Jozef, I looked into this and opened a ticket with a proposed patch to
fix this issue: http://dev.clojure.org/jira/browse/CLJ-1650

Jozef Wagner writes:

> With CLJ-979 applied, lein may crash when doing :aot :all. This is caused
> when lein forces recompilation of already compiled classes. Not sure
> whether this should be considered a lein of clojure bug though.
>
> See https://github.com/wagjo/aotbug for contrived example.
>
> Jozef
>
> On Saturday, January 10, 2015 at 4:37:04 PM UTC+1, Alex Miller wrote:
>>
>> Clojure 1.7.0-alpha5 is now available.
>>
>> Try it via
>> - Download:
>> https://repo1.maven.org/maven2/org/clojure/clojure/1.7.0-alpha5/
>> - Leiningen: [org.clojure/clojure "1.7.0-alpha5"]
>>
>> A few of the highlights in alpha5:
>>
>> 1) New transducer arities for map-indexed, distinct, and interpose.
>> The transducer versions are generally faster than the sequence versions.
>> See CLJ-1601 for more details.
>>
>> 2) The set and vec functions should now be faster in many cases. Some of
>> the
>> vec improvements will not kick in until CLJ-1499 is committed in the
>> future.
>> See CLJ-1546 and CLJ-1618 for more details.
>>
>> 3) Two particularly troublesome AOT classloading bugs have been addressed
>> -
>> CLJ-979 and CLJ-1544. Many other tickets were found to be duplicates of
>> one of
>> these as well. Big thanks to Nicola Mometto for doing the hard work on
>> debugging and providing fixes for these.
>>
>> For all changes new in alpha5, see the issues marked "(alpha5)" in the
>> full changes below.
>>
>> ------------------------------------------------------------
>> Clojure 1.7.0-alpha5 has the changes below from 1.6.0:
>>
>> ## 1 New and Improved Features
>>
>> ### 1.1 Transducers
>>
>> Transducers is a new way to decouple algorithmic transformations from their
>> application in different contexts. Transducers are functions that transform
>> reducing functions to build up a "recipe" for transformation.
>>
>> Also see: http://clojure.org/transducers
>>
>> Many existing sequence functions now have a new arity (one fewer argument
>> than before). This arity will return a transducer that represents the same
>> logic but is independent of lazy sequence processing. Functions included
>> are:
>>
>> * conj (conjs to [])
>> * map
>> * mapcat
>> * filter
>> * remove
>> * take
>> * take-while
>> * drop
>> * drop-while
>> * cycle
>> * take-nth
>> * replace
>> * partition-by
>> * partition-all
>> * keep
>> * keep-indexed
>> * map-indexed (alpha5)
>> * distinct (alpha5)
>> * interpose (alpha5)
>>
>> Additionally some new transducer functions have been added:
>>
>> * cat - concatenates the contents of each input
>> * de-dupe - removes consecutive duplicated values
>> * random-sample - returns items from coll with random probability
>>
>> And this function can be used to make completing transforms:
>>
>> * completing
>>
>> There are also several new or modified functions that can be used to apply
>> transducers in different ways:
>>
>> * sequence - takes a transformation and a coll and produces a lazy seq
>> * transduce - reduce with a transformation (eager)
>> * eduction - returns a reducible/seqable/iterable seq of applications of
>> the transducer to items in coll. Applications are re-performed with every
>> reduce/seq/iterator.
>> * run! - run the transformation for side effects on the collection
>>
>> There have been a number of internal changes to support transducers:
>>
>> * volatiles - there are a new set of functions (volatile!, vswap!,
>> vreset!, volatile?) to create and use volatile "boxes" to hold state in
>> stateful transducers. Volatiles are faster than atoms but give up atomicity
>> guarantees so should only be used with thread isolation.
>> * array iterators - added support for iterators over arrays
>>
>> Some related issues addressed during development:
>> * [CLJ-1511](http://dev.clojure.org/jira/browse/CLJ-1511)
>> * [CLJ-1497](http://dev.clojure.org/jira/browse/CLJ-1497)
>> * [CLJ-1549](http://dev.clojure.org/jira/browse/CLJ-1549)
>> * [CLJ-1537](http://dev.clojure.org/jira/browse/CLJ-1537)
>> * [CLJ-1554](http://dev.clojure.org/jira/browse/CLJ-1554)
>> * [CLJ-1601](http://dev.clojure.org/jira/browse/CLJ-1601) (alpha5)
>> * [CLJ-1606](http://dev.clojure.org/jira/browse/CLJ-1606) (alpha5)
>> * [CLJ-1621](http://dev.clojure.org/jira/browse/CLJ-1621) (alpha5)
>> * [CLJ-1600](http://dev.clojure.org/jira/browse/CLJ-1600) (alpha5)
>>
>> ### 1.2 Keyword and Symbol Construction
>>
>> In response to issues raised in [CLJ-1439](
>> http://dev.clojure.org/jira/browse/CLJ-1439),
>> several changes have been made in symbol and keyword construction:
>>
>> 1) The main bottleneck in construction of symbols (which also occurs
>> inside keywords) was
>> interning of the name and namespace strings. This interning has been
>> removed, resulting
>> in a performance increase.
>>
>> 2) Keywords are cached and keyword construction includes a cache check. A
>> change was made
>> to only clear the cache reference queue when there is a cache miss.
>>
>> ### 1.3 Warn on Boxed Math
>>
>> One source of performance issues is the (unintended) use of arithmetic
>> operations on
>> boxed numbers. To make detecting the presence of boxed math easier, a
>> warning will now
>> be emitted about boxed math if \*unchecked-math* is set to :warn-on-boxed
>> (any truthy
>> value will enable unchecked-math, only this specific value enables the
>> warning).
>>
>> Example use:
>>
>>     user> (defn plus-2 [x] (+ x 2))  ;; no warning, but boxed
>> #'user/plus-2
>>     user> (set! *unchecked-math* :warn-on-boxed)
>> true
>>     user> (defn plus-2 [x] (+ x 2)) ;; now we see a warning
>>     Boxed math warning, NO_SOURCE_PATH:10:18 - call: public static
>> java.lang.Number
>> clojure.lang.Numbers.unchecked_add(java.lang.Object,long).
>>     #'user/plus-2
>> user> (defn plus-2 [^long x] (+ x 2)) ;; use a hint to avoid boxing
>> #'user/plus-2
>>
>> * [CLJ-1325](http://dev.clojure.org/jira/browse/CLJ-1325)
>> * [CLJ-1535](http://dev.clojure.org/jira/browse/CLJ-1535)
>>
>> ### 1.4 update - like update-in for first level
>>
>> `update` is a new function that is like update-in specifically for
>> first-level keys:
>>
>>     (update m k f args...)
>>
>> Example use:
>>
>>     user> (update {:a 1} :a inc)
>> {:a 2}
>> user> (update {:a 1} :a + 2)
>> {:a 3}
>> user> (update {} :a identity)  ;; missing returns nil
>> {:a nil}
>>
>> * [CLJ-1251](http://dev.clojure.org/jira/browse/CLJ-1251)
>>
>> ## 2 Enhancements
>>
>> ### 2.1 Error messages
>>
>> * [CLJ-1261](http://dev.clojure.org/jira/browse/CLJ-1261)
>>   Invalid defrecord results in exception attributed to consuming ns
>> instead of defrecord ns
>> * [CLJ-1169](http://dev.clojure.org/jira/browse/CLJ-1169)
>>   Report line,column, and source in defmacro errors
>> * [CLJ-1297](http://dev.clojure.org/jira/browse/CLJ-1297)
>>   Give more specific hint if namespace with "-" not found to check file
>> uses "_"
>>
>> ### 2.2 Documentation strings
>>
>> * [CLJ-1417](http://dev.clojure.org/jira/browse/CLJ-1417)
>>   clojure.java.io/input-stream has incorrect docstring
>> * [CLJ-1357](http://dev.clojure.org/jira/browse/CLJ-1357)
>>   Fix typo in gen-class doc-string
>> * [CLJ-1479](http://dev.clojure.org/jira/browse/CLJ-1479)
>>   Fix typo in filterv example
>> * [CLJ-1480](http://dev.clojure.org/jira/browse/CLJ-1480)
>>   Fix typo in defmulti docstring
>> * [CLJ-1477](http://dev.clojure.org/jira/browse/CLJ-1477)
>>   Fix typo in deftype docstring
>> * [CLJ-1478](http://dev.clojure.org/jira/browse/CLJ-1378)
>>   Fix typo in clojure.main usage
>>
>> ### 2.3 Performance
>>
>> * [CLJ-1430](http://dev.clojure.org/jira/browse/CLJ-1430)
>>   Improve performance of partial with more unrolling
>> * [CLJ-1384](http://dev.clojure.org/jira/browse/CLJ-1384)
>>   clojure.core/set should use transients for better performance
>> * [CLJ-1429](http://dev.clojure.org/jira/browse/CLJ-1429)
>>   Cache unknown multimethod value default dispatch
>> * [CLJ-1529](http://dev.clojure.org/jira/browse/CLJ-1529)
>>   Reduce compile times by avoiding unnecessary calls to Class.forName()
>> * [CLJ-1546](http://dev.clojure.org/jira/browse/CLJ-1546) (alpha5)
>>   vec is now faster on almost all inputs
>> * [CLJ-1618](http://dev.clojure.org/jira/browse/CLJ-1618) (alpha5)
>>   set is now faster on almost all inputs
>>
>> ### 2.4 Other enhancements
>>
>> * [CLJ-1191](http://dev.clojure.org/jira/browse/CLJ-1191)
>>   Improve apropos to show some indication of namespace of symbols found
>> * [CLJ-1378](http://dev.clojure.org/jira/browse/CLJ-1378)
>>   Hints don't work with #() form of function
>> * [CLJ-1498](http://dev.clojure.org/jira/browse/CLJ-1498)
>>   Removes owner-thread check from transients - this check was preventing
>> some valid usage of transients in core.async where a transient is created
>> on one thread and then used again in another pooled thread (while still
>> maintaining thread isolation).
>> * [CLJ-803](http://dev.clojure.org/jira/browse/CLJ-803)
>>   Extracted IAtom interface implemented by Atom.
>> * [CLJ-1315](http://dev.clojure.org/jira/browse/CLJ-1315)
>>   Don't initialize classes when importing them
>> * [CLJ-1330](http://dev.clojure.org/jira/browse/CLJ-1330)
>>   Class name clash between top-level functions and defn'ed ones
>> * [CLJ-1349](http://dev.clojure.org/jira/browse/CLJ-1349)
>>   Update to latest test.generative and add dependency on test.check
>> * [CLJ-1546](http://dev.clojure.org/jira/browse/CLJ-1546) (alpha5)
>>   vec now works with things that only implement Iterable or IReduceInit
>> * [CLJ-1618](http://dev.clojure.org/jira/browse/CLJ-1618) (alpha5)
>>   set now works with things that only implement Iterable or IReduceInit
>> * [CLJ-1633](http://dev.clojure.org/jira/browse/CLJ-1633) (alpha5)
>>   PersistentList/creator doesn't handle ArraySeqs correctly
>>
>> ## 3 Bug Fixes
>>
>> * [CLJ-1362](http://dev.clojure.org/jira/browse/CLJ-1362)
>>   Reduce broken on some primitive vectors
>> * [CLJ-1388](http://dev.clojure.org/jira/browse/CLJ-1388)
>>   Equality bug on records created with nested calls to map->record
>> * [CLJ-1274](http://dev.clojure.org/jira/browse/CLJ-1274)
>>   Unable to set compiler options via system properties except for AOT
>> compilation
>> * [CLJ-1241](http://dev.clojure.org/jira/browse/CLJ-1241)
>>   NPE when AOTing overrided clojure.core functions
>> * [CLJ-1185](http://dev.clojure.org/jira/browse/CLJ-1185)
>>   reductions does not check for reduced value
>> * [CLJ-1039](http://dev.clojure.org/jira/browse/CLJ-1039)
>>   Using def with metadata {:type :anything} throws ClassCastException
>> during printing
>> * [CLJ-887](http://dev.clojure.org/jira/browse/CLJ-887)
>>   Error when calling primitive functions with destructuring in the arg
>> vector
>> * [CLJ-823](http://dev.clojure.org/jira/browse/CLJ-823)
>>   Piping seque into seque can deadlock
>> * [CLJ-738](http://dev.clojure.org/jira/browse/CLJ-738)
>>   <= is incorrect when args include Double/NaN
>> * [CLJ-1408](http://dev.clojure.org/jira/browse/CLJ-1408)
>>   Make cached string value of Keyword and Symbol transient
>> * [CLJ-1466](http://dev.clojure.org/jira/browse/CLJ-1466)
>>   clojure.core/bean should implement Iterable
>> * [CLJ-1578](http://dev.clojure.org/jira/browse/CLJ-1578)
>>   Make refer of Clojure core function not throw exception on reload
>> * [CLJ-1501](http://dev.clojure.org/jira/browse/CLJ-1501)
>>   LazySeq equals() should not use equiv() logic
>> * [CLJ-1572](http://dev.clojure.org/jira/browse/CLJ-1572) (alpha5)
>>   into (and other fns that rely on reduce) require only IReduceInit
>> * [CLJ-1619](http://dev.clojure.org/jira/browse/CLJ-1619) (alpha5)
>>   PersistentVector now directly implements reduce without init
>> * [CLJ-1580](http://dev.clojure.org/jira/browse/CLJ-1580) (alpha5)
>>   Transient collections should guarantee thread visibility
>> * [CLJ-1590](http://dev.clojure.org/jira/browse/CLJ-1590) (alpha5)
>>   Some IReduce/IReduceInit implementors don't respect reduced
>> * [CLJ-979](http://dev.clojure.org/jira/browse/CLJ-979) (alpha5)
>>   Clojure resolves to wrong deftype classes when AOT compiling or reloading
>> * [CLJ-1544](http://dev.clojure.org/jira/browse/CLJ-1544) (alpha5)
>>   AOT bug involving namespaces loaded before AOT compilation started
>>

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