run.vbs error – agent fails with error 80070002 "The system cannot find the file specified"

[trongtrd]

Overview

I installed the PapersGPT‑for‑Zotero plug‑in (version v0.3.4) in Zotero 7 on my Windows 11 x64 system. After installation the plug‑in UI loads, but nothing happens when I attempt to use it with either a paid ChatGPT model (gpt‑5 via the OpenAI API) or the built‑in quick‑actions. When the plug‑in window is open, a Windows Script Host error appears stating that run.vbs cannot find the specified file. Uninstalling and reinstalling the plug‑in did not resolve the problem.

Environment

• Operating system: Windows 11 x64
• Zotero version: 7.0
• PapersGPT plug‑in version: v0.3.4 (latest at the time of writing)
• User profile path: C:\Users\… — note that my user name contains a space.

Symptoms and evidence

Plug‑in UI not responding

After installing the plug‑in I opened a PDF in Zotero and invoked PapersGPT. The plug‑in window opened and I selected OpenAI → gpt‑5 and provided my OpenAI API key (I have a ChatGPT Plus subscription). The UI shows the prompt field and the quick‑action buttons, but clicking the send button does nothing and no response is returned. A screen capture of the unresponsive UI is shown below:

run.vbs error

When the plug‑in is invoked a Windows Script Host dialog appears with the following information:

• Script: C:\Users\…\.papersgpt\run.vbs
• Line: 7
• Char: 9
• Error: The system cannot find the file specified.
• Code: 80070002

The dialog is reproduced below:

.papersgpt folder contents

The plug‑in creates a .papersgpt folder in my user profile, but no local‑models directory is created even after several minutes of waiting. The folder contains various DLLs, a SQLite database, and two items named papersgpt‑agent‑v0.3.4 – one is an application and the other appears as a mysterious “4 File” entry. There is also the run.vbs script. A screen capture of the folder is shown here:

Investigations

1. Checked documentation: The usage tips on the official website note that antivirus software may quarantine the agent executables and advise verifying the existence of ~\.papersgpt\local‑models\bin\llm‑server‑deploy‑package\papersgpt‑local‑llm and deleting the folder if it is missing:contentReference[oaicite:0]{index=0}. In my case no local‑models folder exists at all, and Windows Defender never displayed a warning.
2. Examined run.vbs: The VBScript wrapper in .papersgpt simply launches the agent executable based on the first argument. Line 7 reads objShell.Run cmdExec, 0, False, which fails if the path to the agent is not properly quoted. Since my user name contains a space, it appears that the script is receiving a truncated path (e.g., C:\Users\TRONG), leading to the “file not found” error.
3. Confirmed plug‑in version: According to the release notes for version 0.3.0, the developers fixed a Windows‑specific bug where the built‑in embedding server failed to start:contentReference[oaicite:1]{index=1}. However, there is also a warning in the 0.2.1 beta release that the new Windows agent is not yet stable and that users should use version v0.1.3 for a stable experience (version v0.3.4 still exhibits the same agent issues).
4. Tried reinstalling: Completely removing the plug‑in and the .papersgpt folder, then reinstalling, produced the same result: the plug‑in installs, the .papersgpt folder is created, but the agent cannot be started and no local‑models folder is downloaded.

Hypothesis

The plug‑in appears to rely on an external agent (papersgpt‑agent‑v0.3.4) to perform all backend operations, even for remote API models. run.vbs is used to start or stop this agent. On Windows systems where the user profile contains a space, the path is not quoted when passed to the VBScript. As a result, the script receives an incomplete file name and fails with error code 80070002. Because the agent never starts, the plug‑in UI cannot communicate with either local or remote models, and no local‑models folder is created.

Request for assistance

I would appreciate guidance from the PapersGPT maintainers on the following:

• Is there a known fix or workaround for the run.vbs quoting issue on Windows profiles with spaces? Editing run.vbs to wrap the argument in quotes appears to be a potential workaround.
• What is the purpose of the “4 File” version of papersgpt‑agent‑v0.3.4? The inability to open it suggests it may be part of a multi‑part archive.
• Are there instructions for using an older, more stable version of PapersGPT on Windows while the new agent is under development?

Thank you!

[papersgpt]

Thanks for feedback! I have never heard the problem of quoting issue before, I will check it soon!
In order to improve the efficiency, the agent is all implemented by C++, in version v0.3.4, it not only supply the pdf parsing, but also includes the full text bm25 search engine.
You can delete ~/.papersgpt directory, and then install v0.3.3, thanks!

[trongtrd]

Thanks for the suggestion. I deleted the .papersgpt folder and installed v0.3.3 as recommended, but unfortunately I’m seeing the same behaviour: no response from the plug‑in and the same script error.
This might be related to my Zotero environment, so I’ll dig into my settings and report back once I have more information.
Thanks!

[papersgpt]

Yes, this bug is related to the home dir path including space, thanks for your feedback again.
I have just fixed it in the latest v0.3.4, you can download and have a try.

[ljeagle]

@trongtrd Hi, does it work for you now? Thank you.

[trongtrd]

Thank you for your efforts.

The error warning no longer appears, but I still cannot see any output generated, regardless of what I type in the chatbox or which suggested buttons I select (such as “Summary” or “Topic”). I even tried disabling all other plugins in Zotero and reinstalling the PapersGPT plugin, but it didn’t help.

If no one else is experiencing this issue, it might be a problem with my Zotero setup or my Windows environment. I’ll try to look into it further when I have time.

Thank you.

[ljeagle]

Is your OpenAI API KEY valid or does it have enough quota? The LLM API KEY you should created on the API platform of OpenAI, Gemini, Claude, DeepSeek or OpenRouter.
Generally, the problem of not being able to access is that the API KEY is invalid or there is not enough quota.

[ljeagle]

Accessing GPT 5 should do the identity check on the OpenAI's platform base on the OpenAI's requirement.

[trongtrd]

I accessed the OpenAI Platform (https://platform.openai.com/api-keys) to remove my old API key and generate a new one. I then copied this key and pasted it into the PapersGPT box.

However, even with this new key, I still didn’t see any output generated. A small notification appeared (as shown in the attached image) summarizing the process, but it stopped at “Answering.” I don't think there is a problem with quota because I have never reached the quota of ChatGPT with my daily usage.

You wrote: “Accessing GPT‑5 should do the identity check on the OpenAI platform based on OpenAI’s requirement.” I don’t quite understand this sentence. I didn’t see any “identity check” from OpenAI. Where would I find this check?

It would be great if you could provide instructions in your README file on how to obtain an API key and enter it into the PapersGPT plugin.

If I did something wrong during the API key generation process, please let me know.

Thank you.

[ljeagle]

If possible, please take a screenshot of the Zotero output error log.

[trongtrd]

My PapersGPT plugin trial has expired, so I cannot export the output error log. However, I noticed that the latest reported issue (#109) describes a similar problem, so perhaps you could ask that user to take a screenshot of their error log.

By the way, even if the plugin were working, I think its interface could be improved for convenience. It would be better if there were a mode that integrates the plugin interface into Zotero’s right panel (context panel) rather than displaying it as a floating window, as it currently does. This would make it easier for users to read the document in the main window while viewing the chat in the right panel.

It would also be great if users could select a specific paragraph in the document and have a context menu appear, allowing them to ask questions about that paragraph.

Better still, if the right panel could display both the note and the LLM chat at the same time—for example, with the note window above the LLM chat window—that would be excellent. This way, users could easily copy content from the LLM chat into their notes.

I look forward to seeing improvements to your plugin in the future. I will close this issue later today.