jbuilder fails if there is any unreadable directory under the current directory:

~$ jbuilder external-lib-deps --missing @install
Error: exception Sys_error("cloj/popco-x: Permission denied")
... [long, ugly stacktrace]

It's arguable that this isn't a serious problem for building one's own projects, but it's common to be told to run the above command e.g. when there's a problem with an installation of some package via opam. If you run that command from e.g. your $HOME directory (why wouldn't you?), then any unreadable directory under that location that can be found e.g. via links stop the process. (In my case, I have a couple of directories of my own that I've set to be unreadable for my own reasons. One could imagine cases in which someone has a link into a tree belonging to another user or root or something like that, where only some of the directories are readable.)

It seems like it would make more sense to simply ignore unreadable directories, or possibly issue a warning and continue.