Bug Report: ClaudeR stops working after first command

[boragurel]

Summary

I''ve been using ClaudeR for data analysis in my research. It has been working just fine for the past week, but today, after successfully running one R command, all subsequent commands fail with an error message. I have to restart the server after every single command, making ClaudeR unusable for my workflow.

My Setup

• Computer: Windows 11
• R Version: 4.5.0
• RStudio: Latest version
• Python: 3.13.5 (I followed the ClaudeR installation guide)
• ClaudeR Version: 0.2.0
• Location: UK

What Happens

1. I start RStudio and run library(ClaudeR) then claudeAddin()
2. Click "Start Server" - everything looks fine, shows "HTTP Server running"
3. Ask Claude to run any R command → This always works perfectly
4. Ask Claude to run any second command → This always fails
5. Every command after that fails until I restart the server

Error Message

When the second command fails, I see this error in Claude Desktop:
"Failed to call tool execute_r: TypeError: Cannot convert undefined or null to object"

Examples of What I've Tested

First command (always works):

• Simple math: 1+1 ✅
• Complex analysis of my cancer data ✅
• Loading packages and data manipulation ✅

Second command (always fails):

• Simple math: 2+2 ❌
• Just typing "hello" ❌
• Any R command at all ❌

It doesn't matter if the first command is complex or the second is simple - the pattern is always the same.

Additional Issue: Console Access

When the ClaudeR connection is active, I lose access to the R console. The console shows a red "running" indicator and I don't get the normal > prompt anymore. If I press Escape to try to get the prompt back, the ClaudeR server shuts down completely and the viewer pane goes blank.

This means I can't:

• Run any R commands manually while ClaudeR is connected
• Check my data or variables directly in the console
• Troubleshoot issues by testing commands myself
• Work on other parts of my analysis while ClaudeR is running

What I've Tried

• Restarting RStudio, Claude Desktop and the workstation completely
• Trying different port numbers in the settings
• Working both inside and outside R projects
• Following the troubleshooting guide exactly
• Checking that Python packages are installed (they are)

The same pattern happens every time regardless of what I try.

My Configuration

I followed the installation guide and my configuration file contains:

{
  "mcpServers": {
    "r-studio": {
      "command": "py",
      "args": ["-3.13", "C:/Users/[USERNAME]/.R/library/ClaudeR/scripts/persistent_r_mcp.py"],
      "env": {
        "PYTHONPATH": "C:/Users/[USERNAME]/AppData/Local/Programs/Python/Python313/Lib/site-packages",
        "PYTHONUNBUFFERED": "1"
      }
    }
  }
}

What I Notice

• The ClaudeR interface always shows "Server running" even when commands fail
• No error messages appear in R itself
• The log file shows successful commands but failed ones don't appear at all
• Restarting the ClaudeR server temporarily fixes it (one command works, then it breaks again)

I'd be happy to provide any additional information or test specific scenarios if it would help resolve this issue. Thanks!

[boragurel]

Update:

After further searching on the web, this issue appears to be related to the critical Claude Desktop MCP parameter serialization bug reported in anthropics/claude-code#4192.

The exact same pattern occurs with ClaudeR:

First MCP call with parameters: SUCCESS
Subsequent MCP calls with parameters: FAIL with "Cannot convert undefined or null to object"

This suggests the issue is not specific to ClaudeR but affects all MCP servers on Claude Desktop. The timing aligns with the widespread reports - this started happening today without any changes to the ClaudeR installation.

[IMNMV]

Thank you for this wonderfully detailed bug report! It seems your assessment is correct and this issue stems from the parameter serialization bug. While I can't fix this I can address the other issue you mentioned:

When the ClaudeR connection is active, I lose access to the R console. The console shows a red "running" indicator and I don't get the normal > prompt anymore. If I press Escape to try to get the prompt back, the ClaudeR server shuts down completely and the viewer pane goes blank.

I originally made this to make Claude completely autonomous and the Desktop App (or Cursor interface) to be the way to interact with Claude. However, a few people have noted they would prefer to still interact with the console. While I didn't mean to do this, if you press the stop button in the console (to the left of the broom) that will allow you to still use the console and Claude will still be connected to the server. This, in turn, means the only way to end the connection in that window's instance will be to restart it, but you will be able to use the console and Claude will still be able to execute code.

I will work on an update making this more a feature and less of a bug.

[boragurel]

Brilliant. Thank you for the update. I have been using claudeR for only a few days now but it has been GAME CHANGING! On top of what is available within ClaudeR, just by using execute_r I am able to utilize the rstudioapi package commands to do almost anything. On the other hand, this also allows claude, theoretically, to have access to the system terminal through the R studio terminal pane.

I wrote an instruction set that I paste into Claude project instructions to forbid such access. I could share that if anyone is interested :)

[IMNMV]

Oh, thanks for catching this. Are there certain prompts you noticed Claude did this for?

As a precaution, I've pushed an update for the validate_code_security function in the ui.R script to block any function call matching the pattern rstudioapi::terminal.

However, Claude wouldn't even try when I asked it to execute terminal commands. When I explicitly told it to do it for testing reasons, the Desktop app threw a red warning that Claude was not able to do that and to start a new chat (first time I had seen that).

Would love to see your project instructions though! More security never hurts when it comes to computer files!

[Apollo7777777]

感谢您提交如此详细的错误报告！看来您的评估是正确的，这个问题源于参数序列化错误。虽然我无法修复这个问题，但可以解决您提到的另一个问题：

当 ClaudeR 连接处于活动状态时，我无法访问 R 控制台。控制台显示一个红色的“正在运行”指示，并且我再也看不到正常的 > 提示符了。如果我按 Esc 键尝试恢复提示符，ClaudeR 服务器就会完全关闭，查看器窗格会变成空白。

我最初这样做是为了让 Claude 完全自主运行，并通过桌面应用程序（或光标界面）与 Claude 交互。然而，一些人表示他们仍然更喜欢与控制台交互。虽然我并非_有意_为之，但如果您按下控制台上的停止按钮（位于扫帚左侧），您仍然可以使用控制台，Claude 也仍然会连接到服务器。这意味着在该窗口实例中结束连接的唯一方法是重新启动它，但您将能够使用控制台，Claude 仍然可以执行代码。

我将致力于更新，使其成为一个功能，而不是一个错误。

Can I use Claude code in RStudio? I previously set it up in VSCode, and it was fantastic, but I couldn't view variables.

[IMNMV]

Can I use Claude code in RStudio? I previously set it up in VSCode, and it was fantastic, but I couldn't view variables.

Not currently, though you are the second person to ask - so I will add in Google Gemini CLI and Claude Code support this week!

[Apollo7777777]

Can I use Claude code in RStudio? I previously set it up in VSCode, and it was fantastic, but I couldn't view variables.

Not currently, though you are the second person to ask - so I will add in Google Gemini CLI and Claude Code support this week!

Thank you very much, it will be very helpful !!! I'm using a third-party Claude Code API that offers the same sonnet4 capabilities at a lower price, and I'm really looking forward to you integrating it into Rstudio.

[Apollo7777777]

Can I use Claude code in RStudio? I previously set it up in VSCode, and it was fantastic, but I couldn't view variables.

Not currently, though you are the second person to ask - so I will add in Google Gemini CLI and Claude Code support this week!

I follow your progress 🙂

[Apollo7777777]

Can I use Claude code in RStudio? I previously set it up in VSCode, and it was fantastic, but I couldn't view variables.

Not currently, though you are the second person to ask - so I will add in Google Gemini CLI and Claude Code support this week!

Hey, is it available now?

[IMNMV]

Sorry for the delay. It is now available for both Claude Code and Gemini cli as well. I tested it to work on my conda env using Mac OS, so if there are any installation troubles (especially if you have another configuration), let me know.

Thanks for your interest in the project :)

[Apollo7777777]

Sorry for the delay. It is now available for both Claude Code and Gemini cli as well. I tested it to work on my conda env using Mac OS, so if there are any installation troubles (especially if you have another configuration), let me know.

Thanks for your interest in the project :)

[Apollo7777777]

have

Sorry for the delay. It is now available for both Claude Code and Gemini cli as well. I tested it to work on my conda env using Mac OS, so if there are any installation troubles (especially if you have another configuration), let me know.
Thanks for your interest in the project :)

Thank you very much😊 I'm sure many people who use Rstudio will need it. I want to know can I use it in the Windows 11？

[Apollo7777777]

Sorry for the delay. It is now available for both Claude Code and Gemini cli as well. I tested it to work on my conda env using Mac OS, so if there are any installation troubles (especially if you have another configuration), let me know.
Thanks for your interest in the project :)

I try to install it in Windows11 today, but failed, can I chat with you in IG or Whatsapp?

[IMNMV]

Ah, unfortunately the only social I use is twitter. If you don't have that feel free to post any errors here and I'd be happy to troubleshoot.

[Apollo7777777]

Ah, unfortunately the only social I use is twitter. If you don't have that feel free to post any errors here and I'd be happy to troubleshoot.

Hey, this is my twitter account.
David2530048841