To anyone running in the same problem, you have to pass the --vs2015 
command line argument even for the activate command!

emsdk activate --vs2015 emscripten-master-64bit sdk-master-64bit

I feel dumb now since it's actually written in the usage of emsdk...

--vs2013/--vs2015: If building from source, overrides to build
> using the specified compiler. When installing
> precompiled packages, this has no effect.
> Note: The same compiler specifier must be
> passed to the emsdk activate command to
> activate the desired version.


On Sunday, February 12, 2017 at 10:21:56 AM UTC+1, Jean-Marc Le Roux wrote:
>
> Hello,
>
> for some reason, I cannot activate any clang-* or sdk-* using emsdk.
> Running the following command works:
>
> emsdk install --vs2015 sdk-master-64bit
>
> and ends with:
>
> Done installing tool 'emscripten-master-64bit'. 
> Done installing SDK 'sdk-master-64bit'.
>
> but then this fails:
>
> emsdk activate sdk-master-64bit 
> Writing .emscripten configuration file to user home directory C:\Users\
> jeanm/ 
> The SDK/tool 'clang-master-64bit' cannot be activated since it is not 
> installed! Skipping this tool... 
> The SDK/tool 'sdk-master-64bit' cannot be activated since it is not 
> installed! Skipping this tool...
>
> When I run emsdk list, sdk-master-64bit is not marked as installed.
> Yet running the install command again says it is installed...
>
> I tried doing the same with sdk-tag-1.37.2-64bit and I got the same 
> behavior.
>
> I can only use the pre-built 1.35 package.
> I'm on Windows 10 64bit.
>
> How can we fix this?
>

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