I have encountered the same problem with vboxsf mounted folders when using Debian guest on VirtualBox 6.1 hosted by Windows 10.

The general VirtualBox issue of vboxsf not supporting rmdir when there are open file descriptors is difficult to solve, and out of scope for Python.

However, it looks like the shutil.rmtree implementation can be easily modified to change the order of operations so that the rmdir is performed after the directory file descriptor is closed, which makes shutil.rmtree work under vboxsf shared folders.

Example of the change against Python 3.7 is inlined below. The changed order matches the behavior of "rm -r" and to my understanding should not change the security implications of the code, but as the code is related to the prevention of a symlink attack https://bugs.python.org/issue4489 careful review would be needed.


--- /usr/lib/python3.7/shutil.py--orig  2021-01-23 05:04:44.000000000 +0900
+++ /usr/lib/python3.7/shutil.py        2021-12-09 20:42:36.795338346 +0900
@@ -427,10 +427,6 @@
                 try:
                     if os.path.samestat(orig_st, os.fstat(dirfd)):
                         _rmtree_safe_fd(dirfd, fullname, onerror)
-                        try:
-                            os.rmdir(entry.name, dir_fd=topfd)
-                        except OSError:
-                            onerror(os.rmdir, fullname, sys.exc_info())
                     else:
                         try:
                             # This can only happen if someone replaces
@@ -442,6 +438,10 @@
                             onerror(os.path.islink, fullname, sys.exc_info())
                 finally:
                     os.close(dirfd)
+                try:
+                    os.rmdir(entry.name, dir_fd=topfd)
+                except OSError:
+                    onerror(os.rmdir, fullname, sys.exc_info())
         else:
             try:
                 os.unlink(entry.name, dir_fd=topfd)
@@ -489,10 +489,6 @@
         try:
             if os.path.samestat(orig_st, os.fstat(fd)):
                 _rmtree_safe_fd(fd, path, onerror)
-                try:
-                    os.rmdir(path)
-                except OSError:
-                    onerror(os.rmdir, path, sys.exc_info())
             else:
                 try:
                     # symlinks to directories are forbidden, see bug #1669
@@ -501,6 +497,10 @@
                     onerror(os.path.islink, path, sys.exc_info())
         finally:
             os.close(fd)
+        try:
+            os.rmdir(path)
+        except OSError:
+            onerror(os.rmdir, path, sys.exc_info())
     else:
         try:
             if os.path.islink(path):