simba command fails after installation

[AnnabelPerry]

I am trying to install simba on Ubuntu 18.04 I used the following commands to install simba:

conda create -n simbaenv python=3.6.10
conda activate simbaenv
pip install simba-uw-tf-dev
pip uninstall shapely
conda install -c conda-forge shapely
sudo apt install simba

When I initially ran pip install simba-uw-tf-dev, I got the error at the bottom of this post (it's very long, so I did not include it within text). I assumed this was the forewarned shapely error and continued.

When I ran sudo apt install simba, I successfully encountered a purple GUI asking me to name and assign a password to a mysql server. However, after entering the requested information, I reached the following error message:

ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2 "No such file or directory") 

I clicked "abort", deactivated my conda environment, and attempted install mysql: sudo apt-get install mysql-server This reopened the purple GUI and the password was requested After entering the password, I got the following error:

ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2 "No such file or directory") 

I reentered conda environment and tried to run simba, getting the following error: Error in configuration filePermission denied

So, I instead ran sudo simba and got following error: Access denied for user 'mirrors'@'localhost' (using password: YES)

So I tried deactivating the environment, removing it, then running back through the environment creation and installation steps listed at the top of this post. I still get the filePermission denied error when I run simba and sudo apt install simba yields the following message:

Reading package lists... Done
Building dependency tree       
Reading state information... Done
simba is already the newest version (0.8.4-4.3).
The following packages were automatically installed and are no longer required:
  libconfig-inifiles-perl libdbd-mysql-perl libjemalloc1 libreadline5 libterm-readkey-perl linux-hwe-5.4-headers-5.4.0-71 linux-hwe-5.4-headers-5.4.0-72 linux-hwe-5.4-headers-5.4.0-73
  linux-hwe-5.4-headers-5.4.0-74 linux-hwe-5.4-headers-5.4.0-77 linux-hwe-5.4-headers-5.4.0-80 linux-hwe-5.4-headers-5.4.0-81 linux-hwe-5.4-headers-5.4.0-84 linux-hwe-5.4-headers-5.4.0-86
  linux-hwe-5.4-headers-5.4.0-87 linux-hwe-5.4-headers-5.4.0-89 mariadb-common nvidia-container-runtime shim
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded.

I'm not entirely sure where to go from here. Help would be greatly appreciated

Original install error:

Collecting simba-uw-tf-dev
  Using cached Simba_UW_tf_dev-0.88.8-py3-none-any.whl (10.5 MB)
Requirement already satisfied: scipy==1.1.0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (1.1.0)
Requirement already satisfied: yellowbrick==0.9.1 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (0.9.1)
Requirement already satisfied: graphviz==0.11 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (0.11)
Requirement already satisfied: numba==0.48.0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (0.48.0)
Requirement already satisfied: numpy==1.18.1 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (1.18.1)
Requirement already satisfied: Pillow==5.4.1 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (5.4.1)
Requirement already satisfied: dash-colorscales==0.0.4 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (0.0.4)
Collecting wxpython==4.0.4
  Using cached wxPython-4.0.4.tar.gz (68.8 MB)
  Preparing metadata (setup.py) ... done
Requirement already satisfied: numexpr==2.6.9 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (2.6.9)
Requirement already satisfied: tables==3.6.1 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (3.6.1)
Requirement already satisfied: imgaug==0.4.0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (0.4.0)
Requirement already satisfied: opencv-python==3.4.5.20 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (3.4.5.20)
Requirement already satisfied: pyarrow==0.17.1 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (0.17.1)
Requirement already satisfied: dtreeviz==0.8.1 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (0.8.1)
Requirement already satisfied: statsmodels==0.9.0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (0.9.0)
Requirement already satisfied: tqdm==4.30.0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (4.30.0)
Requirement already satisfied: tabulate==0.8.3 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (0.8.3)
Requirement already satisfied: scikit-image==0.14.2 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (0.14.2)
Requirement already satisfied: imutils==0.5.2 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (0.5.2)
Requirement already satisfied: dash-core-components==1.10.2 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (1.10.2)
Collecting shapely==1.7
  Using cached Shapely-1.7.0-cp36-cp36m-manylinux1_x86_64.whl (1.8 MB)
Requirement already satisfied: h5py==2.9.0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (2.9.0)
Requirement already satisfied: eli5==0.10.1 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (0.10.1)
Requirement already satisfied: plotly==4.9.0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (4.9.0)
Requirement already satisfied: pandas==0.25.3 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (0.25.3)
Requirement already satisfied: shap==0.35.0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (0.35.0)
Requirement already satisfied: dash-color-picker==0.0.1 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (0.0.1)
Requirement already satisfied: matplotlib==3.0.3 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (3.0.3)
Requirement already satisfied: cefpython3==66.0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (66.0)
Requirement already satisfied: imblearn==0.0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (0.0)
Requirement already satisfied: xgboost==0.90 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (0.90)
Requirement already satisfied: dash==1.14.0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (1.14.0)
Requirement already satisfied: pyyaml==5.3.1 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (5.3.1)
Requirement already satisfied: seaborn==0.9.0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (0.9.0)
Requirement already satisfied: scikit-learn==0.22.2 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (0.22.2)
Requirement already satisfied: dash-html-components==1.0.3 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from simba-uw-tf-dev) (1.0.3)
Requirement already satisfied: future in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from dash==1.14.0->simba-uw-tf-dev) (0.18.2)
Requirement already satisfied: Flask>=1.0.2 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from dash==1.14.0->simba-uw-tf-dev) (2.0.2)
Requirement already satisfied: flask-compress in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from dash==1.14.0->simba-uw-tf-dev) (1.10.1)
Requirement already satisfied: dash-table==4.9.0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from dash==1.14.0->simba-uw-tf-dev) (4.9.0)
Requirement already satisfied: dash-renderer==1.6.0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from dash==1.14.0->simba-uw-tf-dev) (1.6.0)
Requirement already satisfied: colour in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from dtreeviz==0.8.1->simba-uw-tf-dev) (0.1.5)
Requirement already satisfied: attrs>16.0.0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from eli5==0.10.1->simba-uw-tf-dev) (21.2.0)
Requirement already satisfied: six in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from eli5==0.10.1->simba-uw-tf-dev) (1.11.0)
Requirement already satisfied: jinja2 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from eli5==0.10.1->simba-uw-tf-dev) (3.0.3)
Requirement already satisfied: imbalanced-learn in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from imblearn==0.0->simba-uw-tf-dev) (0.6.2)
Requirement already satisfied: imageio in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from imgaug==0.4.0->simba-uw-tf-dev) (2.3.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/blackmonlab/.local/lib/python3.6/site-packages (from matplotlib==3.0.3->simba-uw-tf-dev) (2.4.7)
Requirement already satisfied: python-dateutil>=2.1 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from matplotlib==3.0.3->simba-uw-tf-dev) (2.7.3)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/blackmonlab/.local/lib/python3.6/site-packages (from matplotlib==3.0.3->simba-uw-tf-dev) (1.3.1)
Requirement already satisfied: cycler>=0.10 in /home/blackmonlab/.local/lib/python3.6/site-packages (from matplotlib==3.0.3->simba-uw-tf-dev) (0.10.0)
Requirement already satisfied: llvmlite<0.32.0,>=0.31.0dev0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from numba==0.48.0->simba-uw-tf-dev) (0.31.0)
Requirement already satisfied: setuptools in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from numba==0.48.0->simba-uw-tf-dev) (58.0.4)
Requirement already satisfied: pytz>=2017.2 in /home/blackmonlab/.local/lib/python3.6/site-packages (from pandas==0.25.3->simba-uw-tf-dev) (2021.1)
Requirement already satisfied: retrying>=1.3.3 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from plotly==4.9.0->simba-uw-tf-dev) (1.3.3)
Requirement already satisfied: networkx>=1.8 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from scikit-image==0.14.2->simba-uw-tf-dev) (2.5.1)
Requirement already satisfied: PyWavelets>=0.4.0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from scikit-image==0.14.2->simba-uw-tf-dev) (1.1.1)
Requirement already satisfied: dask[array]>=1.0.0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from scikit-image==0.14.2->simba-uw-tf-dev) (2021.3.0)
Requirement already satisfied: cloudpickle>=0.2.1 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from scikit-image==0.14.2->simba-uw-tf-dev) (2.0.0)
Requirement already satisfied: joblib>=0.11 in /home/blackmonlab/.local/lib/python3.6/site-packages (from scikit-learn==0.22.2->simba-uw-tf-dev) (1.0.1)
Requirement already satisfied: patsy in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from statsmodels==0.9.0->simba-uw-tf-dev) (0.5.2)
Requirement already satisfied: toolz>=0.8.2 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from dask[array]>=1.0.0->scikit-image==0.14.2->simba-uw-tf-dev) (0.11.2)
Requirement already satisfied: Werkzeug>=2.0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from Flask>=1.0.2->dash==1.14.0->simba-uw-tf-dev) (2.0.2)
Requirement already satisfied: itsdangerous>=2.0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from Flask>=1.0.2->dash==1.14.0->simba-uw-tf-dev) (2.0.1)
Requirement already satisfied: click>=7.1.2 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from Flask>=1.0.2->dash==1.14.0->simba-uw-tf-dev) (8.0.3)
Requirement already satisfied: MarkupSafe>=2.0 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from jinja2->eli5==0.10.1->simba-uw-tf-dev) (2.0.1)
Requirement already satisfied: decorator<5,>=4.3 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from networkx>=1.8->scikit-image==0.14.2->simba-uw-tf-dev) (4.4.2)
Requirement already satisfied: brotli in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from flask-compress->dash==1.14.0->simba-uw-tf-dev) (1.0.9)
Requirement already satisfied: importlib-metadata in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from click>=7.1.2->Flask>=1.0.2->dash==1.14.0->simba-uw-tf-dev) (4.8.3)
Requirement already satisfied: dataclasses in /home/blackmonlab/.local/lib/python3.6/site-packages (from Werkzeug>=2.0->Flask>=1.0.2->dash==1.14.0->simba-uw-tf-dev) (0.8)
Requirement already satisfied: zipp>=0.5 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from importlib-metadata->click>=7.1.2->Flask>=1.0.2->dash==1.14.0->simba-uw-tf-dev) (3.6.0)
Requirement already satisfied: typing-extensions>=3.6.4 in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from importlib-metadata->click>=7.1.2->Flask>=1.0.2->dash==1.14.0->simba-uw-tf-dev) (3.7.4.3)
Building wheels for collected packages: wxpython
  Building wheel for wxpython (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/blackmonlab/anaconda3/envs/simbaenv/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-v9j3pe3f/wxpython_f456f9634ae548d3a4861fa0f1763df0/setup.py'"'"'; __file__='"'"'/tmp/pip-install-v9j3pe3f/wxpython_f456f9634ae548d3a4861fa0f1763df0/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-if_jd4n3
       cwd: /tmp/pip-install-v9j3pe3f/wxpython_f456f9634ae548d3a4861fa0f1763df0/
  Complete output (525 lines):
  /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages/setuptools/dist.py:720: UserWarning: Usage of dash-separated 'license-file' will not be supported in future versions. Please use the underscore name 'license_file' instead
    % (opt, underscore_opt)
  /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages/setuptools/dist.py:294: DistDeprecationWarning: use_2to3 is ignored.
    warnings.warn(f"{attr} is ignored.", DistDeprecationWarning)
  running bdist_wheel
  running build
  WARNING: Building this way assumes that all generated files have been
  generated already.  If that is not the case then use build.py directly
  to generate the source and perform the build stage.  You can use
  --skip-build with the bdist_* or install commands to avoid this
  message and the wxWidgets and Phoenix build steps in the future.

  "/home/blackmonlab/anaconda3/envs/simbaenv/bin/python" -u build.py build
  Will build using: "/home/blackmonlab/anaconda3/envs/simbaenv/bin/python"
  3.6.10 |Anaconda, Inc.| (default, May  8 2020, 02:54:21)
  [GCC 7.3.0]
  Python's architecture is 64bit
  cfg.VERSION: 4.0.4

  Running command: build
  Running command: build_wx
  wxWidgets build options: ['--wxpython', '--unicode', '--gtk3']
  Configure options: ['--enable-unicode', '--with-gtk=3', '--with-opengl', '--enable-sound', '--enable-graphics_ctx', '--enable-mediactrl', '--enable-display', '--enable-geometry', '--enable-debug_flag', '--enable-optimise', '--disable-debugreport', '--enable-uiactionsim', '--enable-autoidman', '--with-sdl']
  /tmp/pip-install-v9j3pe3f/wxpython_f456f9634ae548d3a4861fa0f1763df0/ext/wxWidgets/configure --enable-unicode --with-gtk=3 --with-opengl --enable-sound --enable-graphics_ctx --enable-mediactrl --enable-display --enable-geometry --enable-debug_flag --enable-optimise --disable-debugreport --enable-uiactionsim --enable-autoidman --with-sdl
  checking build system type... x86_64-pc-linux-gnu
  checking host system type... x86_64-pc-linux-gnu
  checking for --disable-gui... no
  checking for --enable-monolithic... no
  checking for --enable-plugins... no
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  checking for toolkit... gtk
  checking for --with-libpng... yes
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  configure: WARNING: wxMediaCtrl can't be built because GStreamer not available
  configure: error: wxMediaCtrl was explicitly requested but can't be built.

      Fix the problems reported above or don't use --enable-mediactrl configure option.

  Error running configure
  ERROR: failed building wxWidgets
  Traceback (most recent call last):
    File "build.py", line 1321, in cmd_build_wx
      wxbuild.main(wxDir(), build_options)
    File "/tmp/pip-install-v9j3pe3f/wxpython_f456f9634ae548d3a4861fa0f1763df0/buildtools/build_wxwidgets.py", line 375, in main
      "Error running configure")
    File "/tmp/pip-install-v9j3pe3f/wxpython_f456f9634ae548d3a4861fa0f1763df0/buildtools/build_wxwidgets.py", line 85, in exitIfError
      raise builder.BuildError(msg)
  buildtools.builder.BuildError: Error running configure
  Finished command: build_wx (0m7.750s)
  Finished command: build (0m7.751s)
  Command '"/home/blackmonlab/anaconda3/envs/simbaenv/bin/python" -u build.py build' failed with exit code 1.
  ----------------------------------------
  ERROR: Failed building wheel for wxpython
  Running setup.py clean for wxpython
Failed to build wxpython
Installing collected packages: shapely, wxpython, simba-uw-tf-dev
    Running setup.py install for wxpython ... error
    ERROR: Command errored out with exit status 1:
     command: /home/blackmonlab/anaconda3/envs/simbaenv/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-v9j3pe3f/wxpython_f456f9634ae548d3a4861fa0f1763df0/setup.py'"'"'; __file__='"'"'/tmp/pip-install-v9j3pe3f/wxpython_f456f9634ae548d3a4861fa0f1763df0/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-0yd87w4f/install-record.txt --single-version-externally-managed --compile --install-headers /home/blackmonlab/anaconda3/envs/simbaenv/include/python3.6m/wxpython
         cwd: /tmp/pip-install-v9j3pe3f/wxpython_f456f9634ae548d3a4861fa0f1763df0/
    Complete output (525 lines):
    /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages/setuptools/dist.py:720: UserWarning: Usage of dash-separated 'license-file' will not be supported in future versions. Please use the underscore name 'license_file' instead
      % (opt, underscore_opt)
    /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages/setuptools/dist.py:294: DistDeprecationWarning: use_2to3 is ignored.
      warnings.warn(f"{attr} is ignored.", DistDeprecationWarning)
    running install
    running build
    WARNING: Building this way assumes that all generated files have been
    generated already.  If that is not the case then use build.py directly
    to generate the source and perform the build stage.  You can use
    --skip-build with the bdist_* or install commands to avoid this
    message and the wxWidgets and Phoenix build steps in the future.

    "/home/blackmonlab/anaconda3/envs/simbaenv/bin/python" -u build.py build
    Will build using: "/home/blackmonlab/anaconda3/envs/simbaenv/bin/python"
    3.6.10 |Anaconda, Inc.| (default, May  8 2020, 02:54:21)
    [GCC 7.3.0]
    Python's architecture is 64bit
    cfg.VERSION: 4.0.4

    Running command: build
    Running command: build_wx
    wxWidgets build options: ['--wxpython', '--unicode', '--gtk3']
    Configure options: ['--enable-unicode', '--with-gtk=3', '--with-opengl', '--enable-sound', '--enable-graphics_ctx', '--enable-mediactrl', '--enable-display', '--enable-geometry', '--enable-debug_flag', '--enable-optimise', '--disable-debugreport', '--enable-uiactionsim', '--enable-autoidman', '--with-sdl']
    /tmp/pip-install-v9j3pe3f/wxpython_f456f9634ae548d3a4861fa0f1763df0/ext/wxWidgets/configure --enable-unicode --with-gtk=3 --with-opengl --enable-sound --enable-graphics_ctx --enable-mediactrl --enable-display --enable-geometry --enable-debug_flag --enable-optimise --disable-debugreport --enable-uiactionsim --enable-autoidman --with-sdl
    checking build system type... x86_64-pc-linux-gnu
    checking host system type... x86_64-pc-linux-gnu
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    checking for sdl-config... no
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    *** The sdl-config script installed by SDL could not be found
    *** If SDL was installed in PREFIX, make sure PREFIX/bin is in
    *** your path, or set the SDL_CONFIG environment variable to the
    *** full path to sdl-config.
    checking for GTKPRINT... yes
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    checking for WEBKIT... configure: WARNING: webkit2gtk not found, falling back to webkitgtk
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    configure: WARNING: WebKit not available, disabling wxWebView
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    configure: WARNING: wxMediaCtrl can't be built because GStreamer not available
    configure: error: wxMediaCtrl was explicitly requested but can't be built.

        Fix the problems reported above or don't use --enable-mediactrl configure option.

    Error running configure
    ERROR: failed building wxWidgets
    Traceback (most recent call last):
      File "build.py", line 1321, in cmd_build_wx
        wxbuild.main(wxDir(), build_options)
      File "/tmp/pip-install-v9j3pe3f/wxpython_f456f9634ae548d3a4861fa0f1763df0/buildtools/build_wxwidgets.py", line 375, in main
        "Error running configure")
      File "/tmp/pip-install-v9j3pe3f/wxpython_f456f9634ae548d3a4861fa0f1763df0/buildtools/build_wxwidgets.py", line 85, in exitIfError
        raise builder.BuildError(msg)
    buildtools.builder.BuildError: Error running configure
    Finished command: build_wx (0m7.773s)
    Finished command: build (0m7.773s)
    Command '"/home/blackmonlab/anaconda3/envs/simbaenv/bin/python" -u build.py build' failed with exit code 1.
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/blackmonlab/anaconda3/envs/simbaenv/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-v9j3pe3f/wxpython_f456f9634ae548d3a4861fa0f1763df0/setup.py'"'"'; __file__='"'"'/tmp/pip-install-v9j3pe3f/wxpython_f456f9634ae548d3a4861fa0f1763df0/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-0yd87w4f/install-record.txt --single-version-externally-managed --compile --install-headers /home/blackmonlab/anaconda3/envs/simbaenv/include/python3.6m/wxpython Check the logs for full command output.

[sronilsson]

Hi @AnnabelPerry! First, SimBA has no SQL dependencies or currently store data in SQL format, and not sure why it would try to connect to SQL server. If you see those error again: terminate your session, and make sure you are installing SimBA in a fresh conda environment.

The rest of the errors, however, seems very similar to the errors reported by another user this morning, who is also working in Linux or MacOS. https://github.com/sgoldenlab/simba/issues/154

Can you try to install simba with pip install simba-uw-tf-dev --no-deps and see if that fixes it? It seems related to MacOS/Linus and the installation of wxpython. Also make sur you are running python 3.6.10

[AnnabelPerry]

Thank you for your rapid response! So I'd actually tried re-installing SimBA with no dependencies a couple days ago. It installed properly, but I encountered an issue in the GUI where it would fail with an error when I tried to crop videos. I tried replicating the error just now, but it appears to have installed successfully this time. Here's what I did: I removed the old environment and reran these steps (with the no dependencies flag):

conda create -n simbaenv python=3.6.10 

conda activate simbaenv 

pip install simba-uw-tf-dev --no-deps

pip uninstall shapely 

conda install -c conda-forge shapely 

I then ran the simba command, getting this error:

Traceback (most recent call last):
  File "/home/blackmonlab/anaconda3/envs/simbaenv/bin/simba", line 5, in 
    from simba.SimBA import main
  File "/home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages/simba/SimBA.py", line 6, in 
    import seaborn as sns
ModuleNotFoundError: No module named 'seaborn'

I ran pip install seaborn, getting this error:

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
simba-uw-tf-dev 0.88.8 requires cefpython3==66.0, which is not installed.
simba-uw-tf-dev 0.88.8 requires dash==1.14.0, which is not installed.
simba-uw-tf-dev 0.88.8 requires dash-color-picker==0.0.1, which is not installed.
simba-uw-tf-dev 0.88.8 requires dash-colorscales==0.0.4, which is not installed.
simba-uw-tf-dev 0.88.8 requires dash-core-components==1.10.2, which is not installed.
simba-uw-tf-dev 0.88.8 requires dash-html-components==1.0.3, which is not installed.
simba-uw-tf-dev 0.88.8 requires dtreeviz==0.8.1, which is not installed.
simba-uw-tf-dev 0.88.8 requires eli5==0.10.1, which is not installed.
simba-uw-tf-dev 0.88.8 requires graphviz==0.11, which is not installed.
simba-uw-tf-dev 0.88.8 requires h5py==2.9.0, which is not installed.
simba-uw-tf-dev 0.88.8 requires imblearn==0.0, which is not installed.
simba-uw-tf-dev 0.88.8 requires imgaug==0.4.0, which is not installed.
simba-uw-tf-dev 0.88.8 requires imutils==0.5.2, which is not installed.
simba-uw-tf-dev 0.88.8 requires numba==0.48.0, which is not installed.
simba-uw-tf-dev 0.88.8 requires numexpr==2.6.9, which is not installed.
simba-uw-tf-dev 0.88.8 requires opencv-python==3.4.5.20, which is not installed.
simba-uw-tf-dev 0.88.8 requires plotly==4.9.0, which is not installed.
simba-uw-tf-dev 0.88.8 requires pyarrow==0.17.1, which is not installed.
simba-uw-tf-dev 0.88.8 requires pyyaml==5.3.1, which is not installed.
simba-uw-tf-dev 0.88.8 requires scikit-image==0.14.2, which is not installed.
simba-uw-tf-dev 0.88.8 requires scikit-learn==0.22.2, which is not installed.
simba-uw-tf-dev 0.88.8 requires shap==0.35.0, which is not installed.
simba-uw-tf-dev 0.88.8 requires statsmodels==0.9.0, which is not installed.
simba-uw-tf-dev 0.88.8 requires tables==3.6.1, which is not installed.
simba-uw-tf-dev 0.88.8 requires tabulate==0.8.3, which is not installed.
simba-uw-tf-dev 0.88.8 requires tqdm==4.30.0, which is not installed.
simba-uw-tf-dev 0.88.8 requires wxpython==4.0.4, which is not installed.
simba-uw-tf-dev 0.88.8 requires xgboost==0.90, which is not installed.
simba-uw-tf-dev 0.88.8 requires yellowbrick==0.9.1, which is not installed.
simba-uw-tf-dev 0.88.8 requires matplotlib==3.0.3, but you have matplotlib 3.3.4 which is incompatible.
simba-uw-tf-dev 0.88.8 requires numpy==1.18.1, but you have numpy 1.19.5 which is incompatible.
simba-uw-tf-dev 0.88.8 requires pandas==0.25.3, but you have pandas 1.1.5 which is incompatible.
simba-uw-tf-dev 0.88.8 requires Pillow==5.4.1, but you have pillow 8.4.0 which is incompatible.
simba-uw-tf-dev 0.88.8 requires scipy==1.1.0, but you have scipy 1.5.4 which is incompatible.
simba-uw-tf-dev 0.88.8 requires seaborn==0.9.0, but you have seaborn 0.11.2 which is incompatible.
simba-uw-tf-dev 0.88.8 requires shapely==1.7, but you have shapely 1.7.1 which is incompatible.

I pip installed all the requested package versions. All except wxpython installed without error. pip install wxpython==4.0.4 yielded the error at the bottom of the post (incredibly lengthy, so I included it outside the flow of the text so you could see the rest of my message)

I then ran the simba command, successfully entering the GUI. I have yet to encounter any issues preprocessing videos, but if the wxpython error becomes a problem I'll open a new issue! Thanks again for the help!

pip install wxpython==4.0.4 error:

Collecting wxpython==4.0.4
  Using cached wxPython-4.0.4.tar.gz (68.8 MB)
Requirement already satisfied: six in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from wxpython==4.0.4) (1.16.0)
Requirement already satisfied: Pillow in /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages (from wxpython==4.0.4) (5.4.1)
Building wheels for collected packages: wxpython
  Building wheel for wxpython (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/blackmonlab/anaconda3/envs/simbaenv/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/setup.py'"'"'; __file__='"'"'/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-ee4j772p
       cwd: /tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/
  Complete output (525 lines):
  /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages/setuptools/dist.py:720: UserWarning: Usage of dash-separated 'license-file' will not be supported in future versions. Please use the underscore name 'license_file' instead
    % (opt, underscore_opt)
  /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages/setuptools/dist.py:294: DistDeprecationWarning: use_2to3 is ignored.
    warnings.warn(f"{attr} is ignored.", DistDeprecationWarning)
  running bdist_wheel
  running build
  WARNING: Building this way assumes that all generated files have been
  generated already.  If that is not the case then use build.py directly
  to generate the source and perform the build stage.  You can use
  --skip-build with the bdist_* or install commands to avoid this
  message and the wxWidgets and Phoenix build steps in the future.

  "/home/blackmonlab/anaconda3/envs/simbaenv/bin/python" -u build.py build
  Will build using: "/home/blackmonlab/anaconda3/envs/simbaenv/bin/python"
  3.6.10 |Anaconda, Inc.| (default, May  8 2020, 02:54:21)
  [GCC 7.3.0]
  Python's architecture is 64bit
  cfg.VERSION: 4.0.4

  Running command: build
  Running command: build_wx
  wxWidgets build options: ['--wxpython', '--unicode', '--gtk3']
  Configure options: ['--enable-unicode', '--with-gtk=3', '--with-opengl', '--enable-sound', '--enable-graphics_ctx', '--enable-mediactrl', '--enable-display', '--enable-geometry', '--enable-debug_flag', '--enable-optimise', '--disable-debugreport', '--enable-uiactionsim', '--enable-autoidman', '--with-sdl']
  /tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/ext/wxWidgets/configure --enable-unicode --with-gtk=3 --with-opengl --enable-sound --enable-graphics_ctx --enable-mediactrl --enable-display --enable-geometry --enable-debug_flag --enable-optimise --disable-debugreport --enable-uiactionsim --enable-autoidman --with-sdl
  checking build system type... x86_64-pc-linux-gnu
  checking host system type... x86_64-pc-linux-gnu
  checking for --disable-gui... no
  checking for --enable-monolithic... no
  checking for --enable-plugins... no
  checking for --without-subdirs... no
  checking for --enable-official_build... no
  checking for --disable-all-features... no
  checking for --enable-universal... no
  checking for --enable-nanox... no
  checking for --enable-gpe... no
  checking for toolkit... gtk
  checking for --with-libpng... yes
  checking for --with-libjpeg... yes
  checking for --with-libtiff... yes
  checking for --without-libjbig... no
  checking for --without-liblzma... no
  checking for --with-libxpm... yes
  checking for --with-libiconv... yes
  checking for --with-libmspack... no
  checking for --without-gtkprint... no
  checking for --with-gnomevfs... no
  checking for --with-libnotify... yes
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  configure: WARNING: wxMediaCtrl can't be built because GStreamer not available
  configure: error: wxMediaCtrl was explicitly requested but can't be built.

      Fix the problems reported above or don't use --enable-mediactrl configure option.

  Error running configure
  ERROR: failed building wxWidgets
  Traceback (most recent call last):
    File "build.py", line 1321, in cmd_build_wx
      wxbuild.main(wxDir(), build_options)
    File "/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/buildtools/build_wxwidgets.py", line 375, in main
      "Error running configure")
    File "/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/buildtools/build_wxwidgets.py", line 85, in exitIfError
      raise builder.BuildError(msg)
  buildtools.builder.BuildError: Error running configure
  Finished command: build_wx (0m8.126s)
  Finished command: build (0m8.126s)
  Command '"/home/blackmonlab/anaconda3/envs/simbaenv/bin/python" -u build.py build' failed with exit code 1.
  ----------------------------------------
  ERROR: Failed building wheel for wxpython
  Running setup.py clean for wxpython
Failed to build wxpython
Installing collected packages: wxpython
    Running setup.py install for wxpython ... error
    ERROR: Command errored out with exit status 1:
     command: /home/blackmonlab/anaconda3/envs/simbaenv/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/setup.py'"'"'; __file__='"'"'/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-_jggwalf/install-record.txt --single-version-externally-managed --compile --install-headers /home/blackmonlab/anaconda3/envs/simbaenv/include/python3.6m/wxpython
         cwd: /tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/
    Complete output (525 lines):
    /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages/setuptools/dist.py:720: UserWarning: Usage of dash-separated 'license-file' will not be supported in future versions. Please use the underscore name 'license_file' instead
      % (opt, underscore_opt)
    /home/blackmonlab/anaconda3/envs/simbaenv/lib/python3.6/site-packages/setuptools/dist.py:294: DistDeprecationWarning: use_2to3 is ignored.
      warnings.warn(f"{attr} is ignored.", DistDeprecationWarning)
    running install
    running build
    WARNING: Building this way assumes that all generated files have been
    generated already.  If that is not the case then use build.py directly
    to generate the source and perform the build stage.  You can use
    --skip-build with the bdist_* or install commands to avoid this
    message and the wxWidgets and Phoenix build steps in the future.

    "/home/blackmonlab/anaconda3/envs/simbaenv/bin/python" -u build.py build
    Will build using: "/home/blackmonlab/anaconda3/envs/simbaenv/bin/python"
    3.6.10 |Anaconda, Inc.| (default, May  8 2020, 02:54:21)
    [GCC 7.3.0]
    Python's architecture is 64bit
    cfg.VERSION: 4.0.4

    Running command: build
    Running command: build_wx
    wxWidgets build options: ['--wxpython', '--unicode', '--gtk3']
    Configure options: ['--enable-unicode', '--with-gtk=3', '--with-opengl', '--enable-sound', '--enable-graphics_ctx', '--enable-mediactrl', '--enable-display', '--enable-geometry', '--enable-debug_flag', '--enable-optimise', '--disable-debugreport', '--enable-uiactionsim', '--enable-autoidman', '--with-sdl']
    /tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/ext/wxWidgets/configure --enable-unicode --with-gtk=3 --with-opengl --enable-sound --enable-graphics_ctx --enable-mediactrl --enable-display --enable-geometry --enable-debug_flag --enable-optimise --disable-debugreport --enable-uiactionsim --enable-autoidman --with-sdl
    checking build system type... x86_64-pc-linux-gnu
    checking host system type... x86_64-pc-linux-gnu
    checking for --disable-gui... no
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    configure: WARNING: wxMediaCtrl can't be built because GStreamer not available
    configure: error: wxMediaCtrl was explicitly requested but can't be built.

        Fix the problems reported above or don't use --enable-mediactrl configure option.

    Error running configure
    ERROR: failed building wxWidgets
    Traceback (most recent call last):
      File "build.py", line 1321, in cmd_build_wx
        wxbuild.main(wxDir(), build_options)
      File "/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/buildtools/build_wxwidgets.py", line 375, in main
        "Error running configure")
      File "/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/buildtools/build_wxwidgets.py", line 85, in exitIfError
        raise builder.BuildError(msg)
    buildtools.builder.BuildError: Error running configure
    Finished command: build_wx (0m7.750s)
    Finished command: build (0m7.751s)
    Command '"/home/blackmonlab/anaconda3/envs/simbaenv/bin/python" -u build.py build' failed with exit code 1.
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/blackmonlab/anaconda3/envs/simbaenv/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/setup.py'"'"'; __file__='"'"'/tmp/pip-install-2l9g9bkk/wxpython_2695da00068440fd9b9c0b88c3250ba0/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-_jggwalf/install-record.txt --single-version-externally-managed --compile --install-headers /home/blackmonlab/anaconda3/envs/simbaenv/include/python3.6m/wxpython Check the logs for full command output.

[catubc]

Hi @AnnabelPerry , I just had this same issue this week. It seems wxpython is still a pain to work with. My recollection was that conda installing wxpython might have helped. See issue here;

https://github.com/sgoldenlab/simba/issues/154