Kernel supervisor times out between creating a session and connecting to it

[eutanatos]

Type: Bug

Fresh install of Positron, default configuration, no extensions added after clean install. No previously installed Positron on this system. OS - Windows 11, all updates installed. R version - 4.5.0.

Message on opening console:
R 4.5.0 failed to start.
Error
The supervisor process exited before the server was ready.

VS Code version: Positron 1.100.0 (e7e5d55, 2025-05-29T21:27:54.586Z)
OS version: Windows_NT x64 10.0.26100
Modes:

System Info

Item	Value
CPUs	12th Gen Intel(R) Core(TM) i5-12400 (12 x 2496)
GPU Status	2d_canvas: enabled canvas_oop_rasterization: enabled_on direct_rendering_display_compositor: disabled_off_ok gpu_compositing: enabled multiple_raster_threads: enabled_on opengl: enabled_on rasterization: enabled raw_draw: disabled_off_ok skia_graphite: disabled_off video_decode: enabled video_encode: enabled vulkan: disabled_off webgl: enabled webgl2: enabled webgpu: enabled webnn: disabled_off
Load (avg)	undefined
Memory (System)	15.71GB (3.78GB free)
Process Argv
Screen Reader	no
VM	0%

Extensions (14)

Extension	Author (truncated)	Version
ruff	cha	2025.22.0
vscode-pull-request-github	Git	0.110.0
pyright	ms-	1.1.401
debugpy	ms-	2025.6.0
jupyter	ms-	2025.4.1
jupyter-keymap	ms-	1.1.2
vscode-jupyter-cell-tags	ms-	0.1.9
vscode-jupyter-slideshow	ms-	0.1.6
air-vscode	Pos	0.12.0
publisher	pos	1.16.1
shiny	Pos	1.2.2
shinyuieditor	pos	0.5.0
quarto	qua	1.122.0
claude-dev	sao	3.17.11

[juliasilge]

Does this happen every time you start Positron? If so, can you share (from the Output panel) the R Console logs and the Kernel Supervisor logs?

If you are up for it, you might consider trying out the daily builds, which have some recent fixes from the kernel supervisor.

[rodrigosf672]

[Edit: root cause does not seem to be related to what the user is experiencing. For issue reported in this comment, it seems more related to #7991)

If that's the same issue, here are some further details (I'm also seeing similar behavior in the dev version).

R 4.5.0 failed to start up (exit code 0)

Failed to connect to session's ZeroMQ sockets: Failed to complete JEP 66 handshake: JEP 66 handshake failed for session r-5494ebc4: Timeout waiting for handshake
R 4.5.0 failed to start up (exit code 0)

Failed to connect to session's ZeroMQ sockets: Failed to complete JEP 66 handshake: JEP 66 handshake failed for session r-5494ebc4: Timeout waiting for handshake

Positron Dev Version: 2025.07.0 build 0
Code - OSS Version: 1.100.0
Commit: Unknown
Date: Unknown
Electron: 34.5.1
Chromium: 132.0.6834.210
Node.js: 20.19.0
V8: 13.2.152.41-electron.0
OS: Darwin arm64 24.5.0

[jmcphers]

@rodrigosf672 I couldn't reproduce this in a dev build -- can you share the output that @juliasilge requested?

[immanuelazn]

EDIT: Found that every build prior to this has R working properly.

Also seeing this error on the following build:

Positron Version: 2025.06.0 (system setup) build 167
Code - OSS Version: 1.100.0
Commit: e7e5d5590adc6bf7b760f837051cd2f57ea9e3dc
Date: 2025-05-29T21:27:54.586Z
Electron: 34.5.1
Chromium: 132.0.6834.210
Node.js: 20.19.0
V8: 13.2.152.41-electron.0
OS: Windows_NT x64 10.0.26100

Running on Windows 11 remoting into WSL. Previous versions of positron were working. Getting this on console, after restarting wsl, resetting ports etc.

R 4.4.1 failed to start up (exit code 0)

Failed to connect to session's ZeroMQ sockets: Failed to complete JEP 66 handshake: JEP 66 handshake failed for session r-79bdbfe7: Timeout waiting for handshake

Output on Kernel Supervisor:

FILE: /home/imman/.config/Positron/positron-supervisor-781.json
2025-06-09 16:47:34.177 [info] Reconnecting to Kallichore server at http://127.0.0.1:22850 (PID 823)
2025-06-09 16:47:34.177 [info] Streaming Kallichore server logs at /home/imman/.config/Positron/positron-supervisor-781.log
2025-06-09 16:47:34.177 [info] 23:47:30 [INFO] Generated random auth token: 42a7016132cbdc48
2025-06-09 16:47:34.177 [info] 23:47:30 [INFO] Wrote connection details to /home/imman/.config/Positron/positron-supervisor-781.json
2025-06-09 16:47:34.177 [info] 23:47:30 [INFO] Starting Kallichore server at 127.0.0.1:22850
2025-06-09 16:47:34.177 [info] Kallichore 0.1.42 server reconnected with 0 sessions
2025-06-09 16:47:34.177 [info] Connected to previously established supervisor.
Creating session: {"sessionId":"r-79bdbfe7","sessionMode":"console","createdTimestamp":1749512855633,"startReason":"Affiliated runtime for workspace"}
Creating session: {"sessionId":"python-7efc375d","sessionMode":"console","createdTimestamp":1749512856186,"startReason":"Affiliated runtime for workspace"}
23:47:33 [INFO] set_server_configuration - X-Span-ID: "e6de9133-65fa-4a2f-b2f1-1fed2ba21496"
23:47:33 [INFO] Updating idle shutdown hours to Some(1)
23:47:35 [INFO] new_session("r-79bdbfe7") - X-Span-ID: "7bd3ae3b-ca22-485b-b9a8-c2895f8ad4ac"
23:47:35 [INFO] start_session("r-79bdbfe7") - X-Span-ID: "cf449e19-d6b8-4351-af84-21465d714b21"
23:47:35 [INFO] [session r-79bdbfe7] Kernel supports JEP 66 (protocol version 5.5) - creating registration socket for handshake
23:47:35 [INFO] [session r-79bdbfe7] Waiting for JEP 66 handshake
23:47:35 [INFO] Child process for session r-79bdbfe7 exited with status: exit status: 1
23:47:24 [INFO] new_session("python-7efc375d") - X-Span-ID: "c469a9a3-1dba-49a3-a8f9-997e90d0da6b"
23:47:24 [INFO] start_session("python-7efc375d") - X-Span-ID: "48d3ef75-d3d3-4e8c-9e50-1410e802bbd3"
23:47:25 [INFO] [session python-7efc375d] Connected to heartbeat socket at tcp://127.0.0.1:18901.
23:47:25 [INFO] [session python-7efc375d] Received initial heartbeat from kernel
23:47:25 [INFO] [client python-7efc375d-0] Connecting to websocket
23:47:25 [INFO] [client python-7efc375d-0] Got message 62564da141 of type comm_open; sending to Jupyter socket Shell
23:47:25 [INFO] [client python-7efc375d-0] Got message 351d0087de of type comm_open; sending to Jupyter socket Shell
23:47:25 [INFO] [client python-7efc375d-0] Got message ddcae51503 of type comm_info_request; sending to Jupyter socket Shell
23:47:25 [INFO] [client python-7efc375d-0] Got message 7c063e211b of type comm_info_request; sending to Jupyter socket Shell
23:47:25 [INFO] [client python-7efc375d-0] Got message 94e724e758 of type comm_info_request; sending to Jupyter socket Shell
23:47:25 [INFO] [client python-7efc375d-0] Got message 5415c179 of type comm_msg; sending to Jupyter socket Shell
23:47:25 [INFO] [client python-7efc375d-0] Got message 7597796a of type comm_msg; sending to Jupyter socket Shell
23:47:26 [INFO] [client python-7efc375d-0] Got message fcdfca0500 of type comm_open; sending to Jupyter socket Shell
23:47:26 [INFO] [client python-7efc375d-0] Got message 5237324a40 of type comm_open; sending to Jupyter socket Shell
23:47:41 [INFO] client_heartbeat - X-Span-ID: "9efce755-6cac-4cbb-8984-fbb3c37e4d1c"
23:47:53 [ERROR] [session r-79bdbfe7] Timeout waiting for handshake
23:47:53 [ERROR] [session r-79bdbfe7] JEP 66 handshake failed: JEP 66 handshake failed for session r-79bdbfe7: Timeout waiting for handshake
23:48:01 [INFO] client_heartbeat - X-Span-ID: "d1f150e7-1032-495e-922f-1142596bff9d"
23:48:21 [INFO] client_heartbeat - X-Span-ID: "ffe06c81-38d5-4e55-a129-0343edaf7d16"
23:48:41 [INFO] client_heartbeat - X-Span-ID: "46c24a26-08d1-444c-8d09-446c2dda2ba6"
23:49:01 [INFO] client_heartbeat - X-Span-ID: "c9b1c331-82bb-4a73-94a0-163af7e71324"
23:49:21 [INFO] client_heartbeat - X-Span-ID: "df41a94b-2f06-4fa5-a51b-6503b3b81677"
23:49:41 [INFO] client_heartbeat - X-Span-ID: "6730a88c-e00a-461f-858e-19a6decebb8e"
23:50:01 [INFO] client_heartbeat - X-Span-ID: "9ffe73ab-d7fa-4a59-9aae-4899f55872ab"
23:50:21 [INFO] client_heartbeat - X-Span-ID: "3c3c1261-b277-4db4-b297-b069e95887ba"

Output on R console:

2025-06-09 16:47:35.737 [info] R 4.4.1 session 'r-79bdbfe7' created in /mnt/c/Users/Immanuel/PycharmProjects/BPCellsProjects with command:
2025-06-09 16:47:35.737 [info] /home/imman/.positron-server/bin/e7e5d5590adc6bf7b760f837051cd2f57ea9e3dc/extensions/positron-r/resources/ark/ark --connection_file {connection_file} --log /tmp/kernel-c4wL2u/kernel.log --startup-file /home/imman/.positron-server/bin/e7e5d5590adc6bf7b760f837051cd2f57ea9e3dc/extensions/positron-r/resources/scripts/startup.R --session-mode console -- --interactive --no-restore-data 
2025-06-09 16:47:35.738 [debug] State: uninitialized => starting (invoking start API)
2025-06-09 16:47:24.377 [debug] No UI comm open yet; queueing request 'setConsoleWidth'
2025-06-09 16:47:26.510 [debug] No UI comm open yet; queueing request 'packageVersion'
2025-06-09 16:47:28.606 [debug] Queuing LSP activation. Reason: foreground session changed. Queue size: 0, pending: 0
2025-06-09 16:47:28.606 [debug] LSP activation started. Reason: foreground session changed. Queue size: 0, pending: 1
2025-06-09 16:47:28.606 [info] Starting Positron LSP server
2025-06-09 16:47:28.606 [info] Starting LSP server positron-lsp-r-7db3e14a for 127.0.0.1
2025-06-09 16:47:53.350 [debug] State: starting => exited (startup failed)
2025-06-09 16:47:53.350 [debug] Queuing LSP deactivation. Reason: session exited. Queue size: 0, pending: 1

[Mengzhiyaa]

I've encountered the same issue.

Here are the circumstances under which I'm experiencing it:

This issue first appeared in version 2025.06.0-146. Previous versions did not have this problem. All versions from 2025.06.0-146 onwards have this issue.
The problem occurs exclusively on remote Linux systems (accessed via SSH). My local Windows machine does not have this issue. I have not tested it on a non-remote Linux environment.
Specific log information is as follows:
R console:

2025-06-10 21:07:23.245 [info] R 4.4.2 session 'r-32a5c151' created in /data1/test/ with command:
2025-06-10 21:07:23.245 [info] /home/test/.positron-server/bin/fe621e856f2e66144c97d30a3c77471947048e61/extensions/positron-r/resources/ark/ark --connection_file {connection_file} --log /tmp/kernel-HrwnYT/kernel.log --startup-file /home/test/.positron-server/bin/fe621e856f2e66144c97d30a3c77471947048e61/extensions/positron-r/resources/scripts/startup.R --session-mode console -- --interactive --no-restore-data
2025-06-10 21:07:23.245 [debug] State: uninitialized => starting (invoking start API)
2025-06-10 21:07:23.989 [debug] No UI comm open yet; queueing request 'setConsoleWidth'
2025-06-10 21:07:53.253 [debug] State: starting => exited (startup failed)
2025-06-10 21:07:53.254 [debug] Queuing LSP deactivation. Reason: session exited. Queue size: 0, pending: 0
2025-06-10 21:07:53.254 [debug] LSP deactivation started. Reason: session exited. Queue size: 0, pending: 1
2025-06-10 21:07:53.254 [debug] LSP already deactivated

Kallichore：

LE: /home/test/.config/Positron/positron-supervisor-4097411.json
2025-06-10 21:06:38.252 [info] Reconnecting to Kallichore server at http://127.0.0.1:23645 (PID 4097422)
2025-06-10 21:06:38.252 [info] Streaming Kallichore server logs at /home/test/.config/Positron/positron-supervisor-4097411.log
2025-06-10 21:06:38.252 [info] 13:06:31 [INFO] Generated random auth token: 8ecbd23e41e95fac
2025-06-10 21:06:38.252 [info] 13:06:31 [INFO] Wrote connection details to /home/test/.config/Positron/positron-supervisor-4097411.json
2025-06-10 21:06:38.252 [info] 13:06:31 [INFO] Starting Kallichore server at 127.0.0.1:23645
2025-06-10 21:06:38.252 [info] Kallichore 0.1.45 server reconnected with 0 sessions
2025-06-10 21:06:38.252 [info] Connected to previously established supervisor.
Creating session: {"sessionId":"r-731623cc","sessionMode":"console","createdTimestamp":1749560800611,"startReason":"Affiliated R runtime for workspace"}
13:06:37 [INFO] set_server_configuration - X-Span-ID: "d0e7817a-0d92-4ebe-afda-f6f5480a5adc"
13:06:37 [INFO] Updating idle shutdown hours to Some(1)
13:06:41 [INFO] new_session("r-731623cc") - X-Span-ID: "d2c58c22-e637-48f4-b1f4-8aafdc3cd868"
13:06:41 [INFO] start_session("r-731623cc") - X-Span-ID: "60fb9380-d885-44f6-9ca5-35785f81b980"
13:06:41 [INFO] [session r-731623cc] Kernel supports JEP 66 (protocol version 5.5) - creating registration socket for handshake
13:06:41 [INFO] [session r-731623cc] Waiting for JEP 66 handshake
13:06:57 [INFO] client_heartbeat - X-Span-ID: "b2a10507-be72-44c9-a76a-40c33b83e77a"
13:07:11 [ERROR] [session r-731623cc] Timeout waiting for handshake
13:07:11 [ERROR] [session r-731623cc] JEP 66 handshake failed: JEP 66 handshake failed for session r-731623cc: Timeout waiting for handshake
13:07:17 [INFO] client_heartbeat - X-Span-ID: "86ed6343-d629-4ba7-861b-0b58549c1c2d"
Creating session: {"sessionId":"r-32a5c151","sessionMode":"console","createdTimestamp":1749560841379,"startReason":"A file with the language ID r was opened."}
13:07:23 [INFO] new_session("r-32a5c151") - X-Span-ID: "04397549-a588-4ad7-b833-409aa311c26f"
13:07:23 [INFO] start_session("r-32a5c151") - X-Span-ID: "70cd0b64-0782-47ae-a6d6-8ef177d97903"
13:07:23 [INFO] [session r-32a5c151] Kernel supports JEP 66 (protocol version 5.5) - creating registration socket for handshake
13:07:23 [INFO] [session r-32a5c151] Waiting for JEP 66 handshake
13:07:37 [INFO] client_heartbeat - X-Span-ID: "16d80fdd-e96e-48bd-9916-b491a4d1a9dd"
13:07:53 [ERROR] [session r-32a5c151] Timeout waiting for handshake
13:07:53 [ERROR] [session r-32a5c151] JEP 66 handshake failed: JEP 66 handshake failed for session r-32a5c151: Timeout waiting for handshake
13:07:57 [INFO] client_heartbeat - X-Span-ID: "a4e2b13c-1c5c-488e-9513-ee0120892868"

[Robinlovelace]

I'm hitting the same issue on my work desktop.

[Robinlovelace]

This is what it says in the Console:

R 4.4.3 failed to start.
Error
The supervisor process exited before the server was ready.

From that point R hangs and nothing works. There is nothing in the OUTPUT tab:

Reverting back to RStudio for now.

[Robinlovelace]

Positron Version: 2025.07.0 (system setup) build 74
Code - OSS Version: 1.100.0
Commit: fe621e8
Date: 2025-06-09T03:58:07.136Z
Electron: 34.5.1
Chromium: 132.0.6834.210
Node.js: 20.19.0
V8: 13.2.152.41-electron.0
OS: Windows_NT x64 10.0.26100

[rodrigosf672]

@rodrigosf672 I couldn't reproduce this in a dev build -- can you share the output that @juliasilge requested?

@jmcphers I believe my issue is unrelated (see edit to my comment above), since deleting the ark processes running in the background solved the issue. However, my output pane was blank when my failure to start R happened.