If it is AOT, then you're probably seeing this issue: 
http://dev.clojure.org/jira/browse/CLJ-130

On Tuesday, December 16, 2014 11:02:22 AM UTC-6, Nick Gonzalez wrote:
> I'm using codox to generate api documentation for a fairly large Cojure 
> project, and it is ignoring namespace doc strings for all but some of my 
> namespaces.  i have moved the :aot directives into the uberjar profile, so 
> the :apt option should not be the problem.  but who knows.  
> 
> 
> 1. Has anyone else experienced this issue?  
> 2. Is there a better way to generate API docs?
> 
> 
> FYI - I am also using Marginalia, and it is working great.  There are no 
> missing doc strings in the output.
> 
> 
> Thanks,
> -NG

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