Issue installing moseq2-model

[donglabimaging]

We are trying to install the moseq2 pipeline on a Win10 machine with pip install git+https://github.com/dattalab/moseq2-model.git, but we are getting the following error. We are not sure what is causing this error. Any help would be greatly appreciated. Thank you!

ERROR: Command errored out with exit status 1:
command: 'c:\users\allenli\miniconda3\envs\moseq2\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\setup.py'"'"'; file='"'"'C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d 'C:\Users\AllenLi\AppData\Local\Temp\pip-wheel-wbr8ekm5' --python-tag cp36
cwd: C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive
Complete output (66 lines):
running bdist_wheel
running build
running build_py
creating build
creating build\lib.win-amd64-3.6
creating build\lib.win-amd64-3.6\autoregressive
copying autoregressive\distributions.py -> build\lib.win-amd64-3.6\autoregressive
copying autoregressive\models.py -> build\lib.win-amd64-3.6\autoregressive
copying autoregressive\util.py -> build\lib.win-amd64-3.6\autoregressive
copying autoregressive_init_.py -> build\lib.win-amd64-3.6\autoregressive
running build_ext
building 'autoregressive.messages' extension
creating build\temp.win-amd64-3.6
creating build\temp.win-amd64-3.6\Release
creating build\temp.win-amd64-3.6\Release\autoregressive
C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.22.27905\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MT -Iautoregressive -Ic:\users\allenli\miniconda3\envs\moseq2\lib\site-packages\numpy\core\include -Ideps -Ic:\users\allenli\miniconda3\envs\moseq2\include -Ic:\users\allenli\miniconda3\envs\moseq2\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.22.27905\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.18362.0\cppwinrt" /EHsc /Tpautoregressive\messages.cpp /Fobuild\temp.win-amd64-3.6\Release\autoregressive\messages.obj -O2 -fopenmp -std=c++11 -DEIGEN_NO_MALLOC -DNDEBUG -w
cl : Command line warning D9025 : overriding '/W3' with '/w'
cl : Command line warning D9002 : ignoring unknown option '-fopenmp'
cl : Command line warning D9002 : ignoring unknown option '-std=c++11'
messages.cpp
c:\users\allenli\miniconda3\envs\moseq2\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h(14) : Warning Msg: Using deprecated NumPy API, disable it with #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(44): error C2131: expression did not evaluate to a constant
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(44): note: failure was caused by a read of a variable outside its lifetime
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(44): note: see usage of 'sz'
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(31): note: while compiling class template member function 'Type dummy::resample_arhmm(int,int,int,int,bool,Type *,Type *,Type *,Type *,Type *,Type *,int32_t *,int32_t *,int32_t *,Type *,Type *)'
with
[
Type=double
]
autoregressive\messages.cpp(5902): note: see reference to function template instantiation 'Type dummy::resample_arhmm(int,int,int,int,bool,Type *,Type *,Type *,Type *,Type *,Type *,int32_t *,int32_t *,int32_t *,Type *,Type *)' being compiled
with
[
Type=double
]
autoregressive\messages.cpp(5055): note: see reference to class template instantiation 'dummy' being compiled
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(44): error C2146: syntax error: missing ';' before identifier 'attribute'
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(44): error C3861: 'aligned': identifier not found
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(44): error C3861: 'attribute': identifier not found
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(46): error C2131: expression did not evaluate to a constant
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(46): note: failure was caused by a read of a variable outside its lifetime
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(46): note: see usage of 'sz'
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(46): error C2146: syntax error: missing ';' before identifier 'attribute'
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(46): error C3861: 'aligned': identifier not found
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(46): error C3861: 'attribute': identifier not found
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(48): error C2131: expression did not evaluate to a constant
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(48): note: failure was caused by a read of a variable outside its lifetime
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(48): note: see usage of 'M'
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(48): error C2146: syntax error: missing ';' before identifier 'attribute'
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(48): error C3861: 'aligned': identifier not found
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(48): error C3861: 'attribute': identifier not found
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(50): error C2131: expression did not evaluate to a constant
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(50): note: failure was caused by a read of a variable outside its lifetime
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(50): note: see usage of 'M'
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(50): error C2146: syntax error: missing ';' before identifier 'attribute'
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(50): error C3861: 'aligned': identifier not found
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(50): error C3861: 'attribute': identifier not found
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(52): error C2131: expression did not evaluate to a constant
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(52): note: failure was caused by a read of a variable outside its lifetime
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(52): note: see usage of 'T'
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(55): error C3863: array type 'Type [sz]' is not assignable
with
[
Type=double
]
C:\Users\AllenLi\AppData\Local\Temp\pip-install-7ihbxpxf\autoregressive\autoregressive\messages.h(60): error C3861: '__builtin_expect': identifier not found
error: command 'C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.22.27905\bin\HostX86\x64\cl.exe' failed with exit status 2

ERROR: Failed building wheel for autoregressive

[jmarkow]

How exactly are you installing moseq2-model? Did you follow the instructions here (under Windows 10)?

https://github.com/dattalab/moseq2-docs/wiki/Setup:-moseq2-pipeline

[donglabimaging]

Thank you for the quick response. Yes we did follow the instructions on the wiki page under the Win10. The error showed up after running pip install git+https://github.com/dattalab/moseq2-model.git.

[jmarkow]

I see. So this is running inside of the WSL? That error seems to be related to using a visual studio compiler instead of gcc. What's the output of:

which gcc

and

which g++

You mean need to tab-complete to find the version that was installed, then link to it via,

export CC=/usr/local/bin/gcc-7

and

export CXX=/usr/local/bin/g++-7

Assuming you have version 7, then re-try pip installing.

[jmarkow]

Your error also looks similar to this #37 . Your commands are being run inside of the linux subsytem and not the Windows command prompt?

[donglabimaging]

I was running those in Anaconda Prompt (Miniconda3). Would that be the issue?

[jmarkow]

Yes you need to use the WSL. Once in the Debian prompt try following the rest of the installation instructions.

[donglabimaging]

I will try that and let you know soon. Thank you!

[donglabimaging]

It worked. Thank you!