Plugin is defining pluggable wp_mail() function. My idea was to check if function is defined already and throw warning if other plugin beat me to it.
However this warning causes issues on activation. As far as I understand during normal operation plugin is loaded before pluggable.php but for the purpose of activation check it is loaded after pluggables.
What would be the robust/proper/suggested way to implement such check for pluggable function? There is no obvious (for me) way to distinguish activation and handle it separately.
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Don’t do the check on activation?
Seriously, the best way I can think of is not to check for this on activation, but only in the normal plugin load process. And instead of throwing a warning (I assume you mean a PHP E_WARNING), perhaps putting an admin error box up would make more sense.