This is fixed by 8b221b64a552d31e241701aa5c6d339287a7a15b on master. The
problem was occuring inside "deduplicate" procedure of (guix store
deduplication).
This procedure uses scandir* to check if the path to deduplicate is a
directory. The problem is that JFS does not support d_type so, the file
property returned was 'unknown. As this particular case was not handled,
directories were not detected as such, causing the procedure to call
"link" on a directory, which was failing.
Mathieu