Re: maven-shade-plugin issues with Clojure core (or any clj) AOT compilation

[Philip Aston]

I just tripped over this and 
opened https://issues.apache.org/jira/browse/MSHADE-272 . Affected users 
might like to vote it up.

FWIW, my workaround:



maven-shade-plugin



...


*:*

**/*.class
**/*.properties


clojure/core_instant18.clj








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Re: maven-shade-plugin issues with Clojure core (or any clj) AOT compilation

[Mike Rodriguez]

Thanks for the feedback.  I will try to track this issue via the 
maven-shade-plugin then.  Hopefully there can be some momentum to change it 
there.

On Saturday, December 31, 2016 at 12:09:32 PM UTC-5, Alex Miller wrote:
>
> This seems like a pretty straightforward bug with maven-shade-plugin not 
> preserving information that it should, so it seems like it should be fixed 
> there.
>
> On Wednesday, December 28, 2016 at 7:06:11 AM UTC-6, Mike Rodriguez wrote:
>>
>> Background:
>>
>> This problem is specific to building jars that contain AOT (Ahead Of 
>> Time) compiled Clojure code using Maven and the maven-shade-plugin.
>>
>> Clojure AOT compilation depends on timestamps of .class files vs .clj 
>> files being accurate.  When both .class files and their associated .clj 
>> files exist, the AOT .class files are only used by the compiler if their 
>> last modified timestamp is strictly greater than the last modified 
>> timestamp of the associated .clj file.
>>
>> Also note that the Clojure core jar itself is deployed AOTed.
>>
>> I know that much of the Clojure ecosystem uses Leiningen as a build tool 
>> (and boot now too I guess).  This problem doesn't apply to Leiningen (and I 
>> haven't looked at boot).
>>
>> Problem:
>>
>> The maven-shade-plugin is popular for building shaded/uber/standalone 
>> jars in Maven.  Typically this means the jar will include some/all of its 
>> dependency jars' files.  The maven-shade-plugin has an unfortunate property 
>> though.  It does not preserve the timestamps on files that are added to 
>> this final shaded jar.  The resulting jar actually ends up with all files 
>> inside of it having the same timestamp (when the jar was created).  In 
>> particular, if you originally had AOT Clojure .class files and .clj files 
>> with different last modified timestamps, now they will have the same 
>> timestamps in the shaded jar.
>>
>> I've brought this up before @ 
>> http://stackoverflow.com/questions/19594360/preserving-timestamps-on-clojure-clj-files-when-building-shaded-jar-via-maven-s
>>
>> I have rarely seen people bring up issues around this with 
>> maven-shade-plugin beyond this particular case.  I believe I have seen a 
>> complaint or two around the timestamp loss during shading (I can't find 
>> them now), but nothing that has gained any traction (I may try to bring it 
>> up to the plugin people soon though).
>>
>> When the AOTed .class file is ignored in favor of the .clj file, the 
>> namespace is JIT (Just-In-Time) compiled.  There are several issues with 
>> this.
>>
>> 1) Performance:  It makes the AOT files mostly worthless since they are 
>> not saving you on startup time costs anymore.  Everything is JITed anyways.
>> 2) Errors:  The reloading of the .clj files is a forced reload of the 
>> .clj namespaces involved.  This can cause classpath clashes among 
>> ClassLoaders.
>> - There are quite a few CLJ Jiras out there that faced trouble dealing 
>> with the mix of reloading namespaces and AOT compilation.
>>
>> You may be thinking, "Just don't build your Clojure jars with Maven.  Use 
>> Leiningen instead perhaps?"
>> This is fine when it is something you control.  However, what if I want 
>> to use Clojure to develop a library that may be consumed by Java consumers 
>> who very likely will be using Maven.  If my library is going to be shaded 
>> into a standalone jar with maven-shade-plugin by this Java consumer (again, 
>> likely) then this scenario can happen.
>>
>> Another thought that may occur is to just avoid AOT compilation of my 
>> library application to avoid the problem (this is recommended in the 
>> community I believe).  However, Clojure core is AOT compiled and it will 
>> get included in the shaded jar.  That alone is enough to cause the issue.
>>
>> Example:
>>
>> I have a GitHub repo to show a minimum example of where this can be a 
>> problem.  In particular it shows a way for the problem (2) to occur.
>> @ https://github.com/mrrodriguez/mvn-shade-test
>>
>> This repo has a Java API through shade.ShadeJava that will cause the 
>> Clojure compiler to require the shade.main namespace using JIT compilation. 
>>  However, shade.main uses clojure.pprint, which is AOT compiled via Clojure 
>> core.
>>
>> clojure.pprint was chosen here just because it one of the cases I've seen 
>> come up that actually fail with problem (2) from above.  Even if there were 
>> no failures though, the Clojure core namespaces would be getting recompiled 
>> with problem (1).
>>
>>

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Re: maven-shade-plugin issues with Clojure core (or any clj) AOT compilation

[Alex Miller]

This seems like a pretty straightforward bug with maven-shade-plugin not 
preserving information that it should, so it seems like it should be fixed 
there.

On Wednesday, December 28, 2016 at 7:06:11 AM UTC-6, Mike Rodriguez wrote:
>
> Background:
>
> This problem is specific to building jars that contain AOT (Ahead Of Time) 
> compiled Clojure code using Maven and the maven-shade-plugin.
>
> Clojure AOT compilation depends on timestamps of .class files vs .clj 
> files being accurate.  When both .class files and their associated .clj 
> files exist, the AOT .class files are only used by the compiler if their 
> last modified timestamp is strictly greater than the last modified 
> timestamp of the associated .clj file.
>
> Also note that the Clojure core jar itself is deployed AOTed.
>
> I know that much of the Clojure ecosystem uses Leiningen as a build tool 
> (and boot now too I guess).  This problem doesn't apply to Leiningen (and I 
> haven't looked at boot).
>
> Problem:
>
> The maven-shade-plugin is popular for building shaded/uber/standalone jars 
> in Maven.  Typically this means the jar will include some/all of its 
> dependency jars' files.  The maven-shade-plugin has an unfortunate property 
> though.  It does not preserve the timestamps on files that are added to 
> this final shaded jar.  The resulting jar actually ends up with all files 
> inside of it having the same timestamp (when the jar was created).  In 
> particular, if you originally had AOT Clojure .class files and .clj files 
> with different last modified timestamps, now they will have the same 
> timestamps in the shaded jar.
>
> I've brought this up before @ 
> http://stackoverflow.com/questions/19594360/preserving-timestamps-on-clojure-clj-files-when-building-shaded-jar-via-maven-s
>
> I have rarely seen people bring up issues around this with 
> maven-shade-plugin beyond this particular case.  I believe I have seen a 
> complaint or two around the timestamp loss during shading (I can't find 
> them now), but nothing that has gained any traction (I may try to bring it 
> up to the plugin people soon though).
>
> When the AOTed .class file is ignored in favor of the .clj file, the 
> namespace is JIT (Just-In-Time) compiled.  There are several issues with 
> this.
>
> 1) Performance:  It makes the AOT files mostly worthless since they are 
> not saving you on startup time costs anymore.  Everything is JITed anyways.
> 2) Errors:  The reloading of the .clj files is a forced reload of the .clj 
> namespaces involved.  This can cause classpath clashes among ClassLoaders.
> - There are quite a few CLJ Jiras out there that faced trouble dealing 
> with the mix of reloading namespaces and AOT compilation.
>
> You may be thinking, "Just don't build your Clojure jars with Maven.  Use 
> Leiningen instead perhaps?"
> This is fine when it is something you control.  However, what if I want to 
> use Clojure to develop a library that may be consumed by Java consumers who 
> very likely will be using Maven.  If my library is going to be shaded into 
> a standalone jar with maven-shade-plugin by this Java consumer (again, 
> likely) then this scenario can happen.
>
> Another thought that may occur is to just avoid AOT compilation of my 
> library application to avoid the problem (this is recommended in the 
> community I believe).  However, Clojure core is AOT compiled and it will 
> get included in the shaded jar.  That alone is enough to cause the issue.
>
> Example:
>
> I have a GitHub repo to show a minimum example of where this can be a 
> problem.  In particular it shows a way for the problem (2) to occur.
> @ https://github.com/mrrodriguez/mvn-shade-test
>
> This repo has a Java API through shade.ShadeJava that will cause the 
> Clojure compiler to require the shade.main namespace using JIT compilation. 
>  However, shade.main uses clojure.pprint, which is AOT compiled via Clojure 
> core.
>
> clojure.pprint was chosen here just because it one of the cases I've seen 
> come up that actually fail with problem (2) from above.  Even if there were 
> no failures though, the Clojure core namespaces would be getting recompiled 
> with problem (1).
>
>

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Re: maven-shade-plugin issues with Clojure core (or any clj) AOT compilation

[Mike Rodriguez]

I also forgot to include the error message from my example GitHub project, 
in case it is easier than actually running it.  I understand this issue for 
the most part.  It has still been a bit tricky for me to fully understand 
how this AOT class interface/class is being referred to by any Clojure 
ClassLoader later on causing this.  I dug some and "sort of" understood at 
this point.  I know there have been many AOT + forced reloading of certain 
Clojure namespace issues in the past.  This one doesn't directly look like 
one I've seen.

However, remember, this isn't the only problem I'm bringing up here.  It is 
that AOT files in general would be ignored after shading with 
maven-shade-plugin.

The errors:

Exception in thread "main" java.lang.ClassCastException: 
clojure.pprint.proxy$java.io.Writer$IDeref$PrettyFlush$4923d848 cannot be 
cast to clojure.pprint.PrettyFlush
at 
clojure.pprint$pretty_writer$fn__4700.invoke(pretty_writer.clj:391)
at 
clojure.pprint.proxy$java.io.Writer$IDeref$PrettyFlush$4923d848.flush(Unknown 
Source)
at clojure.core$flush.invokeStatic(core.clj:3609)
at clojure.core$flush.invoke(core.clj:3603)
at clojure.core$prn.invokeStatic(core.clj:3620)
at clojure.core$prn.doInvoke(core.clj:3612)
at clojure.lang.RestFn.invoke(RestFn.java:397)
at clojure.pprint$pprint.invokeStatic(pprint_base.clj:252)
at clojure.pprint$pprint.invoke(pprint_base.clj:241)
at clojure.pprint$pprint.invokeStatic(pprint_base.clj:245)
at clojure.pprint$pprint.invoke(pprint_base.clj:241)
at shade.main$_main.invokeStatic(main.clj:6)
at shade.main$_main.doInvoke(main.clj:4)
at clojure.lang.RestFn.invoke(RestFn.java:397)
at clojure.lang.Var.invoke(Var.java:375)
at shade.ShadeJava.main(ShadeJava.java:14)

On Wednesday, December 28, 2016 at 7:06:11 AM UTC-6, Mike Rodriguez wrote:
>
> Background:
>
> This problem is specific to building jars that contain AOT (Ahead Of Time) 
> compiled Clojure code using Maven and the maven-shade-plugin.
>
> Clojure AOT compilation depends on timestamps of .class files vs .clj 
> files being accurate.  When both .class files and their associated .clj 
> files exist, the AOT .class files are only used by the compiler if their 
> last modified timestamp is strictly greater than the last modified 
> timestamp of the associated .clj file.
>
> Also note that the Clojure core jar itself is deployed AOTed.
>
> I know that much of the Clojure ecosystem uses Leiningen as a build tool 
> (and boot now too I guess).  This problem doesn't apply to Leiningen (and I 
> haven't looked at boot).
>
> Problem:
>
> The maven-shade-plugin is popular for building shaded/uber/standalone jars 
> in Maven.  Typically this means the jar will include some/all of its 
> dependency jars' files.  The maven-shade-plugin has an unfortunate property 
> though.  It does not preserve the timestamps on files that are added to 
> this final shaded jar.  The resulting jar actually ends up with all files 
> inside of it having the same timestamp (when the jar was created).  In 
> particular, if you originally had AOT Clojure .class files and .clj files 
> with different last modified timestamps, now they will have the same 
> timestamps in the shaded jar.
>
> I've brought this up before @ 
> http://stackoverflow.com/questions/19594360/preserving-timestamps-on-clojure-clj-files-when-building-shaded-jar-via-maven-s
>
> I have rarely seen people bring up issues around this with 
> maven-shade-plugin beyond this particular case.  I believe I have seen a 
> complaint or two around the timestamp loss during shading (I can't find 
> them now), but nothing that has gained any traction (I may try to bring it 
> up to the plugin people soon though).
>
> When the AOTed .class file is ignored in favor of the .clj file, the 
> namespace is JIT (Just-In-Time) compiled.  There are several issues with 
> this.
>
> 1) Performance:  It makes the AOT files mostly worthless since they are 
> not saving you on startup time costs anymore.  Everything is JITed anyways.
> 2) Errors:  The reloading of the .clj files is a forced reload of the .clj 
> namespaces involved.  This can cause classpath clashes among ClassLoaders.
> - There are quite a few CLJ Jiras out there that faced trouble dealing 
> with the mix of reloading namespaces and AOT compilation.
>
> You may be thinking, "Just don't build your Clojure jars with Maven.  Use 
> Leiningen instead perhaps?"
> This is fine when it is something you control.  However, what if I want to 
> use Clojure to develop a library that may be consumed by Java consumers who 
> very likely will be using Maven.  If my library is going to be shaded into 
> a standalone jar with maven-shade-plugin by this Java consumer (again, 
> likely) then this scenario can happen.
>
> Another thought that may occur is to just avoid AOT compilation of my 
> library application to avoid the problem 

Re: maven-shade-plugin issues with Clojure core (or any clj) AOT compilation

[Mike Rodriguez]

I appreciate your input.

When we have controlled the Maven shade projects, we have been able to 
workaround the issue as well.  We actually add a 
org.codehaus.mojo/exec-maven-plugin step where we re-open the shaded jar, 
create a new jar, and re-add every file into the new jar via a script. 
 While re-adding the files, we change all .clj files' timestamps to some 
time in the past and all other files just get the current time.  This 
ensures that all .clj files will look "older" than any AOT .class file that 
happens to be in the jar.

My main problem statement is primarily concerning when you *do not* control 
the build.  If I have a Clojure lib that is not-shaded and not AOT-compiled 
and that I have a Java API exposed on (which is what I demonstrate in my 
example project as shade.ShadeJava), this problem will come up for any Java 
consumer who happens to use maven-shade-plugin.  In this sort of case it 
reflects poorly on Clojure if arbitrary consumers have to do workarounds in 
their shade builds just because in my lib I'm wanting to use Clojure as an 
"implementation detail".

So I bring up this issue to just get a sense of what others think and what 
others think should/could be done about it.  Perhaps using Clojure behind 
Java APIs is just not a very common use-case people are working with.  It 
has been a pretty common one for me.  It does seem like a good use-case 
though to be supported to allow Clojure to sneak into existing Java-centric 
ecosystems.

On Wednesday, December 28, 2016 at 7:13:57 AM UTC-6, Gary Trakhman wrote:
>
> My workaround in a multi-module maven shaded java project with a clojure 
> module was to strip out CLJ files in the top-level build (shipped with 
> clojure.core jar). 
>
> I had also stripped CLJ files from my project artifact, but AOT compiles 
> classfiles from all referenced namespaces, so I attempted to strip those 
> out too earlier with the maven jar plugin. This necessitated manually 
> whitelisting AOT'd protocol classes from some of those 3rd party deps to 
> resolve further classloader issues.
>
> On Wed, Dec 28, 2016 at 8:06 AM Mike Rodriguez  > wrote:
>
>> Background:
>>
>> This problem is specific to building jars that contain AOT (Ahead Of 
>> Time) compiled Clojure code using Maven and the maven-shade-plugin.
>>
>> Clojure AOT compilation depends on timestamps of .class files vs .clj 
>> files being accurate.  When both .class files and their associated .clj 
>> files exist, the AOT .class files are only used by the compiler if their 
>> last modified timestamp is strictly greater than the last modified 
>> timestamp of the associated .clj file.
>>
>> Also note that the Clojure core jar itself is deployed AOTed.
>>
>> I know that much of the Clojure ecosystem uses Leiningen as a build tool 
>> (and boot now too I guess).  This problem doesn't apply to Leiningen (and I 
>> haven't looked at boot).
>>
>> Problem:
>>
>> The maven-shade-plugin is popular for building shaded/uber/standalone 
>> jars in Maven.  Typically this means the jar will include some/all of its 
>> dependency jars' files.  The maven-shade-plugin has an unfortunate property 
>> though.  It does not preserve the timestamps on files that are added to 
>> this final shaded jar.  The resulting jar actually ends up with all files 
>> inside of it having the same timestamp (when the jar was created).  In 
>> particular, if you originally had AOT Clojure .class files and .clj files 
>> with different last modified timestamps, now they will have the same 
>> timestamps in the shaded jar.
>>
>> I've brought this up before @ 
>> http://stackoverflow.com/questions/19594360/preserving-timestamps-on-clojure-clj-files-when-building-shaded-jar-via-maven-s
>>
>> I have rarely seen people bring up issues around this with 
>> maven-shade-plugin beyond this particular case.  I believe I have seen a 
>> complaint or two around the timestamp loss during shading (I can't find 
>> them now), but nothing that has gained any traction (I may try to bring it 
>> up to the plugin people soon though).
>>
>> When the AOTed .class file is ignored in favor of the .clj file, the 
>> namespace is JIT (Just-In-Time) compiled.  There are several issues with 
>> this.
>>
>> 1) Performance:  It makes the AOT files mostly worthless since they are 
>> not saving you on startup time costs anymore.  Everything is JITed anyways.
>> 2) Errors:  The reloading of the .clj files is a forced reload of the 
>> .clj namespaces involved.  This can cause classpath clashes among 
>> ClassLoaders.
>> - There are quite a few CLJ Jiras out there that faced trouble dealing 
>> with the mix of reloading namespaces and AOT compilation.
>>
>> You may be thinking, "Just don't build your Clojure jars with Maven.  Use 
>> Leiningen instead perhaps?"
>> This is fine when it is something you control.  However, what if I want 
>> to use Clojure to develop a library that may be consumed by Java consumers 
>> who very likely will 

Re: maven-shade-plugin issues with Clojure core (or any clj) AOT compilation

[Gary Trakhman]

My workaround in a multi-module maven shaded java project with a clojure
module was to strip out CLJ files in the top-level build (shipped with
clojure.core jar).

I had also stripped CLJ files from my project artifact, but AOT compiles
classfiles from all referenced namespaces, so I attempted to strip those
out too earlier with the maven jar plugin. This necessitated manually
whitelisting AOT'd protocol classes from some of those 3rd party deps to
resolve further classloader issues.

On Wed, Dec 28, 2016 at 8:06 AM Mike Rodriguez  wrote:

> Background:
>
> This problem is specific to building jars that contain AOT (Ahead Of Time)
> compiled Clojure code using Maven and the maven-shade-plugin.
>
> Clojure AOT compilation depends on timestamps of .class files vs .clj
> files being accurate.  When both .class files and their associated .clj
> files exist, the AOT .class files are only used by the compiler if their
> last modified timestamp is strictly greater than the last modified
> timestamp of the associated .clj file.
>
> Also note that the Clojure core jar itself is deployed AOTed.
>
> I know that much of the Clojure ecosystem uses Leiningen as a build tool
> (and boot now too I guess).  This problem doesn't apply to Leiningen (and I
> haven't looked at boot).
>
> Problem:
>
> The maven-shade-plugin is popular for building shaded/uber/standalone jars
> in Maven.  Typically this means the jar will include some/all of its
> dependency jars' files.  The maven-shade-plugin has an unfortunate property
> though.  It does not preserve the timestamps on files that are added to
> this final shaded jar.  The resulting jar actually ends up with all files
> inside of it having the same timestamp (when the jar was created).  In
> particular, if you originally had AOT Clojure .class files and .clj files
> with different last modified timestamps, now they will have the same
> timestamps in the shaded jar.
>
> I've brought this up before @
> http://stackoverflow.com/questions/19594360/preserving-timestamps-on-clojure-clj-files-when-building-shaded-jar-via-maven-s
>
> I have rarely seen people bring up issues around this with
> maven-shade-plugin beyond this particular case.  I believe I have seen a
> complaint or two around the timestamp loss during shading (I can't find
> them now), but nothing that has gained any traction (I may try to bring it
> up to the plugin people soon though).
>
> When the AOTed .class file is ignored in favor of the .clj file, the
> namespace is JIT (Just-In-Time) compiled.  There are several issues with
> this.
>
> 1) Performance:  It makes the AOT files mostly worthless since they are
> not saving you on startup time costs anymore.  Everything is JITed anyways.
> 2) Errors:  The reloading of the .clj files is a forced reload of the .clj
> namespaces involved.  This can cause classpath clashes among ClassLoaders.
> - There are quite a few CLJ Jiras out there that faced trouble dealing
> with the mix of reloading namespaces and AOT compilation.
>
> You may be thinking, "Just don't build your Clojure jars with Maven.  Use
> Leiningen instead perhaps?"
> This is fine when it is something you control.  However, what if I want to
> use Clojure to develop a library that may be consumed by Java consumers who
> very likely will be using Maven.  If my library is going to be shaded into
> a standalone jar with maven-shade-plugin by this Java consumer (again,
> likely) then this scenario can happen.
>
> Another thought that may occur is to just avoid AOT compilation of my
> library application to avoid the problem (this is recommended in the
> community I believe).  However, Clojure core is AOT compiled and it will
> get included in the shaded jar.  That alone is enough to cause the issue.
>
> Example:
>
> I have a GitHub repo to show a minimum example of where this can be a
> problem.  In particular it shows a way for the problem (2) to occur.
> @ https://github.com/mrrodriguez/mvn-shade-test
>
> This repo has a Java API through shade.ShadeJava that will cause the
> Clojure compiler to require the shade.main namespace using JIT
> compilation.  However, shade.main uses clojure.pprint, which is AOT
> compiled via Clojure core.
>
> clojure.pprint was chosen here just because it one of the cases I've seen
> come up that actually fail with problem (2) from above.  Even if there were
> no failures though, the Clojure core namespaces would be getting recompiled
> with problem (1).
>
> --
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> your first post.
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> 

maven-shade-plugin issues with Clojure core (or any clj) AOT compilation

[Mike Rodriguez]

Background:

This problem is specific to building jars that contain AOT (Ahead Of Time) 
compiled Clojure code using Maven and the maven-shade-plugin.

Clojure AOT compilation depends on timestamps of .class files vs .clj files 
being accurate.  When both .class files and their associated .clj files 
exist, the AOT .class files are only used by the compiler if their last 
modified timestamp is strictly greater than the last modified timestamp of 
the associated .clj file.

Also note that the Clojure core jar itself is deployed AOTed.

I know that much of the Clojure ecosystem uses Leiningen as a build tool 
(and boot now too I guess).  This problem doesn't apply to Leiningen (and I 
haven't looked at boot).

Problem:

The maven-shade-plugin is popular for building shaded/uber/standalone jars 
in Maven.  Typically this means the jar will include some/all of its 
dependency jars' files.  The maven-shade-plugin has an unfortunate property 
though.  It does not preserve the timestamps on files that are added to 
this final shaded jar.  The resulting jar actually ends up with all files 
inside of it having the same timestamp (when the jar was created).  In 
particular, if you originally had AOT Clojure .class files and .clj files 
with different last modified timestamps, now they will have the same 
timestamps in the shaded jar.

I've brought this up before @ 
http://stackoverflow.com/questions/19594360/preserving-timestamps-on-clojure-clj-files-when-building-shaded-jar-via-maven-s

I have rarely seen people bring up issues around this with 
maven-shade-plugin beyond this particular case.  I believe I have seen a 
complaint or two around the timestamp loss during shading (I can't find 
them now), but nothing that has gained any traction (I may try to bring it 
up to the plugin people soon though).

When the AOTed .class file is ignored in favor of the .clj file, the 
namespace is JIT (Just-In-Time) compiled.  There are several issues with 
this.

1) Performance:  It makes the AOT files mostly worthless since they are not 
saving you on startup time costs anymore.  Everything is JITed anyways.
2) Errors:  The reloading of the .clj files is a forced reload of the .clj 
namespaces involved.  This can cause classpath clashes among ClassLoaders.
- There are quite a few CLJ Jiras out there that faced trouble dealing with 
the mix of reloading namespaces and AOT compilation.

You may be thinking, "Just don't build your Clojure jars with Maven.  Use 
Leiningen instead perhaps?"
This is fine when it is something you control.  However, what if I want to 
use Clojure to develop a library that may be consumed by Java consumers who 
very likely will be using Maven.  If my library is going to be shaded into 
a standalone jar with maven-shade-plugin by this Java consumer (again, 
likely) then this scenario can happen.

Another thought that may occur is to just avoid AOT compilation of my 
library application to avoid the problem (this is recommended in the 
community I believe).  However, Clojure core is AOT compiled and it will 
get included in the shaded jar.  That alone is enough to cause the issue.

Example:

I have a GitHub repo to show a minimum example of where this can be a 
problem.  In particular it shows a way for the problem (2) to occur.
@ https://github.com/mrrodriguez/mvn-shade-test

This repo has a Java API through shade.ShadeJava that will cause the 
Clojure compiler to require the shade.main namespace using JIT compilation. 
 However, shade.main uses clojure.pprint, which is AOT compiled via Clojure 
core.

clojure.pprint was chosen here just because it one of the cases I've seen 
come up that actually fail with problem (2) from above.  Even if there were 
no failures though, the Clojure core namespaces would be getting recompiled 
with problem (1).

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