Restore debugging feature #165

jrwishart · 2024-06-29T06:46:12Z

Allow line highlighting in source buffer during browser and debug calls
of functions.

Allow line highlighting in source buffer during browser and debug calls of functions.

jrwishart · 2024-06-29T06:52:29Z

Apologies for the delay. Full time work was prioritised until this weekend. I removed some code paths that looked like it was unsupported tmux.

PMassicotte · 2024-06-29T10:46:43Z

Thank you for this PR!

I am testing it on my end, and while it appears to enter debug mode, I do not see any visual indication (e.g., line highlighting) of the debug process.

jrwishart · 2024-06-29T11:53:42Z

Thanks for the quick feedback.

Admittedly, I have never tried to debug a function sourced inline into the global environment. I have been doing it solely from a loaded package for package development. e.g. via devtools::load_all().

It works fine when functions are loaded (see video).

debug1080.mov

I can reproduce the same behaviour you have that the functions sourced inline in the console will not trigger the visual highlighting debug/browser.

jrwishart · 2024-06-29T11:58:01Z

Might be related to #147. Perhaps nvimcom doesn't search functions that are sourced into the global env for the debug lines there?

jrwishart · 2024-06-29T11:58:59Z

Just saw the CI checks failing. I'll see if I can fix those

jrwishart · 2024-06-29T12:15:18Z

doc/R.nvim.txt

+Another limitation of R-Nvim is that it might be unable to jump to the line in
+the source code that is being evaluated if either you have sent the function
+directly to the R Console or the function has been sent by the `knitr`
+package, without calling the function `source()`. In either case, R-Nvim will
+try to find the pattern `funcname <- function(` in the buffer being edited. If
+the pattern is found, the cursor will jump to its position.


Seems like it was already a known implementation? (I didn't write the documentation in this PR, I am merely restoring it from the previous state).

I just tried sourcing the function in a file using the source function and I get the same behaviour (no highlighting). So perhaps the documentation could be updated to reflect that loading functions into the environment via devtools will work but not using source?

If I understand correctly, debugging will only work when sourcing a package with devtools.

PMassicotte · 2024-06-29T12:23:33Z

PMassicotte · 2024-06-29T13:16:12Z

I am trying with a package, and still can not get it working. Any ideas?

PMassicotte · 2024-06-29T13:18:50Z

Maybe because I am using an external terminal?

jalvesaq · 2024-06-29T13:53:02Z

Some notes:

I have never used devtools. I only install it when someone reports a bug that requires it to be installed.
When using the debugging feature, I manually sourced the file with the function I wanted to debug. This way, R knew where the function was from.
The terminal emulator should not affect the process because nvimcom reads the R prompt (which indicates the debugging mode) directly from R's memory.

jrwishart · 2024-06-29T21:44:15Z

lua/r/debug.lua

+    local rlines
+    local can_debug = type(config.external_term) == "boolean" and not config.external_term
+    if not can_debug then return end
+
+    s.func_offset = -1 -- Not found
+    local sbopt = vim.o.switchbuf
+    vim.o.switchbuf = "useopen,usetab"
+    local curtab = vim.fn.tabpagenr()
+    local isnormal = vim.fn.mode() == "n"
+    local curwin = vim.fn.winnr()
+    r_bufnr = vim.api.nvim_get_current_buf()
+    vim.cmd("sb " .. r_bufnr)
+    vim.fn.sleep(30) -- Time to fill the buffer lines
+    rlines = vim.fn.getline(1, "$")


In this PR, the debug code only finds rlines (The R source lines I believe) if there is no external_term in the config.

There was vimscript code that defined rlines when debugging with tmux and I could look to convert it. That code is here.

R.nvim/R/start_r.vim

Lines 97 to 102 in 5b55186

elseif string(g:SendCmdToR) == "function('SendCmdToR_Term')"

let tout = system('tmux -L NvimR capture-pane -p -t ' . g:rplugin.tmuxsname)

let rlines = split(tout, "\n")

elseif string(g:SendCmdToR) == "function('SendCmdToR_TmuxSplit')"

let tout = system('tmux capture-pane -p -t ' . g:rplugin.rconsole_pane)

let rlines = split(tout, "\n")

I searched the commit history last week but couldn't determine what the proper way to do this in the lua plugin. As such I removed it. I mentioned it in the initial comment that I removed some code paths that looked like unsupported tmux.

Be happy to be advised on how to fix.

At this point, it's better to no longer look at Nvim-R code. What has to be done is relatively simple:

When beginning the debugging, load the file where the code is or jump to it if it's already open (this is already done in the specific case that I fixed) and store the buffer number (not done yet).

From the second jump onward, move the cursor without switching to its buffer (this will be different from Nvim-R).

jalvesaq · 2024-06-29T22:22:34Z

I'm trying to fix the pull request...

…uns in a external terminal emulator - Replace R-Nvim with `R.nvim` in the documentation. - Rename `M.stop_r_debugging` as `M.stop`. - Rename `M.find_debug_func` as `local find_func`. - Rename `M.r_debug_jump` as `M.jump`. - Fix bugs.

jalvesaq · 2024-06-29T22:54:10Z

It's fixed on my side if R is running in an external terminal emulator and the function being debugged is in another script which was read with the source() command. Here's how to try it:

Uninstall nvimcom:

echo 'remove.packages("nvimcom")' | R

Then, follow the instructions from the documentation:

For example, if you have a file named my_function.R with the following contents:

add.one <- function(x) {
    y <- x + 1
    print(y)
    return(invisible(NULL))
}

You could debug the add.one() function from another script such as:

source("path/to/my_function.R")
debug(add.one)
add.one(7)

jalvesaq · 2024-06-29T23:06:48Z

I removed "r" and "debug" from the names of Lua functions because the information that the function is related to debugging R functions is already present in the module name, "r.debug".

jrwishart · 2024-06-29T23:43:33Z

Thanks for the quick update. I can confirm that it works for source now too 👍

I took the liberty to update the documentation to show the devtools approach. The only loose end is the last commit you made seems to have broken the cursor staying in the R console. Previously I could stay in the R console while debugging but now it is staying in the highlighted source line on every step requiring manually switching cursor to the R console each time.

debug_buf_switch.mov

jalvesaq · 2024-06-30T00:24:38Z

The only loose end is the last commit you made seems to have broken the cursor staying in the R console.

I can look at this on the next weekend. I think the solution will be to implement steps 1 and 2 from my previous comment.

PMassicotte · 2024-06-30T10:45:47Z

No luck on my side.

jalvesaq · 2024-06-30T11:06:20Z

Try an R script with these lines:

source("debug.R")
debug(addone)
addone(1)

In its current buggy state, it only works if the function is in another script which still has to be open.

PMassicotte · 2024-06-30T12:17:20Z

Same thing, nothing happens.

jalvesaq · 2024-06-30T12:26:37Z

It only works if R is running in an external terminal emulator or a Tmux split pane because the code to open and switch buffers is yet to be fixed.

jalvesaq · 2024-06-30T16:09:10Z

@jrwishart, please, see #166 as an alternative to this pull request...

- Update README (remove reference to no implementation of the debugging feature). - Fix spelling of `debug_jump` option in `doc/R.nvim.txt`. - Fix jumps form a buffer to another. - Use `R_GetSrcFilename()` to simplify `nvimcom.c` code.

jalvesaq · 2024-06-30T23:10:28Z

I found some time today and fixed the bugs I knew existed. Of course, instead of merging this pull request, it would be better to have a real DAP plugin.

jrwishart · 2024-07-01T06:19:02Z

Thanks for the speedy reply/fix.

I agree that having dap would be preferable but it doesn't exist in a working state at the moment. (Happy to be proved otherwise)

jrwishart · 2024-07-01T08:02:10Z

The last commit fixed the cursor position but seems to have introduced a new bug where it doesn't find the correct line if debug or browser is called from another function in a different file. E.g. in the video, bar calls hi, bar is in foo.R and hi is in qux.R and it gets the wrong line match for hi if it is a nested browser/debug call.

jump_480.mov

PMassicotte · 2024-07-04T11:22:35Z

It works on my side if I do srouce + debug(fun) in the terminal and then call the function. Should it works also if I place a browser() somewhere in a script and then use the send all lines to the terminal?

jalvesaq · 2024-07-04T11:41:26Z

Thanks for catching this! It should work now.

jalvesaq · 2024-07-04T11:50:52Z

When we source() a script, R knows where a function comes from and this information is available for us in an internal variable that can be accessed from C. When we send the function directly to R Console, R doesn't know where the function comes from. Then, we have to get the contents of R Console and look for the string "^debugging in: " or "Called from: ", extract the function name, and seek for it in the R script currently being edited.

So, the debugging will not work if you send a function directly to the R Console and switch to another buffer before starting to debug the function.

jalvesaq · 2024-07-04T11:57:00Z

There is still one possible improvement. When debugging a function from an installed package or a function sent directly to the R Console from another R script, the source code isn't available, but the whole function is printed in the R Console, and we could copy it from there and paste it in a new temporary R script. However, before investing time in doing this, let's see if the DAP works...

PMassicotte · 2024-07-04T12:12:51Z

When we source() a script, R knows where a function comes from and this information is available for us in an internal variable that can be accessed from C. When we send the function directly to R Console, R doesn't know where the function comes from. Then, we have to get the contents of R Console and look for the string "^debugging in: " or "Called from: ", extract the function name, and seek for it in the R script currently being edited.

So, the debugging will not work if you send a function directly to the R Console and switch to another buffer before starting to debug the function.

Great this is working if I create a script like this:

addone <- function(x) {
  x + 1
}


browser()
addone(10)

and then source() it from the console.

wurli · 2024-07-07T21:22:14Z

Hi all, I've only been somewhat following this thread because I very rarely use R's debugger. But just want to throw this out there in case it's relevant - the guys at Posit are working on a DAP server/LSP server for R called Ark. It's not yet usable by other software than their new Positron IDE, but the README says it will be soon.

jalvesaq · 2024-07-07T22:36:58Z

Thanks for the news, @wurli! This is another reason for not merging this pull request, but we can keep it open until either Ark or debugadapter is ready to be used in Neovim.

akthe-at · 2024-08-13T18:03:49Z

@wurli @jalvesaq It looks like the Ark project is moving along and is starting to be usable outside of positron (Jupyter)...Very exciting times

jalvesaq · 2025-02-17T12:30:51Z

Ark is still usable only by Positron.

https://codeberg.org/dgkf/debugadapter still says "Currently, nothing will happen" when "debugging".

Do we have other options? Should we keep waiting or merge this pull request?

PMassicotte · 2025-02-17T12:40:21Z

Have you been able to test it? Could be nice to have it rather than nothing. Maybe switch later when something else is ready.

jalvesaq · 2025-02-17T12:48:30Z

I'm resolving the conflicts...

jalvesaq · 2025-02-17T13:24:49Z

I fixed the conflicts in Github's online editor.

PMassicotte · 2025-02-17T13:25:41Z

Ok I will test it.

PMassicotte · 2025-02-17T13:34:46Z

Using this as testing code:

addone <- function(x) {
  browser()

  x + 1L

  z <- x / 42L
}


addone(10L)

for (x in 1L:3L) {
  print(x)
}

If I go in the console and type source("file.R"), it works.

However, I use <localleader>ae I get these errors:

Vim(lua):E5108: Error executing lua /media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/debug.lua:56: attempt to call field 'system
' (a nil value)                                                                                                            
stack traceback:                                                                                                           
        /media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/debug.lua:56: in function 'find_func'                                  
        /media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/debug.lua:152: in function 'jump'                                      
        [string ":lua"]:1: in main chunk                                                                                   
        [C]: in function 'execute'                                                                                         
        /media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/job.lua:48: in function 'exec_stdout_cmd'                              
        /media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/job.lua:69: in function </media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/jo
b.lua:58>                                                                                                                  
stack traceback:                                                                                                           
        [C]: in function 'execute'                                                                                         
        /media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/job.lua:48: in function 'exec_stdout_cmd'                              
        /media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/job.lua:69: in function </media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/jo
b.lua:58>                                                                                                                  
Vim(lua):E5108: Error executing lua /media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/debug.lua:56: attempt to call field 'system
' (a nil value)                                                                                                            
stack traceback:                                                                                                           
        /media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/debug.lua:56: in function 'find_func'                                  
        /media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/debug.lua:152: in function 'jump'                                      
        [string ":lua"]:1: in main chunk                                                                                   
        [C]: in function 'execute'                                                                                         
        /media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/job.lua:48: in function 'exec_stdout_cmd'                              
        /media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/job.lua:69: in function </media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/jo
b.lua:58>                                                                                                                  
stack traceback:                                                                                                           
        [C]: in function 'execute'                                                                                         
        /media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/job.lua:48: in function 'exec_stdout_cmd'                              
        /media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/job.lua:69: in function </media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/jo
b.lua:58> function: builtin#18 Vim(lua):E5108: Error executing lua /media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/debug.lua:56
: attempt to call field 'system' (a nil value)                                                                             
stack traceback:                                                                                                           
        /media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/debug.lua:56: in function 'find_func'                                  
        /media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/debug.lua:152: in function 'jump'                                      
        [string ":lua"]:1: in main chunk                                                                                   
        [C]: in function 'execute'                                                                                         
        /media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/job.lua:48: in function 'exec_stdout_cmd'                              
        /media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/job.lua:69: in function </media/LaCie16TB/work/dev/nvim/R.nvim/lua/r/jo
b.lua:58>

jalvesaq · 2025-02-17T13:40:53Z

Fixed: utils.system() replaced with vim.system()

PMassicotte · 2025-02-17T13:37:15Z

lua/r/debug.lua

+            "-t",
+            require("r.external_term").get_tmuxsname(),
+        }
+        local resp = require("r.utils").system(run_cmd, { text = true }):wait()


This is the faulty line when trying to source a file that includes a browser() call.

doc/R.nvim.txt

PMassicotte · 2025-02-17T13:51:41Z

Thanks, fixed small error on keymaping and added a sentence.

Co-authored-by: Philippe Massicotte <[email protected]>

PMassicotte · 2025-02-17T14:11:00Z

Thank you and thanks to @jrwishart for this work.

* Restore debugging feature * Update documentation to mention devtools approach Co-authored-by: Jakson Alves de Aquino <[email protected]> Co-authored-by: Philippe Massicotte <[email protected]>

Restore debugging feature

3646aa5

Allow line highlighting in source buffer during browser and debug calls of functions.

Remove force debugging options set during development

b22e237

Fix issues found by CI

46e72a8

jrwishart commented Jun 29, 2024

View reviewed changes

Update documentation to mention devtools approach

3a4c929

Bug fixes:

d613aba

- Update README (remove reference to no implementation of the debugging feature). - Fix spelling of `debug_jump` option in `doc/R.nvim.txt`. - Fix jumps form a buffer to another. - Use `R_GetSrcFilename()` to simplify `nvimcom.c` code.

Also check for "Called from:"

a6b91b5

jalvesaq added 2 commits July 7, 2024 12:15

Improve buffer switching

94c1705

Merge branch 'main' into restore_debug

510f5d7

jalvesaq added 2 commits February 17, 2025 09:55

Merge branch 'main' into restore_debug

e4e77d5

Increase nvimcom version and make adjustments in R.nvim

266474f

Update the code (fix bug "system is nil")

8448b4d

Fix check of config.external_term

beab05b

PMassicotte reviewed Feb 17, 2025

View reviewed changes

jalvesaq and others added 3 commits February 17, 2025 10:59

Check for error in vim.system()

3f73ed2

Update doc/R.nvim.txt

a79f34d

Co-authored-by: Philippe Massicotte <[email protected]>

Update doc/R.nvim.txt

88d4ad0

Co-authored-by: Philippe Massicotte <[email protected]>

PMassicotte merged commit 2f4b931 into R-nvim:main Feb 17, 2025
1 check passed

	elseif string(g:SendCmdToR) == "function('SendCmdToR_Term')"
	let tout = system('tmux -L NvimR capture-pane -p -t ' . g:rplugin.tmuxsname)
	let rlines = split(tout, "\n")
	elseif string(g:SendCmdToR) == "function('SendCmdToR_TmuxSplit')"
	let tout = system('tmux capture-pane -p -t ' . g:rplugin.rconsole_pane)
	let rlines = split(tout, "\n")

Restore debugging feature #165

Restore debugging feature #165

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