problems installing pyembree and igneous in windows miniconda environment

[Ibrahim Taştekin]

Dear all,

I have some problems installing the fafbseg Flywire python components in Windows OS (working in R with reticulate).  When I run simple simple_python() and fafbseg::dr_fafbseg():

                    module available version
1                  cloudvolume      TRUE   3.8.0
2                  DracoPy      TRUE        
3                  meshparty      FALSE
4                  skeletor      TRUE  0.2.11
5                  pykdtree      TRUE        
6                  pyembree     FALSE        
7                  annotationframeworkclient      FALSE

8                  pychunkedgraph      FALSE
9                  igneous     FALSE     

Somehow, some of the packages are not installed properly. In this case, I can import meshes but cannot do much more.

I installed some of the other packages in the miniconda environment directy and went back to R to run    fafbseg::dr_fafbseg():

module available version
1                  cloudvolume      TRUE   3.8.0
2                  DracoPy      TRUE        
3                  meshparty      TRUE  1.10.2
4                  skeletor      TRUE  0.2.11
5                  pykdtree      TRUE        
6                  pyembree     FALSE        
7                  annotationframeworkclient      TRUE   2.5.0
8                  pychunkedgraph      TRUE 0.1.113
9                  igneous     FALSE 

I am still having difficulties installing pyembree and igneous. 

As for pyembree;

conda install -c conda-forge pyembree

conda install gives the folllowing error:

Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - pyembree

Current channels:

  - https://conda.anaconda.org/conda-forge/win-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/win-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/win-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/msys2/win-64
  - https://repo.anaconda.com/pkgs/msys2/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

Then, I tried to installing pyembree from github: 

git clone https://github.com/scopatz/pyembree.git

cd pyembree

conda install cython numpy

conda install -c conda-forge embree

set INCLUDE=C:\Users\Ribeiro\AppData\Local\r-miniconda\envs\r-reticulate\Library\include

set LIB=C:\Users\Ribeiro\AppData\Local\r-miniconda\envs\r-reticulate\Library\lib

python setup.py install --prefix=C:\Users\Ribeiro\AppData\Local\r-miniconda\envs\r-reticulate

However, I get the following error:

pyembree\mesh_construction.cpp(648): fatal error C1083: Cannot open include file: 'embree2/rtcore.h': No such file or directory
error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio\\2019\\BuildTools\\VC\\Tools\\MSVC\\14.26.28801\\bin\\HostX86\\x64\\cl.exe' failed with exit status 2

For igneous, installing from github seems to work well but I cannot see it installed in  fafbseg::dr_fafbseg().

Does anyone have a solution for these issues?

Sorry for the long message!

Best

Ibo