Troubles with OpenCV/import cv2 on Mac, have tried so many things, now new error

Question

Errors:

• pip3 install opencv-contrib-python
• import cv2
• Original Error: Symbol not found: ___addtf3
• Current Error: Symbol not found: __cg_jpeg_resync_to_restart

Environment:

• opencv-contrib-python 4.1.2.30
• iMac, macOS Catalina 10.15.2
• Python 3.7.5
• pip --version: pip 19.3.1 from /usr/local/lib/python3.7/site-packages/pip (python 3.7)
• Using Homebrew

The 30 or so things that I've tried so far:

Error 1:
  File "/usr/local/lib/python3.7/site-packages/cv2/__init__.py", line 3, in <module>
    from .cv2 import *
  ImportError: numpy.core.multiarray failed to import
Try 1:
    import numpy.core.multiarray before import cv2
Error 2:
  File "/Users/mbennett/Library/Python/3.7/lib/python/site-packages/numpy/__init__.py", line 142, in <module>
    from . import core
  File "/Users/mbennett/Library/Python/3.7/lib/python/site-packages/numpy/core/__init__.py", line 47, in <module>
    raise ImportError(msg)
  ...
  Original error was:
    dlopen(/Users/mbennett/Library/Python/3.7/lib/python/site-packages/numpy/core/_multiarray_umath.cpython-37m-darwin.so, 2): Symbol not found: ___addtf3
  Referenced from: /Users/mbennett/Library/Python/3.7/lib/python/site-packages/numpy/core/../.dylibs/libquadmath.0.dylib
  Expected in: /usr/lib/libSystem.B.dylib
 in /Users/mbennett/Library/Python/3.7/lib/python/site-packages/numpy/core/../.dylibs/libquadmath.0.dylib
 ...
Importing the numpy c-extensions failed.
- x Try uninstalling and reinstalling numpy.
- If you have already done that, then:
  x 1. Check that you expected to use Python3.7 from "/usr/local/opt/python/bin/python3.7",
     and that you have no directories in your PATH or PYTHONPATH that can
     interfere with the Python and numpy version "1.17.4" you're trying to use.
  2. If (1) looks fine, you can open a new issue at
     https://github.com/numpy/numpy/issues.  Please include details on:
     - how you installed Python
     - how you installed numpy
     - your operating system
     - whether or not you have multiple versions of Python installed
     - if you built from source, your compiler versions and ideally a build log
- If you're working with a numpy git repository, try `git clean -xdf`
  (removes all files not under version control) and rebuild numpy.
--
Trying to change symlinks
Python links in 2 places: /usr/bin AND /usr/local/bin
In /usr/bin, AS ROOT, cannot remove or change python link
    rm python
    rm: python: Operation not permitted
    # wtf, whoami -> root
--
Next try: Change order of path, put /usr/local/bin BEFORE /usr/bin, then try changing symlinks there
    or try changing symlink first
(links changed, stopped here)
--
Try 1b: installing again now that pip is really pip3
    No
    # pip now = pip3
    pip uninstall opencv-contrib-python
    pip install opencv-contrib-python
        OK: Successfully installed opencv-contrib-python-4.1.2.30
    No, same errors
Try 1c:
    No
    pip uninstall opencv-contrib-python
    pip install -U opencv-contrib-python
Try 1d:
    No, same version numpy-1.18.1
    pip uninstall numpy
    pip install numpy -U
Try 1e:
    No
    python -c "import numpy;print numpy.version;print numpy.file";
    ^-- and added ()'s to print
Try 1f:
    No
    # put /usr/local/lib before /usr/lib
    export DYLD_LIBRARY_PATH="/usr/local/lib:$DYLD_LIBRARY_PATH"
Try 1g:
    No
    pip install --upgrade --force-reinstall --no-cache-dir numpy
Try 1h:
    No
    pip install --upgrade --force-reinstall --no-cache-dir scipy
        Successfully uninstalled numpy-1.18.1
        Found existing installation: scipy 1.3.3
        Uninstalling scipy-1.3.3:
            Successfully uninstalled scipy-1.3.3
        Successfully installed numpy-1.18.1 scipy-1.4.1
Try 1i:
    No
    Try very old scipy
    # conda uninstall scipy
    # conda install scipy=0.15.0
    pip uninstall scipy
    X pip install scipy=0.15.0   # bad syntax
    x pip install scipy==0.15.0
        ^-- LOTS of errors
    Reintalling w default version it says:
        Requirement already satisfied: numpy>=1.13.3 in /usr/local/lib/python3.7/site-packages (from scipy) (1.18.1)
    Installing collected packages: scipy
    Successfully installed scipy-1.4.1
Try 1j:
    No
    Try rolling back scipy to 1.13.3
    pip uninstall scipy
    pip install scipy==1.13.3
        ^-- not a valid version...
Try 1k:
    No
    Try rolling back scipy to 1.4.0
    (still uninstalled)
    pip install scipy==1.4.0
Try 1l:
    No
    Try uninstalling the Homebrew version of numpy
    # pip uninstall scipy
    # brew update
    # brew upgrade
    brew uninstall numpy
        Uninstalling /usr/local/Cellar/numpy/1.11.2... (474 files, 9.5MB)
Try 1m:
    No  (likely scipy is subset of numpy, vs other way around?)
    Try uninstalling the Homebrew version of scipy
    brew uninstall scipy
        Error: No such keg: /usr/local/Cellar/scipy
Try 1n:
    ? Try installing blas?
    ? "___addtf3 which is a GCC software floating point routine provided by a gfortran"
        ^-- "libquadmath uses the ___addtf3 routine, rather than defines it"
    Try installing gfortran
        x pip install gfortran
        brew install gfortran
        Error:
            Error: No available formula with the name "gfortran" 
            GNU Fortran is part of the GCC formula:
                brew install gcc
Try 1o:
    Install gcc:
        brew install gcc
        Error:
            Error: gcc 6.2.0 is already installed
            To upgrade to 9.2.0_3, run `brew upgrade gcc`.
    ,Then retry installing gfortran
    ,    brew install gfortran
Try 1p:
    No
    brew upgrade gcc
    brew install gfortran
        Error: No available formula with the name "gfortran" 
        GNU Fortran is part of the GCC formula:
            brew install gcc
    # retest import
Try 1q:
    No
    Try installing clang4 or clang4-r
    x brew install clang4
    x brew install clang4-r
    x brew install clang
    --
X install-clang4.sh
--------------------
# Download binary
curl -O http://r.research.att.com/libs/clang-4.0.0-darwin15.6-Release.tar.gz
# Extract binary onto root directory
tar fvxz clang-4.0.0-darwin15.6-Release.tar.gz -C /
# Overwrite the ~/.R/Makevars
cat <<- EOF > ~/.R/Makevars
# The following statements are required to use the clang4 binary
CC=/usr/local/clang4/bin/clang
CXX=/usr/local/clang4/bin/clang++
CXX11=$CXX
CXX14=$CXX
CXX17=$CXX
CXX1X=$CXX
LDFLAGS=-L/usr/local/clang4/lib
# End clang4 inclusion statements
EOF
--
Try 1r:
    x try the Sierra version of gfortran?
    gfortran is part of GCC now, and Web says it's current
--
Try 1s:
    No
    Try overwriting python3 (links?)
    cd /usr/local/Cellar/python
    cp -r 3.7.5 3.7.5.bak
    brew link --overwrite python3
        Warning: Already linked: /usr/local/Cellar/python/3.7.5
        To relink:
            brew unlink python
            brew link python
    brew link --overwrite python
Try 1t:
    X gfortran ... The missing symbol in libgcc isn't surprising
        since you're trying to run code compiled with a 4.6 gfortran in a 4.2 runtime environment.
    No, gfortran part of gcc, remember!
Try 1u:
    No, same import error
    try installing openblas 
    x pip install openblas
    brew install openblas    # ok
Try 1v:
    No:
    Try installing or building gdal2-python
    brew install gdal2-python
        Error: No formulae found in taps.
    x brew reinstall --build-from-source gdal2-python
Try 1w:
    No
    Try fixing gcc?
    cd /usr/local/lib
    x chown -R mbennett gcc  (already done)
    brew link gcc
        Warning: Already linked: /usr/local/Cellar/gcc/9.2.0_3
        To relink:
    brew unlink gcc  # worked
    brew link gcc  # worked
    But same error in python
Try 1x:
    No, and now have different error
    try installing older version of opencv 4x -> 3x
    x pip install opencv-contrib-python==3.3.0.10
        ERROR: Could not find a version that satisfies the requirement opencv-contrib-python==3.3.0.10 (from versions: 3.4.2.16, 3.4.2.17, 3.4.3.18, 3.4.4.19, 3.4.5.20, 3.4.8.29, 4.0.0.21, 4.0.1.24, 4.1.0.25, 4.1.1.26, 4.1.2.30)
        ERROR: No matching distribution found for opencv-contrib-python==3.3.0.10
    pip list | grep opencv
        opencv-contrib-python 4.1.2.30
    pip install opencv-contrib-python==3.4.2.16
        Different error:
        ImportError: dlopen(/usr/local/lib/python3.7/site-packages/cv2/cv2.cpython-37m-darwin.so, 2): Symbol not found: __cg_jpeg_resync_to_restart
        Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
        Expected in: /usr/local/lib/libJPEG.dylib
            in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
    # try latest version 3
    pip install opencv-contrib-python==3.4.8.29
        Different Error:
        File "/usr/local/lib/python3.7/site-packages/cv2/__init__.py", line 3, in <module>
        from .cv2 import *
        ImportError: dlopen(/usr/local/lib/python3.7/site-packages/cv2/cv2.cpython-37m-darwin.so, 2): Library not loaded: @loader_path/libpng16.16.dylib
        Referenced from: /usr/local/lib/python3.7/site-packages/cv2/.dylibs/libfreetype.6.dylib
        Reason: Incompatible library version: libfreetype.6.dylib requires version 54.0.0 or later, but libpng16.16.dylib provides version 43.0.0
    # try first version of 4x
    pip install opencv-contrib-python==4.0.0.21
          File "/usr/local/lib/python3.7/site-packages/cv2/__init__.py", line 3, in <module>
          from .cv2 import *
            ImportError: dlopen(/usr/local/lib/python3.7/site-packages/cv2/cv2.cpython-37m-darwin.so, 2): Symbol not found: __cg_jpeg_resync_to_restart
            Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
            Expected in: /usr/local/lib/libJPEG.dylib
 in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
    # ok, back to latest
    pip install opencv-contrib-python==4.1.2.30
    import cv2
        File "/usr/local/lib/python3.7/site-packages/cv2/__init__.py", line 3, in <module>
            from .cv2 import *
        ImportError: dlopen(/usr/local/lib/python3.7/site-packages/cv2/cv2.cpython-37m-darwin.so, 2): Library not loaded: @loader_path/libpng16.16.dylib
        Referenced from: /usr/local/lib/python3.7/site-packages/cv2/.dylibs/libfreetype.6.dylib
        Reason: Incompatible library version: libfreetype.6.dylib requires version 54.0.0 or later, but libpng16.16.dylib provides version 43.0.0
Try 1y:
    try upgrading libpng
    pip uninstall libpng
        pip uninstall libpng
        WARNING: Skipping libpng as it is not installed.
    pip install libpng
        ERROR: Could not find a version that satisfies the requirement libpng (from versions: none)
        ERROR: No matching distribution found for libpng
    X brew update libpng
    brew upgrade libpng  # ok
    python / import cv2
        New Error:
        File "/usr/local/lib/python3.7/site-packages/cv2/__init__.py", line 3, in <module>
            from .cv2 import *
        ImportError: dlopen(/usr/local/lib/python3.7/site-packages/cv2/cv2.cpython-37m-darwin.so, 2): Library not loaded: @loader_path/libtiff.5.dylib
        Referenced from: /usr/local/lib/python3.7/site-packages/cv2/.dylibs/liblept.5.dylib
        Reason: Incompatible library version: liblept.5.dylib requires version 11.0.0 or later, but libTIFF.dylib provides version 8.0.0
Try 1z:
    try upgrading libtiff
    brew upgrade libtiff   # ok
    import cv2 -> New Error:
        File "/usr/local/lib/python3.7/site-packages/cv2/__init__.py", line 3, in <module>
        from .cv2 import *
        ImportError: dlopen(/usr/local/lib/python3.7/site-packages/cv2/cv2.cpython-37m-darwin.so, 2): Symbol not found: __cg_jpeg_resync_to_restart
        Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
        Expected in: /usr/local/lib/libJPEG.dylib
        in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO
--
Try 1aa:
    No
    Try to fix Symbol not found: __cg_jpeg_resync_to_restart
    cd /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources
    sudo mv libJPEG.dylib libJPEG.dylib.bak
        Error: mv: rename libJPEG.dylib to libJPEG.dylib.bak: Operation not permitted
    sudo ln -sf libJPEG.dylib /usr/local/lib/libJPEG.dylib
    sudo mv libPng.dylib libPng.dylib.bak
    sudo ln -sf libPng.dylib /usr/local/lib/libPng.dylib
    sudo mv libTIFF.dylib libTIFF.dylib.bak
    sudo ln -sf libTIFF.dylib /usr/local/lib/libTIFF.dylib
    sudo mv libGIF.dylib libGIF.dylib.bak
    sudo ln -sf libGIF.dylib /usr/local/lib/libGIF.dylib

Post on Stack Overflow

Answer 1

I agree with the comments, just go with virtual envs and don't interfere with your system's python. But i'd suggest miniconda (reasons: it is easy to uninstall, not size of anaconda, nice docs). [EDIT: i edited for the more reproducible steps that work for me and to address some issues in the comments.]

1. Uninstall Anaconda (https://docs.anaconda.com/anaconda/install/uninstall/) and (https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html#uninstalling-anaconda-or-miniconda) including the OPTIONAL 3rd step(look for blocks starting with # >>> conda init >>>)
2. Follow the installation steps here (https://docs.conda.io/projects/conda/en/latest/user-guide/install/macos.html). When asked for running conda init say no (we'll configure first). After the installation finishes, close and reopen your terminal.

3. configuration (https://docs.conda.io/projects/conda/en/latest/user-guide/configuration/index.html). Mine:

   $ conda config --set auto_activate_base False
   $ conda config --set allow_softlinks False
   $ conda config --set show_channel_urls True
   $ conda config --add channels conda-forge
   

[In the original answer i recommended conda config --set pip_interop_enabled True. Now i think was the wrong thing to suggest. So, leave it out (default is False).]

4. Now issue these commands (i assume the zshell of catalina)

   $ source <your-path-to-miniconda3>/bin/activate
   (base) $ conda update conda
   (base) $ conda init zsh
   

   And close and restart your shell for changes to take effect.

Notes: 1) use the base env only for conda update conda 2) specify a python version when you create your env 3) you always get pip, wheels, setuptools anytime python is installed 4) conda deactivate 5) Concerning the auto_activate_base, if you do set it to False(default is True), remember that the conda python path is only set after an environment is activated.

Create and activate an env:

conda create -n my-env python=3.7
conda activate my-env

or even (for opencv 4.2 from conda-forge assuming the above config):

conda create -n my-opencv-env python=3.7 opencv=4.2
conda activate my-opencv-env

Another note: If you want to install a package in an environment, remember first to activate the environment and then conda install package-name.

Concerning the numpy issue you mention in the comments below, check first whether numpy is included in the packages to be installed when creating your env. And then also, run a file where it imports it as np and print(np.__file__). (you shouldn't have references outside your miniconda env).

more here: https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html . And you can install a package either with conda or with pip (i prefer just conda).