Feature : Enable LLDB Debugging for R Dev Container #260

avinab-neogy · 2025-07-30T11:29:18Z

Added lldb debugging functionality

Closes #196 and #30

hturner

I think you are still missing an update to which_r. This script should manage switching between different versions of R and update any places where the path to the R version that should be used in R terminals is hard-coded.

At the moment which_r edits both r.term.linux and r.path.linux

r-dev-env/scripts/which_r.sh

Lines 63 to 64 in 46b8b6c

    
           updated_settings_data=$(cat "$settings_file_path" | jq --arg subdir "$selected_version" '."r.rterm.linux"=$subdir | ."r.rpath.linux"=$subdir') 
        
           echo "$updated_settings_data" > "$settings_file_path"

Now we are using launch.sh, r.rterm.linux should always stay the same (with r.rpath.linux updated as before), but there are other parts of the code that which_r should change. In particular, I think it should update launch.sh.

hturner · 2025-07-30T17:15:04Z

.devcontainer/devcontainer.json

+                "r.rterm.linux": "/workspaces/r-dev-env/scripts/launch_r.sh",
+                "r.rpath.linux": "/workspaces/r-dev-env/build/r-devel/bin/R",


r.rpath.linux should be /usr/bin/R here as this is the only version of R that exists to begin with.

Suggested change

"r.rterm.linux": "/workspaces/r-dev-env/scripts/launch_r.sh",

"r.rpath.linux": "/workspaces/r-dev-env/build/r-devel/bin/R",

"r.rterm.linux": "/workspaces/r-dev-env/scripts/launch_r.sh",

"r.rpath.linux": "/usr/bin/R",

hturner · 2025-07-30T17:16:09Z

.devcontainer/devcontainer.json

        }
    },
-    "postCreateCommand": "find . -wholename '*.git*'  -type d -prune -o -type f -exec chown vscode:vscode {} \\; && sh /workspaces/r-dev-env/scripts/localscript.sh"
+    "postCreateCommand": "find . -wholename '.git*' -type d -prune -o -type f -exec chown vscode:vscode {} \\; && \\\n  gcc -shared -fPIC -o /workspaces/r-dev-env/scripts/allow_ptrace.so /workspaces/r-dev-env/scripts/allow_ptrace.c && \\\n  chmod +x /workspaces/r-dev-env/scripts/launch_r.sh && \\\n  sh /workspaces/r-dev-env/scripts/localscript.sh"


It is a good idea to compile allow_ptrace.c and change permissions on launch_r.sh as part of the setup. But we should avoid hard-coding the paths as much as possible as the root is different on GitPod and will be different if someone clones the repo to a folder named something other than r-dev-env. I would try to do these steps as part of localscript.sh and then use a relative path:

Suggested change

"postCreateCommand": "find . -wholename '.git*' -type d -prune -o -type f -exec chown vscode:vscode {} \\; && \\\n gcc -shared -fPIC -o /workspaces/r-dev-env/scripts/allow_ptrace.so /workspaces/r-dev-env/scripts/allow_ptrace.c && \\\n chmod +x /workspaces/r-dev-env/scripts/launch_r.sh && \\\n sh /workspaces/r-dev-env/scripts/localscript.sh"

"postCreateCommand": "find . -wholename '.git*' -type d -prune -o -type f -exec chown vscode:vscode {} \\; && \\\n sh ./scripts/localscript.sh"

If this doesn't work, maybe we can use $PWD/scripts/localscript.sh instead.

hturner · 2025-07-30T17:21:17Z

.devcontainer/launch.json

+{
+  "version": "0.2.0",
+  "configurations": [
+    {
+      "name": "Debug R (C debugging)",
+      "type": "cppdbg",
+      "request": "launch",
+      "program": "/workspaces/r-dev-env/scripts/launch_r.sh",
+      "args": ["/workspaces/r-dev-env/build/r-devel/bin/R"],
+      "stopAtEntry": false,
+      "cwd": "${workspaceFolder}",
+      "environment": [],
+      "externalConsole": false,
+      "MIMode": "lldb"
+    }
+  ]
+}


I am not sure why you are using a different launch process from the one proposed. Maybe we can offer alternative debugging configurations if they offer a different debugging experience, or provide some robustness (maybe one works if the other doesn't).

However, you should avoid hard-coding the R version here. Users should be able to select from multiple versions if they have build more than one version of R in the container (as per Multiple R Versions). We could get the which_r script to update the "args" here if necessary.

I have opened a PR with a demo setup that uses CodeLLDB as I discussed in #196. Perhaps you can try it out to see how I got that working - it is still missing the changes to which_r and requires some manual steps that you currently have in the postCreateCommand.

docs/tutorials/building_r.md

hturner · 2025-07-30T17:53:38Z

scripts/launch_r.sh

+
+# If the first argument is a file, use that as R_BINARY; otherwise default.
+if [ -x "$1" ]; then
+  R_BINARY="$1"


Maybe throw an error in this case rather than open a version the user didn't ask for?

But really which_r should handle this: as long as people have defined a valid version of R to switch to, then which_r should set the path correctly here.

…rpath

modify the step for setting CFLAGS for a better explanation Co-authored-by: Heather Turner <ht@heatherturner.net>

avinab-neogy · 2025-07-31T10:01:31Z

Hi @hturner ,
Thanks for running it and opening a PR making sure it works Heather, it really means a lot
But I am still getting > Sys.getenv("LD_PRELOAD") [1] "" as an empty string that is the terminal is not running launch_r , it might be a local issue on my system due to container cache but I tried clearing that and rebuilding the container but it still returns the same empty string.

I have updated this branch in a way that it aligns with your suggestions and comments and should work now logically.

Every time you open a new R terminal , it runs the launch_r.sh instead of calling R directly. This script loads the helper so that the debugger always has permission to attach, and the helper picks whichever R you’ve chosen via the which_r script.

I know this is actually asking a lot but can you please check if this is working on your system once.

hturner · 2025-07-31T14:24:36Z

.devcontainer/devcontainer.json

-                "r.rterm.linux": "/usr/bin/R",
+                "terminal.integrated.env.linux": {
+                    "R_RPATH_LINUX": "${config:r.rpath.linux}"
+                },


I don't think you need this, see below for getting the current version of R.

hturner · 2025-07-31T14:41:02Z

scripts/launch_r.sh

+if [ -n "${R_RPATH_LINUX:-}" ] && [ -x "$R_RPATH_LINUX" ]; then
+  R_BINARY="$R_RPATH_LINUX"
+else
+  R_BINARY="/usr/bin/R"
+fi
+
+exec "$R_BINARY" "$@"


You don't need to do it like this. Define launch_r.sh as

!/bin/bash export LD_PRELOAD=/workspaces/r-dev-env/scripts/allow_ptrace.so exec /usr/bin/R "$@"

then update which_r to replace the old path with the new path as required, e.g. (untested)

sed -i "s|^exec .*R|exec $selected_version|" launch_r.sh

This would be a new step in addition to updating "r.rpath.linux" in the VS Code settings.

For initial testing, just change the path manually, so you don't have to get everything working at once!

hturner · 2025-07-31T14:42:41Z

scripts/localscript.sh

+
+# Remove the .vscode/settings.json file if it exists so that
+# it does not interfere with the devcontainer.json
+rm -f "$WORK_DIR/.vscode/settings.json"


Do not remove this file, this is the one that is being updated on line 32!

hturner · 2025-07-31T14:49:05Z

.devcontainer/launch.json

+      "environment": [
+        {
+          "name": "R_RPATH_LINUX",
+          "value": "${config:r.rpath.linux}"
+        }
+      ],


Should not need this here either. The path to R is only needed when we launch the terminal. The debugger identifies the running R process with the process ID (as returned by Sys.getpid() in R).

Please use the launch.json as I do in #261

hturner · 2025-08-06T08:23:55Z

scripts/which_r.sh

Please only change what is necessary in this file: edit line 63 so it only changes r.rpath.linux and add the new call to sed to update launch_r.sh. Otherwise you risk introducing regressions, e.g. line 67 was added (by you!) in #255 to instruct people how to reload the help to use the version corresponding to the R version that has been switched to.

hturner · 2025-08-06T08:27:32Z

.devcontainer/launch.json

+      "environment": [
+        {
+          "name": "R_RPATH_LINUX",
+          "value": "${config:r.rpath.linux}"
+        }
+      ],


Please use the launch.json as I do in #261

avinab-neogy · 2025-08-08T08:47:33Z

Hi @hturner ,
There were a lot of merge conflicts on this branch so I have brought the current changes into a new branch feature/lldb-debugging-final and have incorporated all the corrections that were needed.

hturner · 2025-08-08T09:37:52Z

@avinab-neogy I just merged #265 that hides the .git dir in vscode file explorer and disables git features inside the devcontainer. It is probably worth branching from the corresponding commit (or later) this so that it is easier to track changes.

avinab-neogy · 2025-08-11T07:15:05Z

Closing this PR as I have opened another PR which is working

avinab-neogy added 6 commits July 30, 2025 09:24

changes to devcontainer.json

b686781

added launch.json

5200db3

added wrapper and launch_r scripts

7131f53

updated documentation to include flags for debugging

0aafb3d

removed settings.json since it overwrites devcontainer.json

12e95fd

Change R debug config to launch through wrapper script

8d169f3

avinab-neogy requested a review from hturner July 30, 2025 11:29

avinab-neogy self-assigned this Jul 30, 2025

hturner reviewed Jul 30, 2025

View reviewed changes

Refactor debugging setup: use wrapper env var and update which_r for …

ecd644a

…rpath

avinab-neogy force-pushed the feature/lldb-debug branch from 4581ad4 to ecd644a Compare July 31, 2025 03:59

pre-commit-ci bot and others added 5 commits July 31, 2025 03:59

[pre-commit.ci] Fixing issues with pre-commit

13a94cd

[pre-commit.ci] Fixing issues with pre-commit

e31cb45

update docs/tutorials/building_r.md

10bb76e

modify the step for setting CFLAGS for a better explanation Co-authored-by: Heather Turner <ht@heatherturner.net>

updated launch config to remove hard coded r version

0ded05f

modified local script

aa3881d

hturner reviewed Jul 31, 2025

View reviewed changes

avinab-neogy and others added 4 commits August 1, 2025 12:05

changes to scripts

c511d20

[pre-commit.ci] Fixing issues with pre-commit

6ff6e5b

updated which_r using sed as suggested by heather

c6e3c74

[pre-commit.ci] Fixing issues with pre-commit

3023bdb

hturner reviewed Aug 6, 2025

View reviewed changes

avinab-neogy and others added 2 commits August 7, 2025 16:07

Updated launch.json

16aab2e

[pre-commit.ci] Fixing issues with pre-commit

8449b16

avinab-neogy closed this Aug 11, 2025

	updated_settings_data=$(cat "$settings_file_path" \| jq --arg subdir "$selected_version" '."r.rterm.linux"=$subdir \| ."r.rpath.linux"=$subdir')
	echo "$updated_settings_data" > "$settings_file_path"

		"r.rterm.linux": "/workspaces/r-dev-env/scripts/launch_r.sh",
		"r.rpath.linux": "/workspaces/r-dev-env/build/r-devel/bin/R",

	"postCreateCommand": "find . -wholename '.git*' -type d -prune -o -type f -exec chown vscode:vscode {} \\; && \\\n gcc -shared -fPIC -o /workspaces/r-dev-env/scripts/allow_ptrace.so /workspaces/r-dev-env/scripts/allow_ptrace.c && \\\n chmod +x /workspaces/r-dev-env/scripts/launch_r.sh && \\\n sh /workspaces/r-dev-env/scripts/localscript.sh"
	"postCreateCommand": "find . -wholename '.git*' -type d -prune -o -type f -exec chown vscode:vscode {} \\; && \\\n sh ./scripts/localscript.sh"

Feature : Enable LLDB Debugging for R Dev Container #260

Feature : Enable LLDB Debugging for R Dev Container #260

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avinab-neogy commented Jul 30, 2025

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avinab-neogy commented Jul 31, 2025

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avinab-neogy commented Aug 8, 2025

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hturner Jul 30, 2025 •

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