Plugin Manager fails to update enabled plugin on Windows due to permission error (when updating Sidekick)

[Marvisak]

Version and Platform (required):

• Binary Ninja Version: 5.3.9757-stable
• Edition: Non-Commercial
• OS: Windows 11
• OS Version: 25H2
• CPU Architecture: x64

Bug Description:
When updating Sidekick (or disabling and enabling without turning binary ninja off, any action that causes dependency update) on a Windows machine, the installation of Python packages fails with a generic error. After digging around I found out it's a permission error connected to markupsafe (might be another package) being used while it's binary is updated.

Steps To Reproduce:

• Install Sidekick on Windows
• Disable and re-enable it

Expected Behavior:
Sidekick should update without any issues

Additional Information:
Reproduced on 2 machines
Workarounds:

• Disable the plugin, restart and update/re-enable
• Turn Binary Ninja off and run the commands displayed in the log (with Binary Ninja turned on the permission error is displayed)

Example traceback:

ERROR: Exception:
Traceback (most recent call last):
  File "C:\Users\jenkins\bundled-python\310\python-3.10.10-packaged-amd64\python310\pip\_internal\cli\base_command.py", line 160, in exc_logging_wrapper
  File "C:\Users\jenkins\bundled-python\310\python-3.10.10-packaged-amd64\python310\pip\_internal\cli\req_command.py", line 247, in wrapper
  File "C:\Users\jenkins\bundled-python\310\python-3.10.10-packaged-amd64\python310\pip\_internal\commands\install.py", line 566, in run
  File "C:\Users\jenkins\bundled-python\310\python-3.10.10-packaged-amd64\python310\pip\_internal\commands\install.py", line 621, in _handle_target_dir
  File "shutil.py", line 750, in rmtree
  File "shutil.py", line 620, in _rmtree_unsafe
  File "shutil.py", line 618, in _rmtree_unsafe
PermissionError: [WinError 5] Přístup byl odepřen: 'C:\\Users\\XXX\\AppData\\Roaming\\Binary Ninja\\python310\\site-packages\\markupsafe\\_speedups.cp310-win_amd64.pyd'

[iamausertoo]

Thanks for the report. This is likely caused by a Windows DLL lifetime issue rather than a normal filesystem permission problem.

Sidekick depends on Jinja2, which depends on MarkupSafe. On Windows, MarkupSafe’s speedups module is a native .pyd DLL. Once Sidekick imports the path that reaches Jinja2/MarkupSafe, markupsafe._speedups remains loaded in the Binary Ninja process. Disabling a running plugin marks it disabled for restart, but it cannot unload already-imported Python modules or native extension DLLs from the process.

The Plugin Manager currently reinstalls/upgrades Python dependencies before update/re-enable using pip with a target site-packages directory. Pip may try to remove or replace the existing MarkupSafe package, including the loaded _speedups...pyd, and Windows rejects that with WinError 5.

We're making a Sidekick change to avoid importing Jinja2/MarkupSafe during ordinary plugin startup, so the disable/re-enable path is less likely to hit this (unless template/skill functionality is used).

But, once the native module has been loaded in the same Binary Ninja process, restarting Binary Ninja is still the reliable workaround. A fuller Plugin Manager-side fix will need to defer dependency reinstalls for running plugins or avoid in-place replacement of packages with loaded native extensions.

[kristopax]

After further investigation, it looks like other modules that are loaded by Sidekick when opening a binary (e.g. numpy) result in the same error. Therefore, we cannot make Sidekick resolve this issue. Binary Ninja's Extension/Plugin Manager will need to be updated to fix this issue.

In order to install updates for Sidekick and avoid this error, you will need to:

1. Disable Sidekick (Click Disable for the Sidekick Plugin within the Plugin Manager)
2. Restart Binary Ninja
3. Update Sidekick (Click Update for the Sidekick Plugin within the Plugin Manager)
4. Enable Sidekick (Click Enable for the Sidekick Plugin within the Plugin Manager)
5. Restart Binary Ninja

I re-titled this issue to attribute the error to the Plugin Manager.