When using the current version (v3 as of March 2017) of Carto.js with maps using Carto's new Builder interface, there are some issues you are likely to run into. Here I run through the common issues and some suggested workarounds.
This is because Carto.js v3 doesn't understand them. Sorry but there is no easy workaround here. In the case of Analysis you could save it as its own layer and use that layer instead.