Ok I opened a new bug 
here: https://github.com/kripken/emscripten/issues/3939
Small test case included.

On Wednesday, November 25, 2015 at 5:40:12 PM UTC-5, Alon Zakai wrote:
>
> I don't know enough cmake to follow that, sorry. Buf if you make a 
> standalone testcase that reproduces the issue I can try to debug that.
>
> On Wed, Nov 25, 2015 at 2:38 PM, Robert Goulet <[email protected] 
> <javascript:>> wrote:
>
>> The test worked. So indeed it must be related to our setup I guess.
>>
>> We build using CMake. And we do the following change to your toolchain 
>> file because we want libs to be bitcode (.bc) :
>>
>> set(CMAKE_STATIC_LIBRARY_SUFFIX ".bc" CACHE STRING "" FORCE)
>> set(CMAKE_SHARED_LIBRARY_SUFFIX ".bc" CACHE STRING "" FORCE)
>> set(CMAKE_FIND_LIBRARY_SUFFIXES ".bc" CACHE STRING "" FORCE)
>> set(CMAKE_C_CREATE_STATIC_LIBRARY "<CMAKE_C_COMPILER> -o <TARGET> 
>> <LINK_FLAGS> <OBJECTS>" CACHE STRING "" FORCE)
>> set(CMAKE_CXX_CREATE_STATIC_LIBRARY "<CMAKE_CXX_COMPILER> -o <TARGET> 
>> <LINK_FLAGS> <OBJECTS>" CACHE STRING "" FORCE)
>>
>> All that used to work fine in 1.35.4 and earlier.
>>
>>
>> On Wednesday, November 25, 2015 at 5:29:57 PM UTC-5, Alon Zakai wrote:
>>>
>>> What does your app do to build? Maybe something very specific in how you 
>>> invoke emcc/em++ is what matters here.
>>>
>>> Does the emscripten test suite work? Try
>>>
>>> emcc --clear-cache
>>> tests/runner.py test_hello_world
>>>
>>>
>>> On Wed, Nov 25, 2015 at 2:26 PM, Robert Goulet <[email protected]> 
>>> wrote:
>>>
>>>> No special steps. I just did a build of Emscripten tag 1.35.10, and 
>>>> tried to build our app with it. All the targets of our app built just 
>>>> fine, 
>>>> its only when it got to generate the Emscripten system libs that it 
>>>> choked. 
>>>> I am running on Windows 8.1 64bit, and doing python --version reveals 
>>>> 2.7.8.
>>>>
>>>> On Wednesday, November 25, 2015 at 5:15:38 PM UTC-5, Alon Zakai wrote:
>>>>>
>>>>> That looks very bad, but unfamiliar, and apparently not something 
>>>>> covered in our test suite. Do you have steps to reproduce it that I can 
>>>>> try?
>>>>>
>>>>> I can suspect it is related to recent emcc/emcc.py/em++ etc. changes. 
>>>>> Maybe platform specific somehow? But all our bots seem ok, so no idea 
>>>>> what's going on.
>>>>>
>>>>> Is the default python on your system 2 or 3? And what OS are you on?
>>>>>
>>>>> On Wed, Nov 25, 2015 at 2:09 PM, Robert Goulet <[email protected]
>>>>> > wrote:
>>>>>
>>>>>> Ok I got 1.35.10 built, but at link time for my project I now get 
>>>>>> this error when it tries to generate the Emscripten system libs. The 
>>>>>> error 
>>>>>> repeats endlessly.
>>>>>>
>>>>>> WARNING:root:generating system library: libcxx_noexcept.a...
>>>>>> Traceback (most recent call last):
>>>>>>   File "<string>", line 1, in <module>
>>>>>>   File 
>>>>>> "D:\emsdk-1.35.0-portable-64bit\python\2.7.5.3_64bit\lib\multiprocessing\forking.py",
>>>>>>  
>>>>>> line 380, in main
>>>>>>     prepare(preparation_data)
>>>>>>   File 
>>>>>> "D:\emsdk-1.35.0-portable-64bit\python\2.7.5.3_64bit\lib\multiprocessing\forking.py",
>>>>>>  
>>>>>> line 489, in prepare
>>>>>>     file, path_name, etc = imp.find_module(main_name, dirs)
>>>>>> ImportError: No module named em++
>>>>>> Traceback (most recent call last):
>>>>>>   File "<string>", line 1, in <module>
>>>>>>   File 
>>>>>> "D:\emsdk-1.35.0-portable-64bit\python\2.7.5.3_64bit\lib\multiprocessing\forking.py",
>>>>>>  
>>>>>> line 380, in main
>>>>>>     prepare(preparation_data)
>>>>>>   File 
>>>>>> "D:\emsdk-1.35.0-portable-64bit\python\2.7.5.3_64bit\lib\multiprocessing\forking.py",
>>>>>>  
>>>>>> line 489, in prepare
>>>>>>     file, path_name, etc = imp.find_module(main_name, dirs)
>>>>>> ImportError: No module named em++
>>>>>> Traceback (most recent call last):
>>>>>>   File "<string>", line 1, in <module>
>>>>>>   File 
>>>>>> "D:\emsdk-1.35.0-portable-64bit\python\2.7.5.3_64bit\lib\multiprocessing\forking.py",
>>>>>>  
>>>>>> line 380, in main
>>>>>>     prepare(preparation_data)
>>>>>>   File 
>>>>>> "D:\emsdk-1.35.0-portable-64bit\python\2.7.5.3_64bit\lib\multiprocessing\forking.py",
>>>>>>  
>>>>>> line 489, in prepare
>>>>>>     file, path_name, etc = imp.find_module(main_name, dirs)
>>>>>> ImportError: No module named em++
>>>>>> ...
>>>>>>
>>>>>> On Wednesday, November 25, 2015 at 4:02:44 PM UTC-5, Alon Zakai wrote:
>>>>>>>
>>>>>>> Yeah, building llvm+clang just takes a lot of memory. You can try 
>>>>>>> using less parallel jobs, or doing a non-debug/no-assertions build.
>>>>>>>
>>>>>>> On Wed, Nov 25, 2015 at 11:15 AM, Robert Goulet <
>>>>>>> [email protected]> wrote:
>>>>>>>
>>>>>>>> Indeed that might be the case. But its very sad since my machine 
>>>>>>>> has 32GB RAM.... oh well.
>>>>>>>>
>>>>>>>> On Wednesday, November 25, 2015 at 1:45:13 PM UTC-5, Alon Zakai 
>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>> Looks like it ran out of memory?
>>>>>>>>>
>>>>>>>>> On Wed, Nov 25, 2015 at 7:00 AM, Robert Goulet <
>>>>>>>>> [email protected]> wrote:
>>>>>>>>>
>>>>>>>>>> incoming fails to build:
>>>>>>>>>>
>>>>>>>>>> D:\emsdk-1.35.0-portable-64bit\clang\fastcomp\src\include\llvm/Support/type_traits.h(46):
>>>>>>>>>>  
>>>>>>>>>> fatal error C1060: compiler is out of heap space (D:\emsdk-
>>>>>>>>>> 1.35.0-portable-64bit\clang\fastcomp\src\tools\clang\lib\CodeGen\CGDebugInfo.cpp)
>>>>>>>>>>  
>>>>>>>>>> [D:\emsdk-1.35.0-portable-64bit\clang\fastcomp\build_incoming_vs201
>>>>>>>>>> 3_64\tools\clang\lib\CodeGen\clangCodeGen.vcxproj]
>>>>>>>>>>
>>>>>>>>>> On Wednesday, November 25, 2015 at 9:40:28 AM UTC-5, Robert 
>>>>>>>>>> Goulet wrote:
>>>>>>>>>>>
>>>>>>>>>>> I'm building incoming right now and will keep you posted about 
>>>>>>>>>>> what code produce this warning on our side.
>>>>>>>>>>>
>>>>>>>>>>> On Tuesday, November 24, 2015 at 9:39:35 PM UTC-5, Alon Zakai 
>>>>>>>>>>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>> I found it's easy to get the LLVM optimizer to emit code that 
>>>>>>>>>>>> hits this warning, see the test I added:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> https://github.com/kripken/emscripten/commit/308e98787f88789431e5210d4defa76c275454ac
>>>>>>>>>>>>
>>>>>>>>>>>> The optimizer sees a union with an int write and a float read, 
>>>>>>>>>>>> and just forwards those bits into a float.
>>>>>>>>>>>>
>>>>>>>>>>>> On Tue, Nov 24, 2015 at 3:27 PM, Jukka Jylänki <
>>>>>>>>>>>> [email protected]> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Btw, I did write a PR for being able to handle such arbitrary 
>>>>>>>>>>>>> NaN literals without warnings, but it was chosen not to merge 
>>>>>>>>>>>>> that in, if I 
>>>>>>>>>>>>> recall correctly, the thinking was that it would be an impossible 
>>>>>>>>>>>>> scenario 
>>>>>>>>>>>>> to occur. The related PR was here: 
>>>>>>>>>>>>> https://github.com/kripken/emscripten-fastcomp/pull/116 which 
>>>>>>>>>>>>> was amended to demote the handling to the warning you are seeing. 
>>>>>>>>>>>>> It would 
>>>>>>>>>>>>> be interesting to hear what kind of code pattern does cause this.
>>>>>>>>>>>>>
>>>>>>>>>>>>> 2015-11-25 0:36 GMT+02:00 Alon Zakai <[email protected]>:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> I added logging of the instruction and function on incoming 
>>>>>>>>>>>>>> now. It will also print out debug info if available.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Tue, Nov 24, 2015 at 8:29 AM, Robert Goulet <
>>>>>>>>>>>>>> [email protected]> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Unfortunately that doesn't really help us track down what 
>>>>>>>>>>>>>>> produced this warning in our code.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Tuesday, November 24, 2015 at 10:51:29 AM UTC-5, arnab 
>>>>>>>>>>>>>>> choudhury wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> This error originates from the JS backend modifications to 
>>>>>>>>>>>>>>>> Clang-++.exe in the emscripten fastcomp project:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> https://github.com/kripken/emscripten-fastcomp/blob/4e83be90903250ec5142edc57971ed4c633c5e25/lib/Target/JSBackend/JSBackend.cpp
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hope this helps.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Tuesday, November 24, 2015 at 7:28:15 AM UTC-8, Robert 
>>>>>>>>>>>>>>>> Goulet wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I got this warning at link time. I searched the code for 
>>>>>>>>>>>>>>>>> this value but couldn't find it. Is there any way to find 
>>>>>>>>>>>>>>>>> which source file 
>>>>>>>>>>>>>>>>> produce this warning? EMCC_DEBUG=1 didn't tell more 
>>>>>>>>>>>>>>>>> details about this. Thanks!
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> emcc: warning: cannot represent a NaN literal 
>>>>>>>>>>>>>>>>> '0x5fec1ef10' with custom bit pattern in NaN-canonicalizing 
>>>>>>>>>>>>>>>>> JS engines 
>>>>>>>>>>>>>>>>> (e.g. Firefox and Safari) without erasing bits!
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thanks!
>>>>>>>>>>>>>>>>>
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>>>>>>>>>>>>>
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