Rainwater catchment and composting toilets.

We have an envirolet co.posting toilet that vents through the metal roof of our home. We need to do rainwater catchment as there is no room for a well where we live. The vent pipe is about a foot above the section of roof. I've noticed a smell of evaporating urine near the vent and wondered if this should be considered when collecting our rainwater. Should we avoid collecting rain from that roof section or will a healthy sized first flush take care of it?

I have written an extensive article on rainfall collection elsewhere on this site.
From my experience in Australia, the vent pipe will not be a problem, you can extend it further if that will make you feel better about it..
Where are you located?

Andy, are you thinking that the smell you are finding means there's some kind of potty substance on the roof?   What you are smelling is a gas from the pipe, and that won't collect on the roof in some black water kind of way.  Don't worry about what's coming out of the pipe.

One thing to consider is what are your roof shingles made out of?  If they are a tar-based composite, then that water has those bits of tar, that are always breaking down, in it.  That's why we have to replace the composite shingles every 15-20 years or so.   Most roof water should be used for landscape, not drinking.  So it's up to you whether you think the slow breakdown of composite roof shingles is something that would affect your vegetable/food garden.

While it might seem obvious that that water would be bad for food, not all plants uptake all substances.  It would take a lab to tell you what's in the water that comes off your roof.  As an example, galvanization of shed panels comes off slowly, breaks down in the soil, but plants don't uptake it.   The molecules are too big.

You could always put a charcoal filter on the water you've collected from the roof that says it will filter out most toxic substances, then use that water on vegetables.

I forgot about shingles.
We use metal roofs and its very suitable for rainfall collection

Thanks everyone. The roof is a new metal roof so shingle breakdown isn't an issue, I was just worried about the potential for pathogens to end up on the roof and therefore into our water supply. We're in Nova Scotia.