-level) symbols
Cross-file reference search for public symbols

Implementation Details

Symbol extraction uses Tree-sitter queries (locals.scm and custom queries)
Workspace indexing with file modification tracking for cache invalidation
R-side resolution via nvimcom:::send_definition() for package functions
Falls back to deparsed source when original source files aren't available

Testing

To test, create this R file with this content:

# Test: gd (definition), gr (references), gi (implementation)

# File-level (public) function
add <- function(a, b) a + b

# Scoping: inner 'x' shadows outer 'x'
outer <- function(x) {
    inner <- function(x) x * 2
    inner(x) + x
}

# Super-assignment (<<-)
make_counter <- function() {
    count <<- 0
    function() count <<- count + 1
}

# Usage (references), use goto definition on these
x <- add(1, 2)
y <- add(x, 3)

# Qualified names (package lookup), use goto definition on these
dplyr::filter()
stats::lm()

# --- Implementation (S3) ---

greet <- function(x) UseMethod("greet")
greet.dog <- function(x) "Woof!"
greet.cat <- function(x) "Meow!"

To test, use lsp keymap directly, or these following lua commands:

:lua vim.lsp.buf.definition()
:lua vim.lsp.buf.references()
:lua vim.lsp.buf.implementation()

Todos

Goto definition on package function is slow the first time you use it
Implement rename functionality. The current infrastructure will allow doing it very easily. We will have to think a bit more about the scoping. For example, renaming a function parameter should only rename it within the function body or renaming a file-level function should rename all its references across the workspace?
Add tests, especially for edge cases like nested functions, anonymous functions, etc.
Add documentation
Use workspace markers to limit the search scope for references?
Remove debug_index() before merging (see also other helper functions)

Add configuration options to let the user to enable/disable these lsp features. Reuse

r_ls = {
    completion = true, -- enable the completion provider
    hover = true, -- enable the hover provider
    signature = true, -- enable the signature help provider
    implementation = true, -- enable the implementation provider
    definition = true, -- enable the goto definition provider
    references = true, -- enable the find references provider
    doc_width = 0,
    fun_data_1 = { "select", "rename", "mutate", "filter" },
    fun_data_2 = { ggplot = { "aes" }, with = { "*" } },
    fun_data_formula = { ggplot = { "facet_wrap", "facet_grid", "vars" } },
    quarto_intel = nil,
}

Basic version of goto-definition. Some speed improvement can be done on package function where we create a temp file to see its source.

…l in queries module This change improves code maintainability and readability by removing redundant query definitions.

…on and definition finding logic for better maintainability feat(lsp/definition.lua): enhance definition search to include enclosing scopes and improve accuracy of symbol resolution refactor(definition.lua): streamline definition search logic and improve code clarity by removing unused functions and comments fix(lsp/init.lua): update require paths for document_symbols and rebuild_index functions to reflect correct module structure feat(workspace.lua): add debug_index function to display workspace index state for easier debugging and verification of indexed symbols

…emoving custom query for enclosing scopes feat(scope.lua): enhance symbol definition lookup with custom query for <<- assignments and improve function signature for better clarity refactor(scope.lua): rename find_definition_in_scope to include cursor position parameters for more precise searching and maintainability

…ee-sitter for better accuracy and robustness fix(lsp/definition.lua): update goto_definition function to handle symbol parsing and response sending more efficiently

jalvesaq · 2026-01-20T11:15:10Z

What is the status of this pull request? I tried the branch, and I can jump to references and definitions, even if the functions are defined in other R scripts. It's a great job so far! And, with more than 2500 lines of code, it certainly has taken a lot of your time. Thank you!

When starting nvim, I get this warning:

  Invalid option `r_ls.references`.
  Invalid option `r_ls.definition`.
  Invalid option `r_ls.implementation`.

Jumping to implementation doesn't work, but it also doesn't work in Lua or C.

PMassicotte · 2026-01-20T12:19:01Z

Thanks for pointing it out for the warnings. These are option to op in/out of the implementation (in case someone would prefer to use r_languageserver).

My plan is to finish this PR by the end of the week or this weekend ;)

For the implementation, it should go to the s3 implementation. I will post an example here when I am back home this afternoon.

…ders to the configuration

…he top level feat(utils.lua): add top_level_only option to extract_symbols for filtering symbols at the top level only

… list, used to build symbol tree to display document symbols

…res with languageserver package Add new options to disable definition, references, and implementation providers in the languageserver package. Update R.nvim config defaults to include these new providers.

Copilot

Pull request overview

This PR implements LSP goto definition, find references, and find implementations functionality for R.nvim. It builds on the existing LSP framework to provide scope-aware symbol resolution, workspace-wide search capabilities, and package source lookup.

Changes:

Added scope-aware symbol resolution using tree-sitter queries and lexical scoping rules
Implemented workspace indexing with file modification tracking for cross-file navigation
Added LSP handlers for textDocument/definition, textDocument/references, textDocument/implementation, and textDocument/documentSymbol

Reviewed changes

Copilot reviewed 20 out of 21 changed files in this pull request and generated 29 comments.

Show a summary per file

File	Description
tests/test_scope_spec.lua	Comprehensive tests for scope resolution and symbol visibility
tests/test_goto_definition_spec.lua	Tests for goto definition with scope awareness
tests/test_helper.lua	Test helper for tree-sitter parser setup
nvimcom/src/apps/tcp.c	Message parsing handlers for definition responses from R
nvimcom/src/apps/rnvimserver.c	LSP request handlers and response builders for new features
nvimcom/bin/rnvimserver	Compiled binary (should not be committed)
nvimcom/R/info.R	R-side definition lookup with package source resolution
lua/r/server.lua	Configuration integration for new LSP features
lua/r/lsp/workspace.lua	Workspace-wide symbol indexing and caching
lua/r/lsp/utils.lua	Shared utilities for symbol extraction and file operations
lua/r/lsp/symbols.lua	Document symbol extraction with hierarchical tree building
lua/r/lsp/scope.lua	Scope management using tree-sitter locals queries
lua/r/lsp/references.lua	Scope-aware reference finding across workspace
lua/r/lsp/queries.lua	Centralized tree-sitter query management
lua/r/lsp/init.lua	Integration points for new LSP features
lua/r/lsp/implementation.lua	S3/S4 method implementation finding
lua/r/lsp/definition.lua	Goto definition with workspace and package lookup
lua/r/lsp/buffer.lua	Buffer management for parsing external files
lua/r/lsp/ast.lua	AST traversal utilities extracted from init.lua
lua/r/config.lua	Configuration options for new LSP features
doc/R.nvim.txt	Documentation for new LSP features and configuration

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

doc/R.nvim.txt

Copilot · 2026-01-25T14:27:02Z

lua/r/lsp/workspace.lua

+function M.index_workspace(force)
+    if indexed and not force then return end
+
+    local cwd = vim.fn.getcwd()
+    local files = {}
+    utils.find_r_files(cwd, files)
+
+    workspace_index = {}
+    file_mtimes = {}
+
+    for _, filepath in ipairs(files) do
+        local stat = vim.uv.fs_stat(filepath)
+        if stat then
+            file_mtimes[filepath] = stat.mtime.sec
+
+            local definitions = utils.parse_file_definitions(filepath)
+            for symbol, locations in pairs(definitions) do
+                if not workspace_index[symbol] then workspace_index[symbol] = {} end
+                for _, loc in ipairs(locations) do
+                    table.insert(workspace_index[symbol], loc)
+                end
+            end
+        end
+    end
+
+    indexed = true
+end


Workspace indexing happens synchronously on first call without user feedback. The index_workspace() function (line 21) scans all R files in the workspace, which could be slow for large projects. This happens during the first LSP operation (goto definition, references, etc.), potentially causing unexpected lag. Consider adding a progress notification or making the initial indexing asynchronous.

nvimcom/src/apps/rnvimserver.c

Copilot · 2026-01-25T14:27:03Z

nvimcom/R/info.R

+        # Check if cached file already exists
+        if (!file.exists(tmpfile)) {
+            header <- sprintf(
+                "# %s::%s (no source available - deparsed)",
+                pkg_name,
+                symbol
+            )
+            body <- deparse(fn)
+            writeLines(c(header, "", body), tmpfile)
+        }


Potential race condition in file-based caching. Line 178 checks if the tmpfile exists, and if not, creates it (lines 179-186). However, in a concurrent environment (e.g., multiple Neovim instances), two processes could both find that the file doesn't exist and try to create it simultaneously, leading to corruption or undefined behavior. Consider using atomic file operations or file locking.

Suggested change

# Check if cached file already exists

if (!file.exists(tmpfile)) {

header <- sprintf(

"# %s::%s (no source available - deparsed)",

pkg_name,

symbol

)

body <- deparse(fn)

writeLines(c(header, "", body), tmpfile)

}

# Always (re)generate the deparsed cache file to avoid race conditions

header <- sprintf(

"# %s::%s (no source available - deparsed)",

pkg_name,

symbol

)

body <- deparse(fn)

writeLines(c(header, "", body), tmpfile)

lua/r/lsp/definition.lua

lua/r/server.lua

lua/r/lsp/utils.lua

nvimcom/src/apps/rnvimserver.c

Copilot · 2026-01-25T14:27:10Z

lua/r/lsp/references.lua

+        for _, filepath in ipairs(files) do
+            if utils.normalize_path(filepath) ~= utils.normalize_path(file) then
+                local temp_bufnr, _, cleanup = buffer.load_file_to_buffer(filepath)
+
+                if temp_bufnr then
+                    local _, temp_root = ast.get_parser_and_root(temp_bufnr)
+
+                    if temp_root then
+                        for _, node in query:iter_captures(temp_root, temp_bufnr) do
+                            local text = vim.treesitter.get_node_text(node, temp_bufnr)
+                            if text == word then
+                                local in_function = ast.find_ancestor(
+                                    node,
+                                    "function_definition"
+                                )
+                                if not in_function then
+                                    local start_row, start_col = node:start()
+                                    table.insert(all_refs, {
+                                        file = filepath,
+                                        line = start_row,
+                                        col = start_col,
+                                    })
+                                end
+                            end
+                        end
+                    end
+
+                    if cleanup then cleanup() end
+                end
+            end
+        end


Potential performance issue with nested loops. In the worst case, for each file in the workspace (outer loop at line 159), we iterate through all captures from the query (inner loop at line 167). For a workspace with many files and many references per file, this could be O(n*m) where n is number of files and m is captures per file. Consider adding early termination or limiting the search scope.

Copilot · 2026-01-25T14:27:10Z

lua/r/lsp/implementation.lua

+--- Find implementations for R.nvim LSP
+--- Provides textDocument/implementation functionality for S3/S4 methods
+
+local M = {}
+
+local workspace = require("r.lsp.workspace")
+local utils = require("r.lsp.utils")
+
+--- Find S3 method implementations for a generic function
+---@param word string The generic function name
+---@return table[] List of locations {file, line, col}
+local function find_s3_methods(word)
+    -- Pattern: word.* (e.g., print.default, print.factor)
+    local pattern = "^" .. vim.pesc(word) .. "%."
+    return workspace.find_symbols_matching(pattern)
+end
+
+--- Find implementations of a generic function (S3/S4 methods)
+---@param req_id string LSP request ID
+function M.find_implementations(req_id)
+    local word, err = utils.get_keyword_safe()
+    if err or not word then
+        utils.send_null(req_id)
+        return
+    end
+
+    utils.prepare_workspace()
+
+    local implementations = find_s3_methods(word)
+
+    -- Strategy 2: Dynamic lookup via nvimcom (if R is running)
+    -- TODO: Implement async R query for runtime method discovery
+    -- if vim.g.R_Nvim_status == 7 then
+    --     local cmd = string.format(
+    --         "nvimcom:::send_implementations('%s', '%s')",
+    --         req_id, word
+    --     )
+    --     require("r.run").send_to_nvimcom("E", cmd)
+    --     return
+    -- end
+
+    -- Return static results
+    if #implementations > 0 then
+        utils.send_response("I", req_id, { locations = implementations })
+    else
+        utils.send_null(req_id)
+    end
+end
+
+return M


Missing test coverage for the find_implementations functionality. The implementation.lua module (which implements textDocument/implementation for S3/S4 methods) lacks tests. This is particularly important given that S3/S4 method resolution has complex edge cases and the pattern-based matching could have subtle bugs that wouldn't be caught without tests.

Co-authored-by: Copilot <[email protected]>

Copilot · 2026-01-25T14:30:22Z

@PMassicotte I've opened a new pull request, #493, to work on those changes. Once the pull request is ready, I'll request review from you.

Co-authored-by: Copilot <[email protected]>

Copilot · 2026-01-25T14:34:26Z

@PMassicotte I've opened a new pull request, #494, to work on those changes. Once the pull request is ready, I'll request review from you.

* Initial plan * refactor: consolidate location-based LSP response functions into single parameterized function Co-authored-by: PMassicotte <[email protected]> * Final update: refactoring complete and validated Co-authored-by: PMassicotte <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: PMassicotte <[email protected]>

* Initial plan * Remove debug logging statements from send_implementation_result Co-authored-by: PMassicotte <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: PMassicotte <[email protected]> Co-authored-by: Philippe Massicotte <[email protected]>

Co-authored-by: Copilot <[email protected]>

PMassicotte added 6 commits January 4, 2026 14:56

First version of goto-definition

2069498

Basic version of goto-definition. Some speed improvement can be done on package function where we create a temp file to see its source.

Removing lint warnings/errors

583403e

refactor(lsp): simplify query handling by centralizing query retrieva…

fbcbd3b

…l in queries module This change improves code maintainability and readability by removing redundant query definitions.

refactor(lsp/definition.lua): improve qualified name parsing using tr…

abe1708

…ee-sitter for better accuracy and robustness fix(lsp/definition.lua): update goto_definition function to handle symbol parsing and response sending more efficiently

PMassicotte force-pushed the lsp-goto-definition branch from 4c5f7b4 to abe1708 Compare January 6, 2026 14:51

PMassicotte changed the title ~~LSP: implementing goto defitnition and reference~~ LSP: implementing goto defitnition/reference/implementation Jan 6, 2026

jalvesaq mentioned this pull request Jan 8, 2026

Rnvim fails to initiate #483

Closed

PMassicotte force-pushed the lsp-goto-definition branch from 0aa8c14 to abe1708 Compare January 19, 2026 23:09

PMassicotte added 6 commits January 20, 2026 07:28

feat(config.lua, server.lua): add references and implementation provi…

40b019a

…ders to the configuration

feat(utils.lua): add is_top_level function to check if a node is at t…

ca4bbc6

…he top level feat(utils.lua): add top_level_only option to extract_symbols for filtering symbols at the top level only

Add tests

6408f52

add functions to convert and build hierarchical symbol tree from flat…

4b1f419

… list, used to build symbol tree to display document symbols

docs(R.nvim.txt): update instructions for disabling overlapping featu…

c7d40c8

…res with languageserver package Add new options to disable definition, references, and implementation providers in the languageserver package. Update R.nvim config defaults to include these new providers.

Merge branch 'main' into lsp-goto-definition

344facd

PMassicotte requested a review from Copilot January 25, 2026 14:18

Copilot started reviewing on behalf of PMassicotte January 25, 2026 14:18 View session

Copilot AI reviewed Jan 25, 2026

View reviewed changes

Update doc/R.nvim.txt

7dfec08

Co-authored-by: Copilot <[email protected]>

Copilot AI mentioned this pull request Jan 25, 2026

Refactor duplicated location-based LSP response handlers #493

Merged

PMassicotte and others added 2 commits January 25, 2026 09:31

Update lua/r/lsp/definition.lua

88cecb4

Co-authored-by: Copilot <[email protected]>

Update lua/r/lsp/utils.lua

91acf98

Co-authored-by: Copilot <[email protected]>

Copilot AI mentioned this pull request Jan 25, 2026

Remove debug logging from send_implementation_result #494

Merged

Copilot AI and others added 2 commits January 25, 2026 09:36

PMassicotte and others added 2 commits January 25, 2026 13:45

improve shadowing resolution

0989953

Update lua/r/server.lua

20da2e5

Co-authored-by: Copilot <[email protected]>

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

LSP: implementing goto defitnition/reference/implementation #482

LSP: implementing goto defitnition/reference/implementation #482

Uh oh!

PMassicotte commented Jan 6, 2026 •

edited

Loading

Uh oh!

jalvesaq commented Jan 20, 2026

Uh oh!

PMassicotte commented Jan 20, 2026 •

edited

Loading

Uh oh!

Copilot AI left a comment

Uh oh!

Uh oh!

Copilot AI Jan 25, 2026

Uh oh!

Uh oh!

Copilot AI Jan 25, 2026

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Copilot AI Jan 25, 2026

Uh oh!

Copilot AI Jan 25, 2026

Uh oh!

Copilot AI commented Jan 25, 2026

Uh oh!

Copilot AI commented Jan 25, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

LSP: implementing goto defitnition/reference/implementation #482

Are you sure you want to change the base?

LSP: implementing goto defitnition/reference/implementation #482

Uh oh!

Conversation

PMassicotte commented Jan 6, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Features

Testing

Todos

Uh oh!

jalvesaq commented Jan 20, 2026

Uh oh!

PMassicotte commented Jan 20, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Reviewed changes

Uh oh!

Uh oh!

Copilot AI Jan 25, 2026

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Copilot AI Jan 25, 2026

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Copilot AI Jan 25, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 25, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI commented Jan 25, 2026

Uh oh!

Copilot AI commented Jan 25, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

PMassicotte commented Jan 6, 2026 •

edited

Loading

PMassicotte commented Jan 20, 2026 •

edited

Loading