I had some code that worked in 3.4 that was broken by 3.5 adding 'pruning.mode' and making the default mode be an error. It's fine for the default to change, but we should have a way to override it without making the code incompatible with earlier Bioconductor versions (i.e. I get an error if I set pruning.mode in 3.4). Probably the easiest way to achieve this is with getOption(). If the option you look for isn't set, it returns NULL, and then you can fall back to the default mode you have now (an error).