The ampersand is ambiguous and can be interpreted by perl as bitwise AND in certain contexts.
Wow, I've never seen that trap sprung.
The trap I have seen sprung quite a few times is sub log { ... }. That is why I follow my own advice in my 'classic' node, (tye)Re: A question of style, and mix case in all of my subroutine names.
But, I sometimes slip and use camelCase and then get lazy and give a routine or two one-word names and... I've actually still been bit by sub log { ... }, just less frequently than before.
So using &func( ... ) is still in my list of optional best practices for two reasons. First, it prevents you from being caught (often very confusingly) if you unintentially give your subroutine a "reserved" name. Second, it is a valid style choice to visually distinguish user sub calls from other similar-looking constructs.
Note that if you import a &log, then log() will call it and so the leading ampersand is not as useful for imported routines. So I don't find the "might disable prototypes" argument too worrisome. Since, if I didn't important the routine, then I'm sure to know whether or not I was stupid enough to use a prototype on it. While, if I imported the routine, I don't need to use the ampersand (and modules that export over the top of built-in functions usually have a good reason for doing so or get bug reports filed against them).
Now, as far as best practices go, I consider "always mix case (or add an underscore) in your subroutine names" to be a better "best practices" then "use &sub(...) when calling your own subs", because there are fewer nearby potential down-sides (such as using &sub w/o parens). But I do get annoyed when I see (every time the subject comes up) a bunch of people spouting poorly justified proclamations against using &sub(...) while also not warning against using subroutine names that might accidentally match a built-in.
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