Bug connecting Claude Desktop to R Studio on windows

[ndtivendale]

Bug: ClaudeR fails to connect on Windows when HOME points to OneDrive (two issues)

Environment

• OS: Windows
• RStudio: 2026.4.0.526 (or similar)
• ClaudeR installed via devtools::install_github("IMNMV/ClaudeR")
• Claude Desktop with clauder-mcp via uvx

Description

On Windows machines where the HOME environment variable points to a OneDrive-synced Documents folder (a common configuration), ClaudeR fails to connect to Claude Desktop. There are two distinct bugs that compound each other.

---

Bug 1: HOME/USERPROFILE mismatch causes discovery file to be written to the wrong location

What happens

ClaudeR (the R addin) writes the session discovery file using R's path.expand("~"), which resolves to the HOME environment variable. On many Windows machines, HOME points to a OneDrive-synced folder such as:

C:\Users\username\OneDrive - Organisation\Documents\.claude_r_sessions\

However, clauder-mcp (the Python MCP bridge) locates the discovery file using Python's os.path.expanduser("~"), which on Windows resolves to USERPROFILE:

C:\Users\username\.claude_r_sessions\

These are different directories, so clauder-mcp never finds the discovery file written by the R addin.

Reproduction

1. On a Windows machine where HOME != USERPROFILE (common when Documents is redirected to OneDrive), install and run ClaudeR.
2. Note that ClaudeR:::discovery_dir() returns a path under HOME (OneDrive).
3. Note that clauder-mcp looks for discovery files under USERPROFILE.
4. Claude Desktop reports "No active R sessions found" despite the addin running.

Fix

In clauder-mcp/server.py, change:

SESSIONS_DIR = os.path.expanduser("~/.claude_r_sessions")

To use USERPROFILE consistently on Windows:

if sys.platform == "win32":
    SESSIONS_DIR = os.path.join(os.environ.get("USERPROFILE", os.path.expanduser("~")), ".claude_r_sessions")
else:
    SESSIONS_DIR = os.path.expanduser("~/.claude_r_sessions")

And update discovery_dir() in the R package to match, using USERPROFILE on Windows:

discovery_dir <- function() {
  base <- if (.Platform$OS.type == "windows") {
    Sys.getenv("USERPROFILE", unset = path.expand("~"))
  } else {
    path.expand("~")
  }
  file.path(base, ".claude_r_sessions")
}

---

Bug 2: os.kill(pid, 0) does not work correctly on Windows, causing discovery files to be deleted immediately

What happens

After the discovery file is written, clauder-mcp calls _pid_alive(pid) to verify the R process is still running before using the session. This function uses os.kill(pid, 0), which is a standard POSIX signal check. However, on Windows, os.kill() does not support signal 0 in the same way — it raises an OSError even for running processes, causing _pid_alive() to incorrectly return False. As a result, clauder-mcp treats every session as dead and deletes the discovery file immediately after finding it.

Reproduction

1. On Windows, get Bug 1 resolved so the discovery file is written to the correct location.
2. Observe that the discovery file appears briefly then disappears.
3. clauder-mcp is pruning valid sessions because os.kill(pid, 0) fails on Windows.

Fix

In clauder-mcp/server.py, update _pid_alive() to use the Windows-appropriate process check:

def _pid_alive(pid: int) -> bool:
    """Check if a process is running."""
    if sys.platform == "win32":
        import ctypes
        SYNCHRONIZE = 0x00100000
        handle = ctypes.windll.kernel32.OpenProcess(SYNCHRONIZE, False, pid)
        if handle == 0:
            return False
        ctypes.windll.kernel32.CloseHandle(handle)
        return True
    try:
        os.kill(pid, 0)
        return True
    except (OSError, ProcessLookupError):
        return False

---

Workaround (until fixed)

1. Set HOME to match USERPROFILE at the Windows system level:

   setx HOME "C:\Users\username"
   

   Then restart RStudio.

2. Patch _pid_alive() in the installed clauder-mcp/server.py to return True unconditionally on Windows:

   def _pid_alive(pid: int) -> bool:
       if sys.platform == "win32":
           return True
       try:
           os.kill(pid, 0)
           return True
       except (OSError, ProcessLookupError):
           return False

[IMNMV]

Thanks a bunch for pointing this out, as well as the detective work.

You're correct that my earlier fix in 3ca60a5 (in response to a similar bug for someone else on Windows) was wrong on the OneDrive case.

Both bugs fixed in d3a415d and shipped as clauder-mcp 0.5.1:

1. R discovery_dir() and Python SESSIONS_DIR now both use USERPROFILE on Windows, ignoring HOME. They will agree regardless of OneDrive redirection.
2. _pid_alive() now uses OpenProcess(SYNCHRONIZE) via ctypes on Windows, per your suggestion.

To pick up the fix:

remove.packages("ClaudeR")
devtools::install_github("IMNMV/ClaudeR")

Then restart R, run claudeAddin(), click Start Server. uvx clauder-mcp will auto-pull 0.5.1 the next time Claude Desktop starts a new session.

Let me know if anything still acts up on your end. Thanks again for the rigor! It makes implementing changes so much easier.

[ndtivendale]

It took me several hours of back and forth with Claude to figure this out!