Ytdyklly

One fine day I woke up and my conda enviroment broke which was really weird because my pip, conda, tensorflow and numpy worked the previous day.

I started the day by accidentally installing a wrong package: pip install telegram-bot

Collecting telegram-bot

  Using cached https://files.pythonhosted.org/packages/0c/89/b5f6cdebf62f1b37dfc0fd53fee0f92760531a51d834e5238b3110429e93/telegram-bot-0.1.tar.gz

    Complete output from command python setup.py egg_info:

    Traceback (most recent call last):

      File "<string>", line 1, in <module>

      File "/private/var/folders/fy/xjkb7k0d3q16fqp1578b63f00000gn/T/pip-build-muqgbeev/telegram-bot/setup.py", line 12, in <module>

        import telegram

      File "/private/var/folders/fy/xjkb7k0d3q16fqp1578b63f00000gn/T/pip-build-muqgbeev/telegram-bot/telegram/__init__.py", line 15, in <module>

        from telegram import Bot, ChatActions

    ImportError: cannot import name 'Bot'



    ----------------------------------------

Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/fy/xjkb7k0d3q16fqp1578b63f00000gn/T/pip-build-muqgbeev/telegram-bot/

At this point conda list failed mysteriously:

$conda list



# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<



    Traceback (most recent call last):

      File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/conda/exceptions.py", line 1001, in __call__

        return func(*args, **kwargs)

      File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/conda/cli/main.py", line 84, in _main

        exit_code = do_call(args, p)

      File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/conda/cli/conda_argparse.py", line 82, in do_call

        exit_code = getattr(module, func_name)(args, parser)

      File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/conda/cli/main_list.py", line 142, in execute

        show_channel_urls=context.show_channel_urls)

      File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/conda/cli/main_list.py", line 80, in print_packages

        show_channel_urls=show_channel_urls)

      File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/conda/cli/main_list.py", line 45, in list_packages

        installed = sorted(PrefixData(prefix, pip_interop_enabled=True).iter_records(),

      File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/conda/core/prefix_data.py", line 116, in iter_records

        return itervalues(self._prefix_records)

      File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/conda/core/prefix_data.py", line 145, in _prefix_records

        return self.__prefix_records or self.load() or self.__prefix_records

      File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/conda/core/prefix_data.py", line 69, in load

        self._load_site_packages()

      File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/conda/core/prefix_data.py", line 258, in _load_site_packages

        python_record = read_python_record(self.prefix_path, af, python_pkg_record.version)

      File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/conda/gateways/disk/read.py", line 245, in read_python_record

        pydist = PythonDistribution.init(prefix_path, anchor_file, python_version)

      File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/conda/common/pkg_formats/python.py", line 78, in init

        return PythonInstalledDistribution(prefix_path, anchor_file, python_version)

      File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/conda/common/pkg_formats/python.py", line 382, in __init__

        super(PythonInstalledDistribution, self).__init__(anchor_full_path, python_version)

      File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/conda/common/pkg_formats/python.py", line 106, in __init__

        self._check_files()

      File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/conda/common/pkg_formats/python.py", line 116, in _check_files

        assert isfile(fpath)

    AssertionError



`$ /Users/sunyitao/anaconda3/bin/conda list`



  environment variables:

                 CIO_TEST=<not set>

               CONDA_ROOT=/Users/sunyitao/anaconda3

                     PATH=/Users/sunyitao/google-cloud-sdk/bin:/Users/sunyitao/anaconda3/bin:/us

                          r/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/share/dotnet:~/.d

                          otnet/tools:/Library/Frameworks/Mono.framework/Versions/Current/Comman

                          ds:/Applications/Xamarin Workbooks.app/Contents/SharedSupport/path-bin

               PYTHONPATH=::/Users/sunyitao/slim

       REQUESTS_CA_BUNDLE=<not set>

            SSL_CERT_FILE=<not set>



     active environment : None

       user config file : /Users/sunyitao/.condarc

 populated config files : /Users/sunyitao/.condarc

          conda version : 4.6.2

    conda-build version : 3.17.7

         python version : 3.6.5.final.0

       base environment : /Users/sunyitao/anaconda3  (writable)

           channel URLs : https://conda.anaconda.org/intel/osx-64

                          https://conda.anaconda.org/intel/noarch

                          https://repo.anaconda.com/pkgs/main/osx-64

                          https://repo.anaconda.com/pkgs/main/noarch

                          https://repo.anaconda.com/pkgs/free/osx-64

                          https://repo.anaconda.com/pkgs/free/noarch

                          https://repo.anaconda.com/pkgs/r/osx-64

                          https://repo.anaconda.com/pkgs/r/noarch

          package cache : /Users/sunyitao/anaconda3/pkgs

                          /Users/sunyitao/.conda/pkgs

       envs directories : /Users/sunyitao/anaconda3/envs

                          /Users/sunyitao/.conda/envs

               platform : osx-64

             user-agent : conda/4.6.2 requests/2.20.0 CPython/3.6.5 Darwin/18.2.0 OSX/10.14.2

                UID:GID : 501:20

             netrc file : None

           offline mode : False

So I googled and did pip install -U setuptools and conda update conda with no errors, but installing telegram-bot still failed.
But what I really wanted to install was pip install python-telegram-bot which succeeded.

So I ran this to check if the first package is completely removed:

$pip uninstall telegram-bot

Cannot uninstall requirement telegram-bot, not installed

Ran conda list again but same error.

I moved on and did some stuff with tensorflow working fine. After a while I install lightgbm with conda.

Downloading and Extracting Packages

lightgbm-2.2.1       | 617 KB    | ##################################################################################################### | 100%

numpy-base-1.15.4    | 6.0 MB    | ##################################################################################################### | 100%

llvm-openmp-4.0.1    | 454 KB    | ##################################################################################################### | 100%

Now when I run import tensorflow as tf I get this:

Using TensorFlow backend.

File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/tensorflow/python/framework/tensor_util.py", line 32, in <module>

    from tensorflow.python.framework import fast_tensor_util

  File "__init__.pxd", line 872, in init tensorflow.python.framework.fast_tensor_util

ValueError: numpy.ufunc has the wrong size, try recompiling. Expected 192, got 216

I originally had numpy 1.16 from pip and another version of numpy from anaconda. So I uninstalled both versions with pip and then did conda uninstall numpy --force so it would not delete all my packages which depended on numpy. I ran conda install numpy which succeeded.

But now when I import numpy I get:

ModuleNotFoundError: No module named 'numpy'

Did a sanity check with:

$which pip

/Users/sunyitao/anaconda3/bin/pip

$which conda

/Users/sunyitao/anaconda3/bin/conda

$which python

/Users/sunyitao/anaconda3/bin/python

pip check:

$pip check

Exception:

Traceback (most recent call last):

  File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/pip-9.0.3-py3.6.egg/pip/_vendor/pkg_resources/__init__.py", line 2797, in _dep_map

    return self.__dep_map

  File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/pip-9.0.3-py3.6.egg/pip/_vendor/pkg_resources/__init__.py", line 2608, in __getattr__

    raise AttributeError(attr)

AttributeError: _DistInfoDistribution__dep_map



During handling of the above exception, another exception occurred:



Traceback (most recent call last):

  File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/pip-9.0.3-py3.6.egg/pip/_vendor/pkg_resources/__init__.py", line 2788, in _parsed_pkg_info

    return self._pkg_info

  File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/pip-9.0.3-py3.6.egg/pip/_vendor/pkg_resources/__init__.py", line 2608, in __getattr__

    raise AttributeError(attr)

AttributeError: _pkg_info



During handling of the above exception, another exception occurred:



Traceback (most recent call last):

  File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/pip-9.0.3-py3.6.egg/pip/basecommand.py", line 215, in main

    status = self.run(options, args)

  File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/pip-9.0.3-py3.6.egg/pip/commands/check.py", line 20, in run

    missing_reqs_dict, incompatible_reqs_dict = check_requirements(dists)

  File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/pip-9.0.3-py3.6.egg/pip/operations/check.py", line 10, in check_requirements

    missing_reqs = list(get_missing_reqs(dist, installed_dists))

  File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/pip-9.0.3-py3.6.egg/pip/operations/check.py", line 30, in get_missing_reqs

    for requirement in dist.requires():

  File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/pip-9.0.3-py3.6.egg/pip/_vendor/pkg_resources/__init__.py", line 2552, in requires

    dm = self._dep_map

  File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/pip-9.0.3-py3.6.egg/pip/_vendor/pkg_resources/__init__.py", line 2799, in _dep_map

    self.__dep_map = self._compute_dependencies()

  File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/pip-9.0.3-py3.6.egg/pip/_vendor/pkg_resources/__init__.py", line 2808, in _compute_dependencies

    for req in self._parsed_pkg_info.get_all('Requires-Dist') or :

  File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/pip-9.0.3-py3.6.egg/pip/_vendor/pkg_resources/__init__.py", line 2790, in _parsed_pkg_info

    metadata = self.get_metadata(self.PKG_INFO)

  File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/pip-9.0.3-py3.6.egg/pip/_vendor/pkg_resources/__init__.py", line 1468, in get_metadata

    value = self._get(self._fn(self.egg_info, name))

  File "/Users/sunyitao/anaconda3/lib/python3.6/site-packages/pip-9.0.3-py3.6.egg/pip/_vendor/pkg_resources/__init__.py", line 1577, in _get

    with open(path, 'rb') as stream:

FileNotFoundError: [Errno 2] No such file or directory: '/Users/sunyitao/anaconda3/lib/python3.6/site-packages/parso-0.3.1.dist-info/METADATA'

You are using pip version 9.0.3, however version 19.0.1 is available.

You should consider upgrading via the 'pip install --upgrade pip' command.

I am deliberating reinstalling everything now but it is really a last resort option that could take the entire day.

Edit:
I have fixed the numpy issue by running

conda config --add channels conda-forge

conda install numpy --force-reinstall

Now tensorflow and numpy are working again, but pip check and conda list still fails. When I activate a different enviroment pip check and conda list will work so it seems to be a issue with my base enviroment.