What means this error message: lsof: WARNING: can't stat() fuse.gvfs-fuse-daemon file system /home/nes/.gvfs
Solution 1:
There is a FUSE virtual filesystem mounted at ~/.gvfs.
For the majority of filesystem accesses, permissions are ignored for the root user. However, FUSE virtual filesystem mounts are one of the rare exceptions. FUSE virtual filesystems are normally restricted to the user who mounted them.
In this case, the gvfs-fuse-daemon command (run as part of your desktop session) created this mount, belonging to you, and no-one else can access it, including root.