I suggest to specify the dependencies in your plugin's composer.json file which is used to register it in our new plugins repository at http://plugins.roundcube.net.
I think http://trac.roundcube.net/ticket/1489785 is related. Composer appears to be not great and checking what is already available on the system.
I'm not sure the description in this ticket is 100% correct. I cannot recreate it. I am wondering if may be its when people have PEAR globally available on their system – Composer can’t tell, adds it and then the two conflict.
I know that both the PEAR class and Net_Sieve are shipped with Roundcube but I thought it was best to include the dependencies for people who have the GPL version installed. May be that was a mistake and I should not include it at all, just put a comment in the readme for people who need it.
Also because Roundcube its self does not use Composer it's not possible to add in "standard" plugins that are required - like jqueryui for example.
Phil