I believe the issue was this, and resolved.
https://github.com/kripken/emscripten/issues/2203


2014-03-10 10:38 GMT+02:00 Mark Callow <[email protected]>:

>  On 2014/03/07 7:03, Michael IV wrote:
>
> Hi All.Sorry for the noob question.I have installed Emscipten 64bit
> version on Windows 64bit.I am trying to compile with clang hello_world.cpp
> and it throws me :
>
>  clang.exe:error:unable to execute command:program not executable
> clang.exe:error:linker command failed with exit code 1
>
>  What do I miss here?I run the command via emscipten command prompt.
>
>  Are you sure the message was "program not executable?" Or was it "the
> system cannot execute the specified program?"
>
> I think the former most likely means that some command clang was trying to
> execute did not have execute permission. That's pretty unusual in Windows
> because files inherit permissions from their parent directories and
> directories have execute permission.
>
> The latter message has been seen by some of us before when running the
> 64-bit tools from Visual Studio, which is a 32-bit application, and the
> solution was to use the 32-bit tools. This would be the first time I am
> aware of it happening when run from the command line. My initial suggestion
> in this case is to make sure you are using a 64-bit command prompt
> executable. Apparently it can happen when dll dependencies are not found
> but that is not the only reason.
>
> <soapbox>
> I have encountered this type of useless error message far too often in my
> career. Developers who save themselves a few minutes by omitting vital
> information from error messages and managers who approve release of such
> error handling should be fired. They cause users and developers who
> encounter these messages to waste hours even days trying to track down
> problems. The minimum acceptable in this case is the name of the program
> that could not be executed and the reason why it couldn't be executed.
> </soapbox>
>
> Regards
>
>     -Mark
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