lein codox classpath problem

[matthewrfellows]

When trying to run lein codox, I'm getting this error:

java.io.FileNotFoundException: Could not locate clojure/tools/reader/impl/ExceptionInfo__init.class or clojure/tools/reader/impl/ExceptionInfo.clj on classpath.

For context, lein version returns Leiningen 2.5.3 on Java 1.7.0_65 Java HotSpot(TM) 64-Bit Server VM. I'm running on OSX 10.9.5.

Perhaps it's related to this issue (taoensso/sente#181 (comment) ; see also http://yogthos.net/posts/2015-12-26-AOTGotchas.html). On the other hand, the project itself compiles just fine, I only get this error when trying to generate the docs.

Here's the project file, for more context.

(defproject api-web "0.2.3"
  :description "REST API"
  :aot :all
  :main api-web.core
  :dependencies [ [org.clojure/clojure "1.7.0"]
                  [compojure "1.4.0" :exclusions [commons-codec]]
                  [ring/ring-devel "1.4.0"]
                  [ring/ring-core "1.4.0" :exclusions [clj-time org.clojure/tools.reader]]
                  [javax.servlet/servlet-api "2.5"] ; necessary for ring
                  [http-kit "2.1.19"]
                  [cheshire "5.5.0"]
                  [simple-time "0.2.0" :exclusions [joda-time]]
                  [com.taoensso/timbre "4.1.4" :exclusions [org.clojure/tools.reader]]
                  [com.fasterxml.jackson.core/jackson-annotations "2.6.0"]
                  [prismatic/schema "1.0.4"]
                  ]
  :profiles {:dev {:dependencies [[org.clojure/test.check "0.9.0"]]}}
  :jvm-opts ["-XX:MaxPermSize=256m"]
  :war-resources-path "war-resources"
  :plugins [[lein-ring "0.9.7"]
            [lein-codox "0.9.1"]]
  :codox {:metadata {:doc/format :markdown}}
  :ring { :handler api-web.core/app
          :init api-web.core/init-app
          :destroy api-web.core/exit-app}
  :repl-options {:timeout 50000})

[weavejester]

It sounds like you're having an issue with out of date class files. What happens if you run:

lein do clean, codox

Does it work then?

[matthewrfellows]

Unfortunately, no, I still get that error.

On Tue, Jan 5, 2016 at 2:18 PM, James Reeves notifications@github.com
wrote:

It sounds like you're having an issue with out of date class files. What
happens if you run lein do clean, codox? Does it work then?

—
Reply to this email directly or view it on GitHub
#113 (comment).

[weavejester]

Do you have any plugins or dependencies in your ~/.lein/profiles.clj file?

[matthewrfellows]

Good thought.
I did have some plugins, but I just removed all those and tried again (lein
clean, lein codox), and the problem still shows up.

On Tue, Jan 5, 2016 at 2:53 PM, James Reeves notifications@github.com
wrote:

Do you have any plugins or dependencies in your ~/.lein/profiles.clj file?

—
Reply to this email directly or view it on GitHub
#113 (comment).

[weavejester]

Hm, I still can't reproduce the problem you have. I've cleared my profiles.clj in case anything in that was making it work on my machine. I have the same Leiningen version. I'm using the project.clj file you supplied. Codox works fine for me no matter what I do.

Is it possible to post your full source, or put together a sample project that reproduces the problem?

[matthewrfellows]

Thanks for looking into it.
The full source would be a bit overwhelming. I will try to whittle it down
to a minimal set that reproduces the issue.

On Tue, Jan 5, 2016 at 6:34 PM, James Reeves notifications@github.com
wrote:

Hm, I still can't reproduce the problem you have. I've cleared my
profiles.clj in case anything in that was making it work on my machine. I
have the same Leiningen version. I'm using the project.clj file you
supplied. Codox works fine for me no matter what I do.

Is it possible to post your full source, or put together a sample project
that reproduces the problem?

—
Reply to this email directly or view it on GitHub
#113 (comment).

[matthewrfellows]

I've found a very minimal project that does reproduce the problem, and it does seem related to the taoensso.timbre, taoensso.encore issue (taoensso/sente#181).

Run lein new app codoxtest2, and then replace the project.clj and core.clj files with the following to reproduce the issue. If you comment out the :aot :all line in the project file, below, lein codox works fine.

project.clj

(defproject codoxtest2 "0.1.0-SNAPSHOT"
  :dependencies [[org.clojure/clojure "1.7.0"]
                 [com.taoensso/timbre "4.1.4"]]
  :plugins [[lein-codox "0.9.1"]]
  :aot :all
  :main codoxtest2.core)

core.clj

(ns codoxtest2.core
  (:gen-class)
  (:require [taoensso.timbre :refer [warnf warn]]))

(defn -main
  "I don't do a whole lot ... yet."
  [& args]
  (println "Hello, World!"))

[matthewrfellows]

Well, here's a resolution, of sorts.

If, in my full project, I remove the :aot :all line from project.clj, and then do lein codox, I get all sorts of errors that look something like:
Could not generate clojure documentation for api-web.core - root cause: clojure.lang.Compiler$CompilerException java.lang.ExceptionInInitializerError ...

In this case, lein codox does "finish" generating documentation, but it is, effectively, empty.

If, on the other hand, I remove :aot :all from the project.clj files for all of my local projects on which the project in question depends, then lein codox works fine.

This definitely seems to be a more general dependency issue, not directly related to codox.

I think I can work around the issue by adding :uberjar {:aot :all} to the profiles map in the project files.