UnResolvedPackage: Anaconda conda Environment O2MConverter

Question

I have been attempting many ways to install this github repository by creating conda environment and installing dependencies and pip packages that are specified in the project O2MConverter (https://github.com/aikkala/O2MConverter.git) with conda_env.yml file.

However, I have multiple unresolved packaged within conda that can't be found any of the channels provided within.

> conda env create --name O2MConverter --file=conda_env.yml
> conda activate O2MConverter
> python O2MConverter.py opensim_model_file.osim /location/where/converted/model/will/be/saved /location/where/geometry/files/are

Can somebody resolve the dependency issues provided within conda_env.yml file? Here is the exhaustive list, where all the unresolved packages can be seen below. I specifically discarded the build numbers to let it resolved with any builds, which is resulting to conflicting packages.

Package names with required versions, which are unresolved but build numbers are discarded.

    - krb5=1.14.6
    - xz=5.2.4
    - hdf4=4.2.13
    - tk=8.5.19
    - xorg-libxdmcp=1.1.3
    - freeglut=3.0.0
    - xorg-libxi=1.7.10
    - openblas=0.3.9
    - jsoncpp=1.8.4
    - expat=2.2.9
    - libssh2=1.8.0
    - libgfortran-ng=7.3.0
    - libxcb=1.13
    - libiconv=1.15
    - vtk=8.2.0
    - xorg-fixesproto=5.0
    - xorg-libx11=1.6.9
    - openssl=1.0.2u
    - xorg-xextproto=7.3.0
    - patchelf=0.10
    - lz4-c=1.8.3
    - freetype=2.10.1
    - _openmp_mutex=4.5
    - pthread-stubs=0.4
    - scipy=1.4.1
    - tbb=2020.1
    - zlib=1.2.11
    - xorg-kbproto=1.0.7
    - icu=64.2
    - libpng=1.6.37
    - readline=6.2
    - xorg-libice=1.0.10
    - sqlite=3.13.0
    - libwebp-base=1.1.0
    - libxml2=2.9.10
    - libstdcxx-ng=9.2.0
    - pandas=1.0.3
    - xorg-libxext=1.3.4
    - llvm-openmp=9.0.1
    - xorg-libxau=1.0.9
    - xorg-libsm=1.2.3
    - xorg-inputproto=2.3.2
    - xorg-libxt=1.2.0
    - curl=7.61.0
    - libnetcdf=4.6.2
    - _libgcc_mutex=0.1
    - zstd=1.4.4
    - libopenblas=0.3.9
    - ncurses=5.9
    - libuuid=2.32.1
    - hdf5=1.10.4
    - libtiff=4.1.0
    - xorg-libxfixes=5.0.3
    - scikit-learn=0.22.2.post1
    - bzip2=1.0.8
    - jpeg=9c
    - libgcc-ng=9.2.0
    - xorg-xproto=7.0.31

Original conda_env.yml file:

name: O2MConverter
channels:
  - conda-forge
  - https://conda.anaconda.org/conda-forge/
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=1_llvm
  - bzip2=1.0.8=h516909a_2
  - ca-certificates=2020.4.5.1=hecc5488_0
  - certifi=2020.4.5.1=py36h9f0ad1d_0
  - curl=7.61.0=h93b3f91_2
  - expat=2.2.9=he1b5a44_2
  - freeglut=3.0.0=hf484d3e_1005
  - freetype=2.10.1=he06d7ca_0
  - future=0.18.2=py36h9f0ad1d_1
  - hdf4=4.2.13=hf30be14_1003
  - hdf5=1.10.4=nompi_h3c11f04_1106
  - icu=64.2=he1b5a44_1
  - joblib=0.14.1=py_0
  - jpeg=9c=h14c3975_1001
  - jsoncpp=1.8.4=hc9558a2_1002
  - krb5=1.14.6=0
  - libblas=3.8.0=16_openblas
  - libcblas=3.8.0=16_openblas
  - libgcc-ng=9.2.0=h24d8f2e_2
  - libgfortran-ng=7.3.0=hdf63c60_5
  - libiconv=1.15=h516909a_1006
  - liblapack=3.8.0=16_openblas
  - libnetcdf=4.6.2=hbdf4f91_1001
  - libopenblas=0.3.9=h5ec1e0e_0
  - libpng=1.6.37=hed695b0_1
  - libssh2=1.8.0=h1ad7b7a_1003
  - libstdcxx-ng=9.2.0=hdf63c60_2
  - libtiff=4.1.0=hc7e4089_6
  - libuuid=2.32.1=h14c3975_1000
  - libwebp-base=1.1.0=h516909a_3
  - libxcb=1.13=h14c3975_1002
  - libxml2=2.9.10=hee79883_0
  - llvm-openmp=9.0.1=hc9558a2_2
  - lz4-c=1.8.3=he1b5a44_1001
  - natsort=7.0.1=py_0
  - ncurses=5.9=10
  - openblas=0.3.9=he1df0ab_0
  - openssl=1.0.2u=h516909a_0
  - pandas=1.0.3=py36h830a2c2_0
  - patchelf=0.10=he1b5a44_0
  - pip=20.0.2=py_2
  - pthread-stubs=0.4=h14c3975_1001
  - python=3.6.1=3
  - python-dateutil=2.8.1=py_0
  - python_abi=3.6=1_cp36m
  - pytz=2019.3=py_0
  - readline=6.2=0
  - scikit-learn=0.22.2.post1=py36hcdab131_0
  - scipy=1.4.1=py36h2d22cac_2
  - setuptools=46.1.3=py36h9f0ad1d_0
  - six=1.14.0=py_1
  - sk-video=1.1.10=pyh24bf2e0_4
  - sqlite=3.13.0=1
  - tbb=2020.1=hc9558a2_0
  - tk=8.5.19=2
  - vtk=8.2.0=py36ha8e561a_202
  - wheel=0.34.2=py_1
  - xmltodict=0.12.0=py_0
  - xorg-fixesproto=5.0=h14c3975_1002
  - xorg-inputproto=2.3.2=h14c3975_1002
  - xorg-kbproto=1.0.7=h14c3975_1002
  - xorg-libice=1.0.10=h516909a_0
  - xorg-libsm=1.2.3=h84519dc_1000
  - xorg-libx11=1.6.9=h516909a_0
  - xorg-libxau=1.0.9=h14c3975_0
  - xorg-libxdmcp=1.1.3=h516909a_0
  - xorg-libxext=1.3.4=h516909a_0
  - xorg-libxfixes=5.0.3=h516909a_1004
  - xorg-libxi=1.7.10=h516909a_0
  - xorg-libxt=1.2.0=h516909a_0
  - xorg-xextproto=7.3.0=h14c3975_1002
  - xorg-xproto=7.0.31=h14c3975_1007
  - xz=5.2.4=h516909a_1002
  - zlib=1.2.11=h516909a_1006
  - zstd=1.4.4=h3b9ef0a_2
  - pip:
    - admesh==0.98.9
    - cffi==1.14.0
    - cloudpickle==1.3.0
    - cycler==0.10.0
    - cython==0.29.16
    - fasteners==0.15
    - glfw==1.11.0
    - imageio==2.8.0
    - kiwisolver==1.1.0
    - matplotlib==3.2.1
    - monotonic==1.5
    - pillow==7.0.0
    - pycparser==2.20
    - pyglet==1.5.0
    - pynput==1.6.8
    - pyparsing==2.4.6
    - pyquaternion==0.9.5
    - python-xlib==0.27
    - redis==3.4.1
    - timeout-decorator==0.4.1
prefix: /home/aleksi/anaconda3/envs/O2MConverter

Can anyone help me to build the environment using anaconda or using virtual environment?

I tried to build the environment with conda, and tried to make the project pip installable with the same packages. In pip installable cases, the pip install admesh did not work. Building with conda, I experienced unresolved packages, then removed all the build versions, which resulted in conflicting packages and conda couldn't resolve them.

Answer 1

It is Linux-specific. One would have to manually prune out packages that are not available for other platforms to get something to work across platforms. Otherwise, run in Docker or something similar. For example, works fine with mambaforge image:

$ docker run --rm -it condaforge/mambaforge:latest
(base) root@ef04142624c1:/# mamba env create -n foo -f https://github.com/aikkala/O2MConverter/raw/master/conda_env.yml