langchain-ai/deepagents · error · SystemExit

Error: Failed to fully delete skill: {e} Warning: Some files

Error message

Error: Failed to fully delete skill: {e} Warning: Some files may have been partially removed. Please inspect: {skill_dir}/

What it means

After validation passes, `_delete` calls `shutil.rmtree(skill_dir)`. If the OS raises `OSError` (permission denied, read-only filesystem, files held open, etc.) some files may already have been removed, so the command prints a combined error plus a partial-removal warning, points the user at the leftover directory, and raises `SystemExit(1)` from the original exception.

Source

Thrown at libs/code/deepagents_code/skills/commands.py:851

            "Refusing to delete for safety."
        )
        raise SystemExit(1)

    is_valid_path, path_error = _validate_skill_path(skill_dir, base_dir)
    if not is_valid_path:
        console.print(f"[bold red]Error:[/bold red] {path_error}")
        raise SystemExit(1)

    # Delete the skill directory
    try:
        shutil.rmtree(skill_dir)
    except OSError as e:
        console.print(
            f"[bold red]Error:[/bold red] Failed to fully delete skill: {e}\n"
            f"[yellow]Warning:[/yellow] Some files may have been partially removed.\n"
            f"Please inspect: {skill_dir}/"
        )
        raise SystemExit(1) from e

    if output_format == "json":
        from deepagents_code.output import write_json

        write_json(
            "skills delete",
            {
                "name": skill_name,
                "path": str(skill_dir),
                "deleted": True,
            },
        )
        return

    checkmark = get_glyphs().checkmark
    console.print(
        f"{checkmark} Skill '{skill_name}' deleted successfully!",
        style=theme.PRIMARY,

View on GitHub (pinned to a1af029e6e)

Solutions

1. Fix the underlying permission problem shown in the OSError message (chmod/chown the files or run with sufficient privileges)
2. Close processes holding files open in the skill directory (editors, running agents)
3. Manually remove whatever remains in the printed `skill_dir/` path
4. Retry the delete after remounting writable if the volume was read-only

Example fix

// before
$ dcode skills delete my-skill
# Error: Failed to fully delete skill: [Errno 13] Permission denied ...
// after
$ chmod -R u+w ~/.deepagents/skills/my-skill
$ rm -rf ~/.deepagents/skills/my-skill  # or retry the CLI

import os

def skill_dir_writable(skill_dir: Path) -> bool:
    return os.access(skill_dir, os.W_OK | os.X_OK) and all(
        os.access(p, os.W_OK) for p in skill_dir.rglob('*')
    )

import shutil
try:
    shutil.rmtree(skill_dir)
except OSError as e:
    print(f'partial delete possible, inspect {skill_dir}: {e}')
    raise SystemExit(1) from e

When it happens

Trigger: `skills delete <name>` where `shutil.rmtree` fails midway: any `OSError` from unlinking files or removing directories inside `skill_dir` (EACCES, EROFS, EBUSY, ENOTEMPTY on odd filesystems).

Common situations: Deleting skills on read-only or network-mounted volumes; files owned by another user or locked by an editor/another agent process; filesystem bugs where rmtree partially completes before failing.

Related errors

• Error: Could not create project skills directory.
• debug log directory is not owned by the current user: {path}
• Cannot determine whether {str(left)!r} is {str(right)!r}: {e
• Invalid DEEPAGENTS_HOME {str(root)!r}: exists but cannot be
• Could not resolve {label} path {raw_path!r}: {exc}. Ensure t

AI-assisted analysis of langchain-ai/deepagents@a1af029e6e (2026-08-29). Data as JSON: /api/errors/2be7f44dc142d0b3. Report an issue: GitHub.