I'm not really a fan of Double/NaN in general, but sometimes it seems like the least evil choice. When I find myself in one of those cases I always hate having to write tests in a way that differs from all the other tests in the codebase. A goal I've always had with expectations is to keep the syntax consistent, and as a result I've chosen to treat Double/NaN as equal to Double/NaN when in the various Clojure data structures.

The following examples demonstrate Double/NaN being treated as equal

;; allow Double/NaN equality in a map
(expect {:a Double/NaN :b {:c Double/NaN}} {:a Double/NaN :b {:c Double/NaN}})

;; allow Double/NaN equality in a set
(expect #{1 Double/NaN} #{1 Double/NaN})

;; allow Double/NaN equality in a list
(expect [1 Double/NaN] [1 Double/NaN])

jfields$ lein expectations
Ran 3 tests containing 3 assertions in 32 msecs
0 failures, 0 errors.

;; allow Double/NaN equality when verifying values are in a map
(expect {:a Double/NaN :b {:c Double/NaN}} (in {:a Double/NaN :b {:c Double/NaN} :d "other stuff"}))

;; allow Double/NaN equality when verifying it is in a set
(expect Double/NaN (in #{1 Double/NaN}))

;; allow Double/NaN equality when verifying it's existence in a list
(expect Double/NaN (in [1 Double/NaN]))

jfields$ lein expectations
Ran 3 tests containing 3 assertions in 32 msecs
0 failures, 0 errors.

;; allow Double/NaN equality in a map
(expect {:a Double/NaN :b {:c Double/NaN}} {:a nil :b {:c Double/NaN}})

;; allow Double/NaN equality with in fn and map
(expect {:a Double/NaN :b {:c nil}} (in {:a Double/NaN :b {:c Double/NaN} :d "other stuff"}))

;; allow Double/NaN equality in a set
(expect #{1 Double/NaN} #{1 nil})

;; allow Double/NaN equality with in fn and set
(expect Double/NaN (in #{1 nil}))

;; allow Double/NaN equality in a list
(expect [1 Double/NaN] [1 nil])

;; allow Double/NaN equality with in fn and list
(expect Double/NaN (in [1 nil]))


jfields$ lein expectations
failure in (core.clj:5) : sample.test.core
           (expect {:a Double/NaN, :b {:c Double/NaN}}
                   {:a nil, :b {:c Double/NaN}})
           expected: {:a NaN, :b {:c NaN}} 
                was: {:a nil, :b {:c NaN}}
           :a expected: NaN
                   was: nil
failure in (core.clj:8) : sample.test.core
           (expect {:a Double/NaN, :b {:c nil}} (in {:a Double/NaN, :b {:c Double/NaN}, :d "other stuff"}))
           expected: {:a NaN, :b {:c nil}} 
                 in: {:a NaN, :b {:c NaN}, :d "other stuff"}
           :b {:c expected: nil
                       was: NaN
failure in (core.clj:11) : sample.test.core
           (expect #{1 Double/NaN} #{nil 1})
           expected: #{NaN 1} 
                was: #{nil 1}
           nil are in actual, but not in expected
           NaN are in expected, but not in actual
failure in (core.clj:14) : sample.test.core
           (expect Double/NaN (in #{nil 1}))
           key NaN not found in #{nil 1}
failure in (core.clj:17) : sample.test.core
           (expect [1 Double/NaN] [1 nil])
           expected: [1 NaN] 
                was: [1 nil]
           nil are in actual, but not in expected
           NaN are in expected, but not in actual
failure in (core.clj:20) : sample.test.core
           (expect Double/NaN (in [1 nil]))
           value NaN not found in [1 nil]
Ran 6 tests containing 6 assertions in 66 msecs
6 failures, 0 errors.

From http://blog.jayfields.com/2011/11/clojure-expectations-and-doublenan.html