I'm trying to create a container for my python project that uses mariaDB. Here there are dockerfile's lines related to the problem:
FROM python:3.10.6-slim-buster
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update && \
apt-get install -yq apt-utils && \
apt-get install -yq procps && \
apt-get install -yq nano && \
apt-get install -yq libmariadb3 libmariadb-dev
RUN rm -rf /var/lib/apt/lists/*
RUN pip install --no-cache-dir -r requirements.txt
In my requirements.txt I have:
mariadb==1.1.4
When I run the docker build it returns me this error:
Collecting mariadb==1.1.4
Downloading mariadb-1.1.4.zip (97 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 97.4/97.4 kB 10.8 MB/s eta 0:00:00
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'error'
error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [8 lines of output]
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "/tmp/pip-install-2uzbllpk/mariadb_4588dbf4d5fc48b989ebd2605c2d7d1c/setup.py", line 27, in <module>
cfg = get_config(options)
File "/tmp/pip-install-2uzbllpk/mariadb_4588dbf4d5fc48b989ebd2605c2d7d1c/mariadb_posix.py", line 64, in get_config
print('MariaDB Connector/Python requires MariaDB Connector/C '
TypeError: not enough arguments for format string
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
As you can see, I installed the required packages for the connector via apt-get, the installation works without error, but I am still having this problem.
Do you have any idea?
Thank you.
Sorry, my bad - When formatting the code in 1.1.4 with Flake8 (PEP-8) the brackets around the tuple accidentally disappeared, this is already fixed in 1.1.5 (not released yet)
Minimum required Connector/C version is 3.2.4. Buster has MariaDB Server 10.3, corresponding C/C version is 3.1.x - so instead of buster you should bookworm (Server version 10.6.8, C/C version 3.2.8).
I'm trying to build an application into a docker container that uses the OSGEO/GDAL libraries in Python, which are wrappers around the GDAL program. The GDAL program appears to install ok (at least Docker reports => CACHED [3/9] RUN apk add --no-cache gdal without any errors from the step that I can see) however, when I get to the step where pip is supposed to bring in the GDAL Python libraries, it fails looking for files that don't exist, which some initial searching shows is likely to mean it can't find the GDAL program. Does anyone know how to resolve or work around this?
Collecting GDAL~=3.5.1
#11 15.03 Downloading GDAL-3.5.1.tar.gz (752 kB)
#11 15.16 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 752.4/752.4 KB 7.3 MB/s eta 0:00:00
#11 15.30 Preparing metadata (setup.py): started
#11 15.71 Preparing metadata (setup.py): finished with status 'error'
#11 15.73 error: subprocess-exited-with-error
#11 15.73
#11 15.73 × python setup.py egg_info did not run successfully.
#11 15.73 │ exit code: 1
#11 15.73 ╰─> [120 lines of output]
#11 15.73 WARNING: numpy not available! Array support will not be enabled
#11 15.73 running egg_info
#11 15.73 creating /tmp/pip-pip-egg-info-2jyd4zlx/GDAL.egg-info
#11 15.73 writing /tmp/pip-pip-egg-info-2jyd4zlx/GDAL.egg-info/PKG-INFO
#11 15.73 writing dependency_links to /tmp/pip-pip-egg-info-2jyd4zlx/GDAL.egg-info/dependency_links.txt
#11 15.73 writing requirements to /tmp/pip-pip-egg-info-2jyd4zlx/GDAL.egg-info/requires.txt
#11 15.73 writing top-level names to /tmp/pip-pip-egg-info-2jyd4zlx/GDAL.egg-info/top_level.txt
#11 15.73 writing manifest file '/tmp/pip-pip-egg-info-2jyd4zlx/GDAL.egg-info/SOURCES.txt'
#11 15.73 Traceback (most recent call last):
#11 15.73 File "/tmp/pip-install-tjr9j_9m/gdal_6b994752ac484434b194dfc7ccf64728/setup.py", line 105, in fetch_config
#11 15.73 p = subprocess.Popen([command, args], stdout=subprocess.PIPE)
#11 15.73 File "/usr/local/lib/python3.9/subprocess.py", line 951, in __init__
#11 15.73 self._execute_child(args, executable, preexec_fn, close_fds,
#11 15.73 File "/usr/local/lib/python3.9/subprocess.py", line 1821, in _execute_child
#11 15.73 raise child_exception_type(errno_num, err_msg, err_filename)
#11 15.73 FileNotFoundError: [Errno 2] No such file or directory: '../../apps/gdal-config'
Here's my dockerfile (the base image is non-negotiable, I'm afraid)
FROM python:3.9.12-alpine3.15
RUN apk add --no-cache gdal
RUN mkdir -p /usr/src/app/file
WORKDIR /usr/src/app
COPY requirements.txt /usr/src/app/
RUN pip install --no-cache-dir -r requirements.txt
COPY src/ /usr/src/app/src/
COPY main.py /usr/src/app/
CMD ["python", "main.py"]
The requirements.txt is as follows.
requests>= 2.25.0
numpy>=1.23.1
pillow>=9.2.0
GDAL~=3.5.1
DateTime~=4.3
bitstring~=3.1.9
behave~=1.2.6
I'm not sure if there is a way to install GDAL to a particular spot so that python can find it when installing its GDAL libraries, or if I need to give pip some kind of hint, or if something else entirely is going on. If anyone has worked with this library before inside a docker container, thanks in advance!
The main thrust of the problem was lacking gdal-dev, an additional package that separately installs the python bindings. However, once pip was able to find gdal and begin installing the python libraries, those are built from C code and several additional tools plus were needed in the image, plus some environment settings to point them to the right place. Here is the dockerfile that ultimately worked:
FROM python:3.9.12-alpine3.15
RUN apk add --no-cache gcc
RUN apk add --no-cache gdal
RUN apk add --no-cache gdal-dev
RUN apk add --no-cache build-base
RUN apk add --no-cache zlib
RUN export CPLUS_INCLUDE_PATH=/usr/include/gdal
RUN export C_INCLUDE_PATH=/usr/include/gdal
RUN export LDFLAGS="-L/usr/local/opt/zlib/lib"
RUN export CPPFLAGS="-I/usr/local/opt/zlib/include"
RUN mkdir -p /usr/src/app/file
WORKDIR /usr/src/app
COPY requirements.txt /usr/src/app/
RUN pip3 install --no-cache-dir -r requirements.txt
COPY src/ /usr/src/app/src/
COPY main.py /usr/src/app/
CMD ["python", "main.py"]
Lastly, in the requirements.txt, the current 3.5.1 GDAL bindings are for Python 3.10, so I had to downgrade the GDAL until I found one that built without errors since the Python version in the base image is pinned.
This question already has answers here:
pg_config executable not found
(54 answers)
Closed 6 months ago.
I am trying to run docker in django using this command docker build -t myimage . Now the docker file tries to run the RUN pip install -r /app/requirements.txt --no-cache-dir but when ot gets to the Downloading psycopg2-2.9.3.tar.gz (380 kB) section, it throws the error.
NOTE: i do not have psycopg2 in my requirements.txt file only the psycopg2-binary.
requirements.txt file
...
dj-database-url==0.5.0
Django==3.2.7
django-filter==21.1
django-formset-js-improved==0.5.0.2
django-heroku==0.3.1
psycopg2-binary
python-decouple==3.5
...
Downloading pytz-2022.2.1-py2.py3-none-any.whl (500 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 500.6/500.6 kB 2.6 MB/s eta 0:00:00
Collecting psycopg2
Downloading psycopg2-2.9.3.tar.gz (380 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 380.6/380.6 kB 2.7 MB/s eta 0:00:00
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'error'
error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [23 lines of output]
running egg_info
creating /tmp/pip-pip-egg-info-383i9hb2/psycopg2.egg-info
writing /tmp/pip-pip-egg-info-383i9hb2/psycopg2.egg-info/PKG-INFO
writing dependency_links to /tmp/pip-pip-egg-info-383i9hb2/psycopg2.egg-info/dependency_links.txt
writing top-level names to /tmp/pip-pip-egg-info-383i9hb2/psycopg2.egg-info/top_level.txt
writing manifest file '/tmp/pip-pip-egg-info-383i9hb2/psycopg2.egg-info/SOURCES.txt'
Error: pg_config executable not found.
pg_config is required to build psycopg2 from source. Please add the directory
containing pg_config to the $PATH or specify the full executable path with the
option:
python setup.py build_ext --pg-config /path/to/pg_config build ...
or with the pg_config option in 'setup.cfg'.
If you prefer to avoid building psycopg2 from source, please install the PyPI
'psycopg2-binary' package instead.
For further information please check the 'doc/src/install.rst' file (also at
<https://www.psycopg.org/docs/install.html>).
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
The command '/bin/sh -c pip install -r /app/requirements.txt --no-cache-dir' returned a non-zero code: 1
Dockerfile
FROM python:3.8.13-slim-buster
WORKDIR /app
COPY ./my_app ./
RUN pip install --upgrade pip --no-cache-dir
RUN pip install -r /app/requirements.txt --no-cache-dir
CMD ["python", "manage.py", "runserver", "0.0.0.0:8000"]
# CMD ["gunicorn", "main_app.wsgi:application", "--bind"]
You need to install the system dependencies (pg_*) if you want to use psycopg2, otherwise, you can use the all-in-one package that include them by remplacing psycopg2 by psycopg2-binary
I'm building a docker image on cloud server via the following docker file:
# base image
FROM python:3
# add python file to working directory
ADD ./ /
# install and cache dependencies
RUN pip install --upgrade pip
RUN pip install RUST
RUN pip install transformers
RUN pip install torch
RUN pip install slack_sdk
RUN pip install slack_bolt
RUN pip install pandas
RUN pip install gensim
RUN pip install nltk
RUN pip install psycopg2
RUN pip install openpyxl
......
When installing the transformers package, the following error occurs:
STEP 5: RUN pip install transformers
Collecting transformers
Downloading transformers-4.15.0-py3-none-any.whl (3.4 MB)
Collecting filelock
......
Downloading click-8.0.3-py3-none-any.whl (97 kB)
Building wheels for collected packages: tokenizers
Building wheel for tokenizers (pyproject.toml): started
ERROR: Command errored out with exit status 1:
command: /usr/local/bin/python /usr/local/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmp_3y7hw5q
cwd: /tmp/pip-install-bsy5f4da/tokenizers_e09b9f903acd40f0af4a997fe1d8fdb4
Complete output (50 lines):
running bdist_wheel
......
copying py_src/tokenizers/trainers/__init__.pyi -> build/lib.linux-x86_64-3.10/tokenizers/trainers
copying py_src/tokenizers/tools/visualizer-styles.css -> build/lib.linux-x86_64-3.10/tokenizers/tools
running build_ext
error: can't find Rust compiler
If you are using an outdated pip version, it is possible a prebuilt wheel is available for this package but pip is not able to install from it. Installing from the wheel would avoid the need for a Rust compiler.
To update pip, run:
pip install --upgrade pip
and then retry package installation.
If you did intend to build this package from source, try installing a Rust compiler from your system package manager and ensure it is on the PATH during installation. Alternatively, rustup (available at https://rustup.rs) is the recommended way to download and update the Rust compiler toolchain.
----------------------------------------
ERROR: Failed building wheel for tokenizers
ERROR: Could not build wheels for tokenizers, which is required to install pyproject.toml-based projects
Building wheel for tokenizers (pyproject.toml): finished with status 'error'
Failed to build tokenizers
subprocess exited with status 1
subprocess exited with status 1
error building at STEP "RUN pip install transformers": exit status 1
time="2022-01-18T07:24:56Z" level=error msg="exit status 1"
Dockerfile build failed - exit status 1exit status 1
I'm not very sure about what's happening here. Can anyone help me? Thanks in advance.
The logs say
error: can't find Rust compiler
You need to install a rust compiler. See https://www.rust-lang.org/tools/install. You can modify the installation instructions for a docker image like this (from https://stackoverflow.com/a/58169817/5666087):
RUN curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
ENV PATH="/root/.cargo/bin:${PATH}"
Just use a clean python=3.8 environment and try again.
I have a docker image that I need to install openCV in it and from yesterday it started to fail because it cannot find the "skbuild" module:
Step 12/24 : RUN pip install opencv-python opencv-contrib-python
---> Running in a0f746a23aed
Collecting opencv-python
Downloading https://files.pythonhosted.org/packages/77/f5/49f034f8d109efcf9b7e98fbc051878b83b2f02a1c73f92bbd37f317288e/opencv-python-4.4.0.42.tar.gz (88.9MB)
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-build-cciracwm/opencv-python/setup.py", line 9, in <module>
import skbuild
ModuleNotFoundError: No module named 'skbuild'
And on the host also I cannot find that module and pip search is either return nothing or returns a server error:
sudo pip3 search skbuild
WARNING: The directory '/home/ali/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
ERROR: Exception:
Traceback (most recent call last):
File "/usr/local/lib/python3.6/dist-packages/pip/_internal/cli/base_command.py", line 216, in _main
status = self.run(options, args)
File "/usr/local/lib/python3.6/dist-packages/pip/_internal/commands/search.py", line 60, in run
pypi_hits = self.search(query, options)
File "/usr/local/lib/python3.6/dist-packages/pip/_internal/commands/search.py", line 80, in search
hits = pypi.search({'name': query, 'summary': query}, 'or')
File "/usr/lib/python3.6/xmlrpc/client.py", line 1112, in __call__
return self.__send(self.__name, args)
File "/usr/lib/python3.6/xmlrpc/client.py", line 1452, in __request
verbose=self.__verbose
File "/usr/local/lib/python3.6/dist-packages/pip/_internal/network/xmlrpc.py", line 45, in request
return self.parse_response(response.raw)
File "/usr/lib/python3.6/xmlrpc/client.py", line 1342, in parse_response
return u.close()
File "/usr/lib/python3.6/xmlrpc/client.py", line 656, in close
raise Fault(**self._stack[0])
xmlrpc.client.Fault: <Fault -32403: 'server error; service unavailable'>
Is this because their server has some problems or it is related to my pip?
Update
I tried it on different python and pip versions, python versions 3.6 and 3.7 and pip version 19.12 and 20.2.2 and 9.0.1 (the one inside image).
Update 2
I added pip install scikit-build one step before opencv installation but I get another error related to cmake:
Step 12/25 : RUN pip install scikit-build
---> Running in afe0c5c0fca0
Collecting scikit-build
Downloading https://files.pythonhosted.org/packages/78/c9/7c2c7397ea64e36ebb292446896edcdecbb8c1aa6b9a1a32f6f67984c3df/scikit_build-0.11.1-py2.py3-none-any.whl (72kB)
Collecting packaging (from scikit-build)
Downloading https://files.pythonhosted.org/packages/46/19/c5ab91b1b05cfe63cccd5cfc971db9214c6dd6ced54e33c30d5af1d2bc43/packaging-20.4-py2.py3-none-any.whl
Requirement already satisfied: wheel>=0.29.0 in /usr/lib/python3/dist-packages (from scikit-build)
Collecting distro (from scikit-build)
Downloading https://files.pythonhosted.org/packages/25/b7/b3c4270a11414cb22c6352ebc7a83aaa3712043be29daa05018fd5a5c956/distro-1.5.0-py2.py3-none-any.whl
Requirement already satisfied: setuptools>=28.0.0; python_version >= "3" in /usr/lib/python3/dist-packages (from scikit-build)
Requirement already satisfied: six in /usr/lib/python3/dist-packages (from packaging->scikit-build)
Collecting pyparsing>=2.0.2 (from packaging->scikit-build)
Downloading https://files.pythonhosted.org/packages/8a/bb/488841f56197b13700afd5658fc279a2025a39e22449b7cf29864669b15d/pyparsing-2.4.7-py2.py3-none-any.whl (67kB)
Installing collected packages: pyparsing, packaging, distro, scikit-build
Successfully installed distro-1.5.0 packaging-20.4 pyparsing-2.4.7 scikit-build-0.11.1
Removing intermediate container afe0c5c0fca0
---> 533658ddf26d
Step 13/25 : RUN pip install opencv-python opencv-contrib-python
---> Running in 0f2c03bc042a
Collecting opencv-python
Downloading https://files.pythonhosted.org/packages/77/f5/49f034f8d109efcf9b7e98fbc051878b83b2f02a1c73f92bbd37f317288e/opencv-python-4.4.0.42.tar.gz (88.9MB)
Collecting opencv-contrib-python
Downloading https://files.pythonhosted.org/packages/48/98/05bd8e00c71b66c4e7847cc051cac404191d904df58b51a7dcc3767ff747/opencv_contrib_python-4.2.0.34-cp37-cp37m-manylinux1_x86_64.whl (34.2MB)
Collecting numpy>=1.14.5 (from opencv-python)
Downloading https://files.pythonhosted.org/packages/3d/d1/90cd7e0b27ee86d77f5386d38b74520486100286d50772377791b6ef22ff/numpy-1.19.1-cp37-cp37m-manylinux1_x86_64.whl (13.4MB)
Building wheels for collected packages: opencv-python
Running setup.py bdist_wheel for opencv-python: started
Running setup.py bdist_wheel for opencv-python: finished with status 'error'
Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-w49xv99a/opencv-python/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 /tmp/tmpycj03zlwpip-wheel- --python-tag cp37:
/usr/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'long_description_content_type'
warnings.warn(msg)
Traceback (most recent call last):
File "/usr/local/lib/python3.7/dist-packages/skbuild/setuptools_wrap.py", line 560, in setup
cmkr = cmaker.CMaker(cmake_executable)
File "/usr/local/lib/python3.7/dist-packages/skbuild/cmaker.py", line 95, in __init__
self.cmake_version = get_cmake_version(self.cmake_executable)
File "/usr/local/lib/python3.7/dist-packages/skbuild/cmaker.py", line 82, in get_cmake_version
"Problem with the CMake installation, aborting build. CMake executable is %s" % cmake_executable)
Problem with the CMake installation, aborting build. CMake executable is cmake
----------------------------------------
Failed building wheel for opencv-python
Running setup.py clean for opencv-python
Failed to build opencv-python
Installing collected packages: numpy, opencv-python, opencv-contrib-python
Found existing installation: numpy 1.13.3
Not uninstalling numpy at /usr/lib/python3/dist-packages, outside environment /usr
Running setup.py install for opencv-python: started
Running setup.py install for opencv-python: finished with status 'error'
Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-w49xv99a/opencv-python/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-maky1uyw-record/install-record.txt --single-version-externally-managed --compile:
/usr/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'long_description_content_type'
warnings.warn(msg)
Traceback (most recent call last):
File "/usr/local/lib/python3.7/dist-packages/skbuild/setuptools_wrap.py", line 560, in setup
cmkr = cmaker.CMaker(cmake_executable)
File "/usr/local/lib/python3.7/dist-packages/skbuild/cmaker.py", line 95, in __init__
self.cmake_version = get_cmake_version(self.cmake_executable)
File "/usr/local/lib/python3.7/dist-packages/skbuild/cmaker.py", line 82, in get_cmake_version
"Problem with the CMake installation, aborting build. CMake executable is %s" % cmake_executable)
Problem with the CMake installation, aborting build. CMake executable is cmake
If you read the opencv-python package FAQ in PyPI, it clearly provides an answer for this specific issue: you must run pip install --upgrade pip. Check pip version afterwards with pip -V.
This is because your pip is too old to understand the new manylinux2014 package format and tries to compile from source. That will also fail because pip is too old to understand how to use pyproject.toml to install build dependencies such as scikit-build.
Another issue I'm spotting is that you install both opencv-python and opencv-contrib-python. You should not do this. It's also explained in the PyPI page of the packages. Most likely you should be using just opencv-contrib-python-headless package since you are using Docker and I assume you do not use the GUI functionalities of OpenCV.
just update the pip and it will work
python -m pip install --upgrade pip
Just update pip.
If you use python3 then:
pip3 install --upgrade pip
pip3 install opencv-python
skbuild is for Scikit-build.
Install it using pip:
As for windows: pip install scikit-build
After the succesfull installation:
pip install cmake
Since I have python3 installed, I had to use
python3 -m pip install --upgrade pip
11/may/2021: faced same issue on a fresh ubuntu18 virtualbox image. this worked for me
sudo -H pip3 install --upgrade pip
pip3 install opencv-python
I also had the error, in my case when executing
python3.7 -m pip install --user opencv-python in order to get catkin_make -j8 working again in a ROS project. Thus, Docker is not needed to get the error.
First the details:
Collecting opencv-python
Cache entry deserialization failed, entry ignored
Downloading https://files.pythonhosted.org/packages/30/46/821920986c7ce5bae5518c1d490e520a9ab4cef51e3e54e35094dadf0d68/opencv-python-4.4.0.46.tar.gz (88.9MB)
100% |████████████████████████████████| 88.9MB 17kB/s
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-build-8jky5692/opencv-python/setup.py", line 9, in <module>
import skbuild
ModuleNotFoundError: No module named 'skbuild'
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-8jky5692/opencv-python/
Just documenting what I did to solve it:
python -m pip install --user opencv-python gives me /usr/bin/python: No module named pip
sudo apt install python-pip (in addition to the already existing sudo apt install python3-pip installation for pip3)
python -m pip -V now gives me pip 9.0.1 from /usr/lib/python2.7/dist-packages (python 2.7)
pip -V gives me pip 20.3.3 from /home/MYUSERNAME/.local/lib/python3.6/site-packages/pip (python 3.6) (because apt-get installs a standard 3.6, independently from existing python versions)
sudo apt-get update && sudo apt-get install cmake libopenmpi-dev python3.7-dev zlib1g-dev (not sure if this step is needed)
pip install opencv-python WORKING
catkin_make -j8 in my catkin workspace in the Python base environment WORKING
Additional hints for the cmake error that is mentioned in the Update 2
This cmake error is perhaps due to a corrupted workspace during or after catkin_make install:
I had a similar cmake error when I executed the catkin_make command inside my Python virtual environment. When I changed back to the base environment (using deactivate), catkin_make ran through. This is probably due to dependency issues in the virtual environment, perhaps also because of the version that is used when you use standard python -m that is used by some internal scripts, see one of the bullet points above. I had to assign python2.7 to the python -m pip -V pip version, probably because ROS gazebo needed 2.7.
Most promising (if this is a catkin issue): simply remove catkin and install it again, see Error 2 Invoking "make -j4 -l4" failed.
Perhaps also see Invoking "cmake" failed.
I had a similar problem and what finally worked was to change from python:3-alpine to python:3.8-slim and install python and openCV similar to what has been done in the selected answer here: Minimal SciPy Dockerfile
If non of these answers works for you try:
pip3 install opencv-python-headless
with python3 you need to use pip3