That looks like the conda package handling package might have issues. Thanks for reporting. We'll take s look.

msarahan on 12 Jul 2019

My 2 cents.

The issue started with a number of inconsistencies like:

sergey@sergey-Bionic:~$ conda update deprecated
WARNING conda.base.context:use_only_tar_bz2(632): Conda is constrained to only using the old .tar.bz2 file format because you have conda-build installed, and it is <3.18.3.  Update or remove conda-build to get smaller downloads and faster extractions.
Collecting package metadata (repodata.json): done
Solving environment: | 
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:

  - conda-forge/noarch::mapclassify==2.1.1=py_0
  - conda-forge/noarch::jupyterlab_server==1.0.0=py_1
  - conda-forge/noarch::qtconsole==4.5.1=py_0
  - defaults/linux-64::_anaconda_depends==2019.03=py36_0
  - conda-forge/noarch::jupyter_client==5.2.4=py_3
  - conda-forge/noarch::jupyter_contrib_core==0.3.3=py_2
  - conda-forge/noarch::jupyter_console==6.0.0=py_0
  - conda-forge/noarch::jupyter==1.0.0=py_2
  - conda-forge/linux-64::widgetsnbextension==3.5.0=py36_0
  - conda-forge/linux-64::jupyter_nbextensions_configurator==0.4.1=py36_0
  - conda-forge/linux-64::jupyter_highlight_selected_word==0.2.0=py36_1000
  - conda-forge/linux-64::jupyter_latex_envs==1.4.4=py36_1000
  - conda-forge/linux-64::jupyterlab==1.0.1=py36_0
  - conda-forge/linux-64::astroid==2.2.5=py36_0
  - conda-forge/noarch::jupyterlab_launcher==0.13.1=py_2
  - conda-forge/linux-64::notebook==5.7.8=py36_1
  - conda-forge/noarch::ipywidgets==7.5.0=py_0
  - defaults/linux-64::_ipyw_jlab_nb_ext_conf==0.1.0=py36_0
  - conda-forge/linux-64::spyder-kernels==0.5.0=py36_0
  - conda-forge/linux-64::spyder==3.3.5=py36_0
  - conda-forge/noarch::deprecated==1.2.5=py_0
  - conda-forge/linux-64::pylint==2.3.1=py36_0
  - conda-forge/linux-64::jupyter_contrib_nbextensions==0.5.1=py36_0
  - conda-forge/linux-64::ipykernel==5.1.1=py36h24bf2e0_0
  - defaults/linux-64::anaconda==custom=py36_1
done

## Package Plan ##

  environment location: /home/sergey/anaconda3

  added / updated specs:
    - deprecated


The following NEW packages will be INSTALLED:

  boto3              conda-forge/noarch::boto3-1.9.187-py_0
  botocore           conda-forge/noarch::botocore-1.12.187-py_0
  conda-package-han~ conda-forge/linux-64::conda-package-handling-1.3.11-py36_0
  cython             conda-forge/linux-64::cython-0.29.12-py36he1b5a44_0
  dask               conda-forge/noarch::dask-2.1.0-py_0
  dask-core          conda-forge/noarch::dask-core-2.1.0-py_0
  distributed        conda-forge/noarch::distributed-2.1.0-py_0
  flask              conda-forge/noarch::flask-1.1.1-py_0
  geopandas          conda-forge/noarch::geopandas-0.5.1-py_0
  json5              conda-forge/noarch::json5-0.8.5-py_0
  libsodium          conda-forge/linux-64::libsodium-1.0.17-h516909a_0
  pyrsistent         conda-forge/linux-64::pyrsistent-0.15.3-py36h516909a_0
  pyzmq              conda-forge/linux-64::pyzmq-18.0.2-py36hc4ba49a_1
  r-blob             conda-forge/noarch::r-blob-1.2.0-r351_0
  r-ellipsis         conda-forge/linux-64::r-ellipsis-0.2.0.1-r351hcdcec82_0
  r-vctrs            conda-forge/linux-64::r-vctrs-0.2.0-r351hcdcec82_0
  wrapt              conda-forge/linux-64::wrapt-1.11.2-py36h516909a_0
  xerces-c           conda-forge/linux-64::xerces-c-3.2.2-hea5cb30_1002
  zeromq             conda-forge/linux-64::zeromq-4.3.2-he1b5a44_2


Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(637): An error occurred while installing package 'None'.
AssertionError()
Attempting to roll back.

Rolling back transaction: done

AssertionError()
()

Then after the rollback I seem to lose conda_package_handling in "/home/sergey/anaconda3/lib/python3.6/site-packages" directory.

After I copied old version of conda_package_handling from another machine and do conda install conda-package-handling conda became functional again, including conda update --all to correct for conflicting packages.

Regards!

sbushmanov on 12 Jul 2019

👍9

The only way this could have happened is if you somehow extracted the contents of a conda .tar.bz2 into the python3.6/site-packages folder. Were you playing with packages and extracting them yourself? I've never seen conda do anything like that.

msarahan on 12 Jul 2019

👎10

In my case, after conda update --all, I got

WARNING conda.base.context:use_only_tar_bz2(632): Conda is constrained to only using the old .tar.bz2 file format because you have conda-build installed, and it is <3.18.3.  Update or remove conda-build to get smaller downloads and faster extractions.
Collecting package metadata (repodata.json): done

and conda removes many packages including some import ones for no reason

The following packages will be REMOVED:

  alabaster-0.7.12-py37_0
  anaconda-project-0.8.2-py37_0
  astroid-2.2.5-py37_0
  astropy-3.1.2-py37h7b6447c_0
  atomicwrites-1.3.0-py37_1
  babel-2.6.0-py37_0
  backports.os-0.1.1-py37_0
  backports.shutil_get_terminal_size-1.0.0-py37_2
  bitarray-0.8.3-py37h14c3975_0
  bkcharts-0.2-py37_0
  blosc-1.15.0-hd408876_0
  bokeh-1.0.4-py37_0
  boto-2.49.0-py37_0
  bottleneck-1.2.1-py37h035aef0_1
  cloudpickle-0.8.0-py37_0
  colorama-0.4.1-py37_0
  contextlib2-0.5.5-py37_0
  curl-7.64.0-hbc83047_2
  ...
  matplotlib-3.0.3-py37h5429711_0
  ...

yzhao30 on 12 Jul 2019

please see #8842

msarahan on 12 Jul 2019

@msarahan

The only way this could have happened is if you somehow extracted the contents of a conda .tar.bz2 into the python3.6/site-packages folder. Were you playing with packages and extracting them yourself? I've never seen conda do anything like that.

conda_package_handling disappeared from "python3.6/site-packages" folder after buggy upgrade. This is why I copied it from another machine and after doing that I was able to conda install conda-package-handling.

sbushmanov on 12 Jul 2019

Bizarre. I'll reopen the issue, but I hope no one else has this problem.

msarahan on 12 Jul 2019

Hi all,

I have the same issue. Every conda command will give me a error of ModuleNotFoundError: No module named 'conda_package_handling'.

The conda_package_handling can be found in:

(base) yichao@host$ ls -lah /path/to/home/yichao/anaconda3/lib/python3.6/site-packages/conda_package_handling-1.3.10.dist-info/
total 76K
drwxr-xr-x   2 yichao tkgreg 4.0K Jul  4 12:13 .
drwxr-xr-x 438 yichao tkgreg  36K Jul 15 09:01 ..
-rw-rw-r--   3 yichao tkgreg  162 Jun 25 03:35 AUTHORS.txt
-rw-rw-r--   3 yichao tkgreg   57 Jun 25 03:35 entry_points.txt
-rw-rw-r--   3 yichao tkgreg    5 Jun 25 03:35 INSTALLER
-rw-rw-r--   3 yichao tkgreg 1.5K Jun 25 03:35 LICENSE
-rw-rw-r--   3 yichao tkgreg  442 Jun 25 03:35 METADATA
-rw-rw-r--   3 yichao tkgreg 2.5K Jun 25 03:35 RECORD
-rw-rw-r--   3 yichao tkgreg   23 Jun 25 03:35 top_level.txt
-rw-rw-r--   3 yichao tkgreg  110 Jun 25 03:35 WHEEL

When I try conda info , a error report was invoked.

/home/yichao/anaconda3/lib/python3.6/importlib/__init__.py", line 126, in import_module
        return _bootstrap._gcd_import(name[level:], package, level)
      File "<frozen importlib._bootstrap>", line 994, in _gcd_import
      File "<frozen importlib._bootstrap>", line 971, in _find_and_load
      File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
      File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
      File "<frozen importlib._bootstrap_external>", line 678, in exec_module
      File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/conda/cli/main_info.py", line 19, in <module>
        from ..core.index import _supplement_index_with_system
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/conda/core/index.py", line 9, in <module>
        from .package_cache_data import PackageCacheData
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/conda/core/package_cache_data.py", line 15, in <module>
        from conda_package_handling.api import InvalidArchiveError
    ModuleNotFoundError: No module named 'conda_package_handling'

`$ /mnt/cbis/home/yichao/anaconda3/bin/conda info`


An unexpected error has occurred. Conda has prepared the above report.

If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers?

[y/N]:

Before this error happens
This stems from another issue that I reported in https://github.com/conda/conda/issues/8863#issuecomment-508339936.

From there, I did conda update conda. It took over 24 hours to solve the environment and also reported a number of inconsistency. The solving results in installation of some packages and I noticed that python 3.6 was downgraded in this update. Messages of roll back also appeared at the end of this update:

AssertionError()
Attempting to roll back.

Rolling back transaction: done

After the update finished, I have the error of ModuleNotFoundError.

Do you have any idea how I can get conda to work properly? Thank you so much!

yichao-cai on 15 Jul 2019

👍4

I am observing the same as above. Wanted to remove numpy package but got an AssertionError() now the conda_package_handling module is missing.

saschahofmann on 15 Jul 2019

As I stated above, there are 2 steps necessary to make conda functional after "conda_package_handling module is missing" error:

copy "conda_package_handling" from a working distribution to "python3.6/site-packages" folder
do conda install conda-package-handling

sbushmanov on 15 Jul 2019

hm after copying conda-package-handling. I am missing libarchive.
Note: I am copied from and to python3.7

saschahofmann on 15 Jul 2019

hm after copying conda-package-handling. I am missing libarchive.
Note: I am copied from and to python3.7

I too tried copying conda-package-handling, and now I'm missing libarchive. I tried downloading libarchive from https://anaconda.org/conda-forge/libarchive/files and manually copying all files in the right subdirectories, but I had no success.

andreadistefano on 15 Jul 2019

As I stated above, there are 2 steps necessary to make conda functional after "conda_package_handling module is missing" error:

copy "conda_package_handling" from a working distribution to "python3.6/site-packages" folder

do conda install conda-package-handling

@sbushmanov Thanks a lot for the tips!

Unfortunately, it did not work for me.

After copying conda_package_handling and conda_package_handling-1.3.10.dist-info from another working distribution.

I got this long error, when I tried conda install conda-package-handling:

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

    Traceback (most recent call last):
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/conda/gateways/connection/__init__.py", line 21, in <module>
        from requests import ConnectionError, HTTPError, Session
    ModuleNotFoundError: No module named 'requests'

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/conda/exceptions.py", line 1043, in __call__
        return func(*args, **kwargs)
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/conda/cli/main.py", line 84, in _main
        exit_code = do_call(args, p)
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/conda/cli/conda_argparse.py", line 80, in do_call
        module = import_module(relative_mod, __name__.rsplit('.', 1)[0])
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/importlib/__init__.py", line 126, in import_module
        return _bootstrap._gcd_import(name[level:], package, level)
      File "<frozen importlib._bootstrap>", line 994, in _gcd_import
      File "<frozen importlib._bootstrap>", line 971, in _find_and_load
      File "<frozen importlib._bootstrap>", line 955, in _find_and_load_unlocked
      File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
      File "<frozen importlib._bootstrap_external>", line 678, in exec_module
      File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/conda/cli/main_install.py", line 8, in <module>
        from .install import install
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/conda/cli/install.py", line 19, in <module>
        from ..core.index import calculate_channel_urls, get_index
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/conda/core/index.py", line 9, in <module>
        from .package_cache_data import PackageCacheData
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/conda/core/package_cache_data.py", line 17, in <module>
        from .path_actions import CacheUrlAction, ExtractPackageAction
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/conda/core/path_actions.py", line 30, in <module>
        from ..gateways.connection.download import download
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/conda/gateways/connection/__init__.py", line 38, in <module>
        from pip._vendor.requests import ConnectionError, HTTPError, Session
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/pip/_vendor/requests/__init__.py", line 94, in <module>
        from pip._internal.utils.compat import WINDOWS
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/pip/_internal/__init__.py", line 40, in <module>
        from pip._internal.cli.autocompletion import autocomplete
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/pip/_internal/cli/autocompletion.py", line 8, in <module>
        from pip._internal.cli.main_parser import create_main_parser
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/pip/_internal/cli/main_parser.py", line 12, in <module>
        from pip._internal.commands import (
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/pip/_internal/commands/__init__.py", line 6, in <module>
        from pip._internal.commands.completion import CompletionCommand
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/pip/_internal/commands/completion.py", line 6, in <module>
        from pip._internal.cli.base_command import Command
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/pip/_internal/cli/base_command.py", line 20, in <module>
        from pip._internal.download import PipSession
      File "/mnt/cbis/home/yichao/anaconda3/lib/python3.6/site-packages/pip/_internal/download.py", line 368, in <module>
        class PipSession(requests.Session):
    AttributeError: module 'pip._vendor.requests' has no attribute 'Session'

`$ /mnt/cbis/home/yichao/anaconda3/bin/conda install conda-package-handling`

  environment variables:
                 CIO_TEST=<not set>
         CONDA_BACKUP_F90=/mnt/cbis/home/yichao/anaconda3/bin/x86_64-conda_cos6-linux-gnu-
                          gfortran
         CONDA_BACKUP_F95=/mnt/cbis/home/yichao/anaconda3/bin/x86_64-conda_cos6-linux-gnu-f95
        CONDA_BACKUP_HOST=x86_64-conda_cos6-linux-gnu
        CONDA_DEFAULT_ENV=base
                CONDA_EXE=/mnt/cbis/home/yichao/anaconda3/bin/conda
CONDA_MKL_INTERFACE_LAYER_BACKUP=
             CONDA_PREFIX=/mnt/cbis/home/yichao/anaconda3
    CONDA_PROMPT_MODIFIER=(base)
         CONDA_PYTHON_EXE=/mnt/cbis/home/yichao/anaconda3/bin/python
               CONDA_ROOT=/mnt/cbis/home/yichao/anaconda3
              CONDA_SHLVL=1
     JAVA_LD_LIBRARY_PATH=/mnt/cbis/home/yichao/anaconda3/jre/lib/amd64/server
               MODULEPATH=/etc/environment-modules/modules:/usr/share/modules/versions:/usr/Modu
                          les/$MODULE_VERSION/modulefiles:/usr/share/modules/modulefiles
                     PATH=/mnt/cbis/home/yichao/anaconda3/bin:/mnt/cbis/home/yichao/icommands:/m
                          nt/cbis/home/yichao/icommands:/mnt/cbis/home/yichao/bin:/mnt/cbis/home
                          /yichao/anaconda3/bin:/mnt/cbis/home/yichao/anaconda3/condabin:/usr/lo
                          cal/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/
                          local/games:/mnt/raid0/tools/homer/bin:/mnt/raid0/tools/cufflinks/cuff
                          links-2.2.1.Linux_x86_64:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/j
                          ava-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/mnt/cbis/home/
                          yichao/software/sratoolkit.2.5.7-ubuntu64/bin:/mnt/cbis/home/yichao/so
                          ftware:/mnt/cbis/home/yichao/software:/mnt/cbis/home/yichao/software/s
                          ratoolkit.2.5.7-ubuntu64/bin:/mnt/cbis/home/yichao/software:/mnt/cbis/
                          home/yichao/software:/mnt/cbis/home/yichao/software/sratoolkit.2.5.7-u
                          buntu64/bin:/mnt/cbis/home/yichao/software:/mnt/cbis/home/yichao/softw
                          are
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : base
    active env location : /mnt/cbis/home/yichao/anaconda3
            shell level : 1
       user config file : /mnt/cbis/home/yichao/.condarc
 populated config files : /mnt/cbis/home/yichao/.condarc
          conda version : 4.7.5
    conda-build version : not installed
         python version : 3.6.7.final.0
       virtual packages : 
       base environment : /mnt/cbis/home/yichao/anaconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://conda.anaconda.org/r/linux-64
                          https://conda.anaconda.org/r/noarch
          package cache : /mnt/cbis/home/yichao/anaconda3/pkgs
                          /mnt/cbis/home/yichao/.conda/pkgs
       envs directories : /mnt/cbis/home/yichao/anaconda3/envs
                          /mnt/cbis/home/yichao/.conda/envs
               platform : linux-64
             user-agent : conda/4.7.5 requests/2.21.0 CPython/3.6.7 Linux/4.4.0-119-generic ubuntu/16.04.5 glibc/2.23
                UID:GID : 3429:2036
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.

If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers?

I checked that there are requests_oauthlib and requests_oauthlib-1.2.0.dist-info in the site-packages directory. Copying in requests and requests-2.18.4-py3.6.egg-info from other working distribution, I got a new error ModuleNotFoundError: No module named 'urllib3'.

It seems that after the rollback in the problematic conda update, a lot of packages is missing from ~/anaconda3/lib/python3.6/site-packages.
At a glance, I can see that the missing packages including: anaconda_client, lxml, pyodbc, pyOpenSSL, Twisted...

I also noticed that conda-build from the conda info output is "not installed".

It seems to get more errors. :(
I will wait to see if other users reported this similar issue. If not, I am planning to reinstall conda.

yichao-cai on 16 Jul 2019

I got the same error today after running conda update conda, it seems the conda install got completely broken doing this.

(note: I've added additional information regarding this here: 8172)

conda info

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

    Traceback (most recent call last):
      File "/home/user/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1043, in __call__
        return func(*args, **kwargs)
      File "/home/user/miniconda3/lib/python3.7/site-packages/conda/cli/main.py", line 84, in _main
        exit_code = do_call(args, p)
      File "/home/user/miniconda3/lib/python3.7/site-packages/conda/cli/conda_argparse.py", line 80, in do_call
        module = import_module(relative_mod, __name__.rsplit('.', 1)[0])
      File "/home/user/miniconda3/lib/python3.7/importlib/__init__.py", line 127, in import_module
        return _bootstrap._gcd_import(name[level:], package, level)
      File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
      File "<frozen importlib._bootstrap>", line 983, in _find_and_load
      File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
      File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
      File "<frozen importlib._bootstrap_external>", line 728, in exec_module
      File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
      File "/home/user/miniconda3/lib/python3.7/site-packages/conda/cli/main_info.py", line 19, in <module>
        from ..core.index import _supplement_index_with_system
      File "/home/user/miniconda3/lib/python3.7/site-packages/conda/core/index.py", line 9, in <module>
        from .package_cache_data import PackageCacheData
      File "/home/user/miniconda3/lib/python3.7/site-packages/conda/core/package_cache_data.py", line 15, in <module>
        from conda_package_handling.api import InvalidArchiveError
    ModuleNotFoundError: No module named 'conda_package_handling'

`$ /home/user/miniconda3/bin/conda info`


An unexpected error has occurred. Conda has prepared the above report.

If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers?

[y/N]: y
Traceback (most recent call last):
  File "/home/user/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1043, in __call__
    return func(*args, **kwargs)
  File "/home/user/miniconda3/lib/python3.7/site-packages/conda/cli/main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "/home/user/miniconda3/lib/python3.7/site-packages/conda/cli/conda_argparse.py", line 80, in do_call
    module = import_module(relative_mod, __name__.rsplit('.', 1)[0])
  File "/home/user/miniconda3/lib/python3.7/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/home/user/miniconda3/lib/python3.7/site-packages/conda/cli/main_info.py", line 19, in <module>
    from ..core.index import _supplement_index_with_system
  File "/home/user/miniconda3/lib/python3.7/site-packages/conda/core/index.py", line 9, in <module>
    from .package_cache_data import PackageCacheData
  File "/home/user/miniconda3/lib/python3.7/site-packages/conda/core/package_cache_data.py", line 15, in <module>
    from conda_package_handling.api import InvalidArchiveError
ModuleNotFoundError: No module named 'conda_package_handling'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/user/miniconda3/lib/python3.7/site-packages/conda/base/context.py", line 665, in requests_version
    from requests import __version__ as REQUESTS_VERSION
ModuleNotFoundError: No module named 'requests'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/user/miniconda3/bin/conda", line 13, in <module>
    sys.exit(main())
  File "/home/user/miniconda3/lib/python3.7/site-packages/conda/cli/main.py", line 150, in main
    return conda_exception_handler(_main, *args, **kwargs)
  File "/home/user/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1335, in conda_exception_handler
    return_value = exception_handler(func, *args, **kwargs)
  File "/home/user/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1046, in __call__
    return self.handle_exception(exc_val, exc_tb)
  File "/home/user/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1090, in handle_exception
    return self.handle_unexpected_exception(exc_val, exc_tb)
  File "/home/user/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1105, in handle_unexpected_exception
    self._execute_upload(error_report)
  File "/home/user/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1267, in _execute_upload
    'User-Agent': self.user_agent,
  File "/home/user/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1065, in user_agent
    return context.user_agent
  File "/home/user/miniconda3/lib/python3.7/site-packages/conda/_vendor/auxlib/decorators.py", line 268, in new_fget
    cache[inner_attname] = func(self)
  File "/home/user/miniconda3/lib/python3.7/site-packages/conda/base/context.py", line 654, in user_agent
    builder = ["conda/%s requests/%s" % (CONDA_VERSION, self.requests_version)]
  File "/home/user/miniconda3/lib/python3.7/site-packages/conda/_vendor/auxlib/decorators.py", line 268, in new_fget
    cache[inner_attname] = func(self)
  File "/home/user/miniconda3/lib/python3.7/site-packages/conda/base/context.py", line 668, in requests_version
    from pip._vendor.requests import __version__ as REQUESTS_VERSION
  File "/home/user/miniconda3/lib/python3.7/site-packages/pip/_vendor/requests/__init__.py", line 94, in <module>
    from pip._internal.utils.compat import WINDOWS
  File "/home/user/miniconda3/lib/python3.7/site-packages/pip/_internal/__init__.py", line 40, in <module>
    from pip._internal.cli.autocompletion import autocomplete
  File "/home/user/miniconda3/lib/python3.7/site-packages/pip/_internal/cli/autocompletion.py", line 8, in <module>
    from pip._internal.cli.main_parser import create_main_parser
  File "/home/user/miniconda3/lib/python3.7/site-packages/pip/_internal/cli/main_parser.py", line 12, in <module>
    from pip._internal.commands import (
  File "/home/user/miniconda3/lib/python3.7/site-packages/pip/_internal/commands/__init__.py", line 6, in <module>
    from pip._internal.commands.completion import CompletionCommand
  File "/home/user/miniconda3/lib/python3.7/site-packages/pip/_internal/commands/completion.py", line 6, in <module>
    from pip._internal.cli.base_command import Command
  File "/home/user/miniconda3/lib/python3.7/site-packages/pip/_internal/cli/base_command.py", line 20, in <module>
    from pip._internal.download import PipSession
  File "/home/user/miniconda3/lib/python3.7/site-packages/pip/_internal/download.py", line 368, in <module>
    class PipSession(requests.Session):
AttributeError: module 'pip._vendor.requests' has no attribute 'Session'

Here's the latest output of conda-meta/history:

==> 2019-04-19 10:25:54 <==
# cmd: /home/user/miniconda3/bin/conda install gdal-2.2.4-py36_0.tar.bz2
# conda version: 4.6.14
+<unknown>::gdal-2.2.4-py36_0
# update specs: ['gdal[url=file:///c/temp/gdal-2.2.4-py36_0.tar.bz2]']
==> 2019-05-14 09:16:26 <==
# cmd: /home/user/miniconda3/bin/conda update conda
# conda version: 4.6.14
-defaults::ca-certificates-2019.1.23-0
-defaults::certifi-2019.3.9-py37_0
-defaults::conda-4.6.14-py37_0
-defaults::openssl-1.1.1b-h7b6447c_1
+conda-forge::ca-certificates-2019.3.9-hecc5488_0
+conda-forge::certifi-2019.3.9-py37_0
+conda-forge::conda-4.6.14-py37_0
+conda-forge::openssl-1.1.1b-h14c3975_1
# update specs: ['conda']
==> 2019-07-10 13:04:17 <==
# cmd: /home/user/miniconda3/bin/conda update -n base conda
# conda version: 4.6.14
-conda-forge::ca-certificates-2019.3.9-hecc5488_0
-conda-forge::certifi-2019.3.9-py37_0
-conda-forge::conda-4.6.14-py37_0
-defaults::asn1crypto-0.24.0-py37_0
-defaults::cffi-1.11.5-py37he75722e_1
-defaults::chardet-3.0.4-py37_1
-defaults::cryptography-2.4.2-py37h1ba5d50_0
-defaults::idna-2.8-py37_0
-defaults::libffi-3.2.1-hd88cf55_4
-defaults::libgcc-ng-8.2.0-hdf63c60_1
-defaults::ncurses-6.1-he6710b0_1
-defaults::pip-18.1-py37_0
-defaults::pycosat-0.6.3-py37h14c3975_0
-defaults::pycparser-2.19-py37_0
-defaults::pyopenssl-18.0.0-py37_0
-defaults::pysocks-1.6.8-py37_0
-defaults::python-3.7.1-h0371630_7
-defaults::readline-7.0-h7b6447c_5
-defaults::requests-2.21.0-py37_0
-defaults::ruamel_yaml-0.15.46-py37h14c3975_0
-defaults::setuptools-40.6.3-py37_0
-defaults::six-1.12.0-py37_0
-defaults::sqlite-3.26.0-h7b6447c_0
-defaults::tk-8.6.8-hbc83047_0
-defaults::urllib3-1.24.1-py37_0
-defaults::wheel-0.32.3-py37_0
-defaults::xz-5.2.4-h14c3975_4
-defaults::yaml-0.1.7-had09818_2
-defaults::zlib-1.2.11-h7b6447c_3
+conda-forge::asn1crypto-0.24.0-py37_1003
+conda-forge::bzip2-1.0.6-h14c3975_1002
+conda-forge::ca-certificates-2019.6.16-hecc5488_0
+conda-forge::certifi-2019.6.16-py37_0
+conda-forge::cffi-1.12.3-py37h8022711_0
+conda-forge::chardet-3.0.4-py37_1003
+conda-forge::conda-4.7.5-py37_0
+conda-forge::conda-package-handling-1.3.10-py37_0
+conda-forge::cryptography-2.7-py37h72c5cf5_0
+conda-forge::icu-58.2-hf484d3e_1000
+conda-forge::idna-2.8-py37_1000
+conda-forge::libarchive-3.3.3-hb44662c_1005
+conda-forge::libffi-3.2.1-he1b5a44_1006
+conda-forge::libiconv-1.15-h516909a_1005
+conda-forge::libxml2-2.9.9-h13577e0_1
+conda-forge::lz4-c-1.8.3-he1b5a44_1001
+conda-forge::lzo-2.10-h14c3975_1000
+conda-forge::ncurses-6.1-hf484d3e_1002
+conda-forge::pip-19.1.1-py37_0
+conda-forge::pycosat-0.6.3-py37h14c3975_1001
+conda-forge::pycparser-2.19-py37_1
+conda-forge::pyopenssl-19.0.0-py37_0
+conda-forge::pysocks-1.7.0-py37_0
+conda-forge::python-3.7.3-h33d41f4_1
+conda-forge::python-libarchive-c-2.8-py37_1004
+conda-forge::readline-8.0-hf8c457e_0
+conda-forge::requests-2.22.0-py37_0
+conda-forge::ruamel_yaml-0.15.71-py37h14c3975_1000
+conda-forge::setuptools-41.0.1-py37_0
+conda-forge::six-1.12.0-py37_1000
+conda-forge::sqlite-3.28.0-hcee41ef_1
+conda-forge::tk-8.6.9-hed695b0_1002
+conda-forge::tqdm-4.32.2-py_0
+conda-forge::urllib3-1.24.3-py37_0
+conda-forge::wheel-0.33.4-py37_0
+conda-forge::xz-5.2.4-h14c3975_1001
+conda-forge::yaml-0.1.7-h14c3975_1001
+conda-forge::zlib-1.2.11-h14c3975_1004
+conda-forge::zstd-1.4.0-h3b9ef0a_0
+defaults::_libgcc_mutex-0.1-main
+defaults::libgcc-ng-9.1.0-hdf63c60_0
# update specs: ['conda']

Sieboldianus on 16 Jul 2019

Bizarre. I'll reopen the issue, but I hope no one else has this problem.

I've got this problem as well

asaou on 16 Jul 2019

Bizarre. I'll reopen the issue, but I hope no one else has this problem.

I've got this problem as well

Likewise :/

joeborrello on 16 Jul 2019

Note from the other issue, this is how I fixed my conda install (however, I am still not able to update conda to latest):

Following part of rgommers comments:

downloaded Miniconda3-latest-Linux-x86_64.sh from https://repo.continuum.io/miniconda/
bash Miniconda3-latest-Linux-x86_64.sh -u
"Do you wish the installer to initialize Miniconda3 by running conda init?" yes

This helped restore the previous state, but not fix the update problem.

Sieboldianus on 16 Jul 2019

👍1

@Sieboldianus your solution seems to have fixed the conda update conda and conda update --all issues I was having, but I still seem to have some broken environment configs, as I still can't run certain packages managed by conda, such as jupyter.

joeborrello on 16 Jul 2019

Note from the other issue, this is how I fixed my conda install (however, I am still not able to update conda to latest):

Following part of rgommers comments:

downloaded Miniconda3-latest-Linux-x86_64.sh from https://repo.continuum.io/miniconda/

bash Miniconda3-latest-Linux-x86_64.sh -u

"Do you wish the installer to initialize Miniconda3 by running conda init?" yes

This helped restore the previous state, but not fix the update problem.

@Sieboldianus Thank you so much for the reference to the other issue. I managed to revert back to my last functionable version of conda. (4.7.5 -> 4.6.14).

I followed rgommers' comments (https://github.com/conda/conda/issues/8172#issuecomment-459580119) which is slightly different from @Sieboldianus :

downloaded Miniconda3-latest-Linux-x86_64.sh from https://repo.continuum.io/miniconda/
bash Miniconda3-latest-Linux-x86_64.sh
"Do you wish the installer to initialize Miniconda3 by running conda init?" NO If you choose this, I think the default environment when startup should be in miniconda3 but not the original anaconda3.
cd ~/miniconda3/bin This conda from miniconda3 should work perfectly without bugs.
Use the conda from miniconda3 to 'heal' your anaconda3. Like this:
./conda install --prefix ~/anaconda3/ ~/anaconda3/pkgs/conda_package_handling_XXX.tar.bz2
This should allow you to reinstall the packages that are missing in the error output of anaconda3.
In my case, I reinstall conda_package_handling, requests, and urllib3.
Try your anaconda3 conda using conda info or conda install PACKAGE.
If you can get a normal output from conda info, you should be able to revert to previous version of conda using conda install --revision. Please see: http://blog.rtwilson.com/conda-revisions-letting-you-rollback-to-a-previous-version-of-your-environment/

Now everything is reverted back to the previous version. Hope this can be of any help!

yichao-cai on 17 Jul 2019

Note from the other issue, this is how I fixed my conda install (however, I am still not able to update conda to latest):
Following part of rgommers comments:

downloaded Miniconda3-latest-Linux-x86_64.sh from https://repo.continuum.io/miniconda/

bash Miniconda3-latest-Linux-x86_64.sh -u

"Do you wish the installer to initialize Miniconda3 by running conda init?" yes

This helped restore the previous state, but not fix the update problem.

@Sieboldianus Thank you so much for the reference to the other issue. I managed to revert back to my last functionable version of conda. (4.7.5 -> 4.6.14).

I followed rgommers' comments (#8172 (comment)) which is slightly different from @Sieboldianus :
1. downloaded `Miniconda3-latest-Linux-x86_64.sh` from https://repo.continuum.io/miniconda/

2. `bash Miniconda3-latest-Linux-x86_64.sh`

3. "Do you wish the installer to initialize Miniconda3 by running conda init?"  **NO** If you choose this, I think the default environment when startup should be in miniconda3 but not the original anaconda3.

4. `cd ~/miniconda3/bin` This conda from miniconda3 should work perfectly without bugs.

5. Use the conda from miniconda3 to 'heal' your anaconda3. Like this:
   `./conda install --prefix ~/anaconda3/ ~/anaconda3/pkgs/conda_package_handling_XXX.tar.bz2`
   This should allow you to reinstall the packages that are missing in the error output of anaconda3.
   In my case, I reinstall `conda_package_handling`, `requests`, and `urllib3`.

6. Try your anaconda3 conda using `conda info` or `conda install PACKAGE`.

7. If you can get a normal output from `conda info`, you should be able to revert to previous version of conda using `conda install --revision`. Please see: http://blog.rtwilson.com/conda-revisions-letting-you-rollback-to-a-previous-version-of-your-environment/
Now everything is reverted back to the previous version. Hope this can be of any help!

Thanks, but I still get

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

    Traceback (most recent call last):
      File "/home/andrea/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1043, in __call__
        return func(*args, **kwargs)
      File "/home/andrea/anaconda3/lib/python3.7/site-packages/conda/cli/main.py", line 84, in _main
        exit_code = do_call(args, p)
      File "/home/andrea/anaconda3/lib/python3.7/site-packages/conda/cli/conda_argparse.py", line 80, in do_call
        module = import_module(relative_mod, __name__.rsplit('.', 1)[0])
      File "/home/andrea/anaconda3/lib/python3.7/importlib/__init__.py", line 127, in import_module
        return _bootstrap._gcd_import(name[level:], package, level)
      File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
      File "<frozen importlib._bootstrap>", line 983, in _find_and_load
      File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
      File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
      File "<frozen importlib._bootstrap_external>", line 728, in exec_module
      File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
      File "/home/andrea/anaconda3/lib/python3.7/site-packages/conda/cli/main_info.py", line 19, in <module>
        from ..core.index import _supplement_index_with_system
      File "/home/andrea/anaconda3/lib/python3.7/site-packages/conda/core/index.py", line 9, in <module>
        from .package_cache_data import PackageCacheData
      File "/home/andrea/anaconda3/lib/python3.7/site-packages/conda/core/package_cache_data.py", line 15, in <module>
        from conda_package_handling.api import InvalidArchiveError
      File "/home/andrea/anaconda3/lib/python3.7/site-packages/conda_package_handling/api.py", line 3, in <module>
        from libarchive.exception import ArchiveError as _LibarchiveArchiveError
    ModuleNotFoundError: No module named 'libarchive'

`$ /home/andrea/anaconda3/bin/conda info`

andreadistefano on 17 Jul 2019

@andystevens91 you can run pip install libarchive to solve this issue.
Or : sudo apt-get install libarchive-dev
Anyone of these should work.

akashpalrecha on 18 Jul 2019

👍1

@akashpalrecha Using external sources of libarchive is likely to cause problems - if not now, then down the line. I strongly advise against using pip for anything other than getting out of a bind.

Many of the problems being reported here appear to involve a python version change, from 3.6 to 3.7. That can definitely cause issues, and it is not allowed to happen from conda 4.7 forward. To restore functionality, you likely need to use an external miniconda (download and install it elsewhere) and restore your broken installation to its original python version. You can do so by activating the separate miniconda install, then running conda install -p <path to your original install> python=<original python version>

msarahan on 18 Jul 2019

👍2

@andystevens91 you can run pip install libarchive to solve this issue.
Or : sudo apt-get install libarchive-dev

I also got the ModuleNotFoundError: No module named 'libarchive' error.

sudo apt-get install libarchive-dev doesn't seem to solve this. pip install libarchive works, however now I'm getting AttributeError: module 'libarchive' has no attribute 'extract'

peterroelants on 18 Jul 2019

Getting the ModuleNotFoundError: No module named 'libarchive' error here after trying to conda update --all . It broke while trying to update the python-libarchive package. I'll try the suggestion to use an external miniconda install to restore python, but this is still a bit concerning because I haven't done much besides basic conda install and update commands, and now my entire conda install is FUBAR and it's throwing that error even on conda list

marcbecc on 20 Jul 2019

hm after copying conda-package-handling. I am missing libarchive.
Note: I am copied from and to python3.7

I too tried copying conda-package-handling, and now I'm missing libarchive. I tried downloading libarchive from https://anaconda.org/conda-forge/libarchive/files and manually copying all files in the right subdirectories, but I had no success.

"～anaconda3/pkgs" here you can find the missing 'libarchive', also the other missing module in anaconda3 (the version installed in your computer ) can be found here.

caofolin on 22 Jul 2019

I am also facing the same issue, I can't even run 'conda info' or 'conda update'. (Also running Python 3.7 on Windows10) I keep getting:

conda update conda-build
Traceback (most recent call last):
File "C:\Users\username\anaconda3\libsite-packagesconda\exceptions.py", line 1062, in __call__
return func(args, *kwargs)
File "C:\Users\username\anaconda3\libsite-packagesconda\cli\main.py", line 84, in _main
exit_code = do_call(args, p)
File "C:\Users\username\anaconda3\libsite-packagesconda\cliconda_argparse.py", line 80, in do_call
module = import_module(relative_mod, __name__.rsplit('.', 1)[0])
File "C:\Users\username\anaconda3\lib\importlib__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1006, in _gcd_import
File "", line 983, in _find_and_load
File "", line 967, in _find_and_load_unlocked
File "", line 677, in _load_unlocked
File "", line 728, in exec_module
File "", line 219, in _call_with_frames_removed
File "C:\Users\username\anaconda3\libsite-packagesconda\cli\main_update.py", line 8, in
from .install import install
File "C:\Users\username\anaconda3\libsite-packagesconda\cli\install.py", line 19, in
from ..core.index import calculate_channel_urls, get_index
File "C:\Users\username\anaconda3\libsite-packagesconda\core\index.py", line 9, in
from .package_cache_data import PackageCacheData
File "C:\Users\username\anaconda3\libsite-packagesconda\core\package_cache_data.py", line 15, in
from conda_package_handling.api import InvalidArchiveError
ModuleNotFoundError: No module named 'conda_package_handling'

nikeiubel on 22 Jul 2019

@msarahan

Many of the problems being reported here appear to involve a python version change, from 3.6 to 3.7. That can definitely cause issues, and it is not allowed to happen from conda 4.7 forward.

Nope. I was already at version 3.7 and still ran into into this bug on Windows 10.

u55 on 22 Jul 2019

Having similar issues. Is there an appropriate fix, nearly identical issues as @andystevens91 after updating last week.
penicillium@pome:~$ conda update
Traceback (most recent call last):
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/conda/exceptions.py", line 1062, in __call__
return func(args, *kwargs)
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/conda/cli/main.py", line 84, in _main
exit_code = do_call(args, p)
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/conda/cli/conda_argparse.py", line 80, in do_call
module = import_module(relative_mod, __name__.rsplit('.', 1)[0])
File "/home/penicillium/anaconda_ete/lib/python3.6/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 994, in _gcd_import
File "", line 971, in _find_and_load
File "", line 955, in _find_and_load_unlocked
File "", line 665, in _load_unlocked
File "", line 678, in exec_module
File "", line 219, in _call_with_frames_removed
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/conda/cli/main_update.py", line 8, in
from .install import install
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/conda/cli/install.py", line 19, in
from ..core.index import calculate_channel_urls, get_index
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/conda/core/index.py", line 9, in
from .package_cache_data import PackageCacheData
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/conda/core/package_cache_data.py", line 15, in
from conda_package_handling.api import InvalidArchiveError
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/conda_package_handling/api.py", line 3, in
from libarchive.exception import ArchiveError as _LibarchiveArchiveError
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/libarchive/__init__.py", line 1, in
from .entry import ArchiveEntry
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/libarchive/entry.py", line 6, in
from . import ffi
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/libarchive/ffi.py", line 27, in
libarchive = ctypes.cdll.LoadLibrary(libarchive_path)
File "/home/penicillium/anaconda_ete/lib/python3.6/ctypes/__init__.py", line 426, in LoadLibrary
return self._dlltype(name)
File "/home/penicillium/anaconda_ete/lib/python3.6/ctypes/__init__.py", line 348, in __init__
self._handle = _dlopen(self._name, mode)
OSError: libiconv.so.2: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/penicillium/anaconda_ete/bin/conda", line 13, in
sys.exit(main())
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/conda/cli/main.py", line 150, in main
return conda_exception_handler(_main, args, *kwargs)
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/conda/exceptions.py", line 1354, in conda_exception_handler
return_value = exception_handler(func, args, *kwargs)
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/conda/exceptions.py", line 1065, in __call__
return self.handle_exception(exc_val, exc_tb)
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/conda/exceptions.py", line 1109, in handle_exception
return self.handle_unexpected_exception(exc_val, exc_tb)
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/conda/exceptions.py", line 1120, in handle_unexpected_exception
self.print_unexpected_error_report(error_report)
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/conda/exceptions.py", line 1190, in print_unexpected_error_report
from .cli.main_info import get_env_vars_str, get_main_info_str
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/conda/cli/main_info.py", line 19, in
from ..core.index import _supplement_index_with_system
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/conda/core/index.py", line 9, in
from .package_cache_data import PackageCacheData
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/conda/core/package_cache_data.py", line 15, in
from conda_package_handling.api import InvalidArchiveError
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/conda_package_handling/api.py", line 7, in
from .tarball import CondaTarBZ2 as _CondaTarBZ2
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/conda_package_handling/tarball.py", line 7, in
import libarchive
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/libarchive/__init__.py", line 1, in
from .entry import ArchiveEntry
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/libarchive/entry.py", line 6, in
from . import ffi
File "/home/penicillium/anaconda_ete/lib/python3.6/site-packages/libarchive/ffi.py", line 27, in
libarchive = ctypes.cdll.LoadLibrary(libarchive_path)
File "/home/penicillium/anaconda_ete/lib/python3.6/ctypes/__init__.py", line 426, in LoadLibrary
return self._dlltype(name)
File "/home/penicillium/anaconda_ete/lib/python3.6/ctypes/__init__.py", line 348, in __init__
self._handle = _dlopen(self._name, mode)
OSError: libiconv.so.2: cannot open shared object file: No such file or directory

fjlicht on 22 Jul 2019

Summary

My installation is also exhibiting similar problems after an update a couple of weeks ago. My usage of conda is pretty much limited to conda install and switching between environments, so I assume the update caused the problem. A miniconda update upgraded the version of python being used from 3.6 to 3.7 in early April, but the problems didn't start until a more recent update a couple of weeks ago. Like others, I get an error due to missing a missing package conda_package_handling when running basic conda commands, even though the package is actually installed.

Details

When I run basic commands I get the following error about a missing package conda_package_handling.

~ $ conda list
Traceback (most recent call last):
  File "/Users/eharkin/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1043, in __call__
    return func(*args, **kwargs)
  File "/Users/eharkin/miniconda3/lib/python3.7/site-packages/conda/cli/main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "/Users/eharkin/miniconda3/lib/python3.7/site-packages/conda/cli/conda_argparse.py", line 80, in do_call
    module = import_module(relative_mod, __name__.rsplit('.', 1)[0])
  File "/Users/eharkin/miniconda3/lib/python3.7/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/Users/eharkin/miniconda3/lib/python3.7/site-packages/conda/cli/main_list.py", line 14, in <module>
    from ..core.prefix_data import PrefixData
  File "/Users/eharkin/miniconda3/lib/python3.7/site-packages/conda/core/prefix_data.py", line 24, in <module>
    from ..gateways.disk.create import write_as_json_to_file
  File "/Users/eharkin/miniconda3/lib/python3.7/site-packages/conda/gateways/disk/create.py", line 17, in <module>
    import conda_package_handling.api
ModuleNotFoundError: No module named 'conda_package_handling'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/eharkin/miniconda3/bin/conda", line 13, in <module>
    sys.exit(main())
  File "/Users/eharkin/miniconda3/lib/python3.7/site-packages/conda/cli/main.py", line 150, in main
    return conda_exception_handler(_main, *args, **kwargs)
  File "/Users/eharkin/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1335, in conda_exception_handler
    return_value = exception_handler(func, *args, **kwargs)
  File "/Users/eharkin/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1046, in __call__
    return self.handle_exception(exc_val, exc_tb)
  File "/Users/eharkin/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1090, in handle_exception
    return self.handle_unexpected_exception(exc_val, exc_tb)
  File "/Users/eharkin/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1101, in handle_unexpected_exception
    self.print_unexpected_error_report(error_report)
  File "/Users/eharkin/miniconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1171, in print_unexpected_error_report
    from .cli.main_info import get_env_vars_str, get_main_info_str
  File "/Users/eharkin/miniconda3/lib/python3.7/site-packages/conda/cli/main_info.py", line 19, in <module>
    from ..core.index import _supplement_index_with_system
  File "/Users/eharkin/miniconda3/lib/python3.7/site-packages/conda/core/index.py", line 9, in <module>
    from .package_cache_data import PackageCacheData
  File "/Users/eharkin/miniconda3/lib/python3.7/site-packages/conda/core/package_cache_data.py", line 15, in <module>
    from conda_package_handling.api import InvalidArchiveError
ModuleNotFoundError: No module named 'conda_package_handling'

This doesn't seem to be caused by a recent change in python version. See the content of my most recent conda update:

==> 2019-07-08 15:41:47 <==
# cmd: /Users/eharkin/miniconda3/bin/conda update -n base -c defaults conda
# conda version: 4.6.14
-defaults::ca-certificates-2019.1.23-0
-defaults::certifi-2019.3.9-py37_0
-defaults::conda-4.6.14-py37_0
-defaults::openssl-1.1.1b-h1de35cc_1
+defaults::bzip2-1.0.7-h1de35cc_0
+defaults::ca-certificates-2019.5.15-0
+defaults::certifi-2019.6.16-py37_0
+defaults::conda-4.7.5-py37_0
+defaults::conda-package-handling-1.3.10-py37_0
+defaults::libarchive-3.3.3-h786848e_5
+defaults::libxml2-2.9.9-hf6e021a_1
+defaults::lz4-c-1.8.1.2-h1de35cc_0
+defaults::lzo-2.10-h362108e_2
+defaults::openssl-1.1.1c-h1de35cc_1
+defaults::python-libarchive-c-2.8-py37_9
+defaults::tqdm-4.32.1-py_0
+defaults::zstd-1.3.7-h5bba6e5_0
# update specs: ['conda']

A previous update in early April (from conda 4.6.7 to 4.6.11) did indeed upgrade python from 3.6 to 3.7, however. Both versions are still in my miniconda installation:

~ $ ls ~/miniconda3/lib | grep "^python"
python3.6
python3.7

Only python 3.7 has conda_package_handling installed:

~ $ find ~/miniconda3/lib -name "conda*package*handling*"
/Users/eharkin/miniconda3/lib/python3.7/site-packages/conda_package_handling-1.3.10.dist-info

efharkin on 23 Jul 2019

Some one seemed to have fixed something?

(base) penicillium@pome:~$ conda update conda
Collecting package metadata: done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
current version: 4.6.14
latest version: 4.7.10

Please update conda by running

$ conda update -n base -c defaults conda

Package Plan

environment location: /home/penicillium/miniconda2

added / updated specs:
- conda

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
_libgcc_mutex-0.1          |             main           3 KB
bzip2-1.0.8                |       h516909a_0         396 KB  conda-forge
ca-certificates-2019.6.16  |       hecc5488_0         145 KB  conda-forge
certifi-2019.6.16          |           py27_1         149 KB  conda-forge
conda-4.7.10               |           py27_0         3.0 MB  conda-forge
conda-package-handling-1.3.11|           py27_0         257 KB  conda-forge
icu-64.2                   |       he1b5a44_0        12.6 MB  conda-forge
libarchive-3.3.3           |    hb44662c_1005         1.4 MB  conda-forge
libiconv-1.15              |    h516909a_1005         2.0 MB  conda-forge
libxml2-2.9.9              |       hee79883_2         1.3 MB  conda-forge
lz4-c-1.8.3                |    he1b5a44_1001         187 KB  conda-forge
lzo-2.10                   |    h14c3975_1000         319 KB  conda-forge
openssl-1.1.1c             |       h516909a_0         2.1 MB  conda-forge
python-libarchive-c-2.8    |        py27_1004          20 KB  conda-forge
tqdm-4.32.2                |             py_0          41 KB  conda-forge
xz-5.2.4                   |    h14c3975_1001         366 KB  conda-forge
zstd-1.4.0                 |       h3b9ef0a_0         928 KB  conda-forge
------------------------------------------------------------
                                       Total:        25.2 MB

The following NEW packages will be INSTALLED:

_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
bzip2 conda-forge/linux-64::bzip2-1.0.8-h516909a_0
conda-package-han~ conda-forge/linux-64::conda-package-handling-1.3.11-py27_0
icu conda-forge/linux-64::icu-64.2-he1b5a44_0
libarchive conda-forge/linux-64::libarchive-3.3.3-hb44662c_1005
libiconv conda-forge/linux-64::libiconv-1.15-h516909a_1005
libxml2 conda-forge/linux-64::libxml2-2.9.9-hee79883_2
lz4-c conda-forge/linux-64::lz4-c-1.8.3-he1b5a44_1001
lzo conda-forge/linux-64::lzo-2.10-h14c3975_1000
python-libarchive~ conda-forge/linux-64::python-libarchive-c-2.8-py27_1004
tqdm conda-forge/noarch::tqdm-4.32.2-py_0
xz conda-forge/linux-64::xz-5.2.4-h14c3975_1001
zstd conda-forge/linux-64::zstd-1.4.0-h3b9ef0a_0

The following packages will be UPDATED:

ca-certificates pkgs/main::ca-certificates-2019.1.23-0 --> conda-forge::ca-certificates-2019.6.16-hecc5488_0
certifi pkgs/main::certifi-2019.3.9-py27_0 --> conda-forge::certifi-2019.6.16-py27_1
conda pkgs/main::conda-4.6.14-py27_0 --> conda-forge::conda-4.7.10-py27_0
openssl pkgs/main::openssl-1.1.1b-h7b6447c_1 --> conda-forge::openssl-1.1.1c-h516909a_0

Proceed ([y]/n)? y

Downloading and Extracting Packages
conda-package-handli | 257 KB | ######################################################################################################################################################################## | 100%
libiconv-1.15 | 2.0 MB | ######################################################################################################################################################################## | 100%
conda-4.7.10 | 3.0 MB | ######################################################################################################################################################################## | 100%
lz4-c-1.8.3 | 187 KB | ######################################################################################################################################################################## | 100%
bzip2-1.0.8 | 396 KB | ######################################################################################################################################################################## | 100%
libarchive-3.3.3 | 1.4 MB | ######################################################################################################################################################################## | 100%
icu-64.2 | 12.6 MB | ######################################################################################################################################################################## | 100%
certifi-2019.6.16 | 149 KB | ######################################################################################################################################################################## | 100%
ca-certificates-2019 | 145 KB | ######################################################################################################################################################################## | 100%
tqdm-4.32.2 | 41 KB | ######################################################################################################################################################################## | 100%
zstd-1.4.0 | 928 KB | ######################################################################################################################################################################## | 100%
_libgcc_mutex-0.1 | 3 KB | ######################################################################################################################################################################## | 100%
openssl-1.1.1c | 2.1 MB | ######################################################################################################################################################################## | 100%
libxml2-2.9.9 | 1.3 MB | ######################################################################################################################################################################## | 100%
xz-5.2.4 | 366 KB | ######################################################################################################################################################################## | 100%
python-libarchive-c- | 20 KB | ######################################################################################################################################################################## | 100%
lzo-2.10 | 319 KB | ######################################################################################################################################################################## | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

fjlicht on 24 Jul 2019

I "fixed" this problem by completely reinstalling anaconda.

backup environments: cp -R ~/anaconda/envs/* /somewhere/else
delete anaconda3 (or miniconda3) folder: rm -rf ~/anaconda3
reinstall anaconda using the latest installer from anaconda.com (say yes when it asks about conda init)
run conda update -n base -c defaults conda
run conda update --all
copy back your environments: cp -R /somewhere/else ~/anaconda3/envs/
test if your environments still work (mine did without problems)

EDIT: I don't know if there are other things to backup before deleting the anaconda folder, I did it this way and nothing went lost, but i'm not responsible for any data loss on your part.

andreadistefano on 24 Jul 2019

👍23 🎉3

I did a complete uninstall and fresh install (as suggested by @andystevens91) and indeed, Conda is working again. It has the latest Conda version (4.7.10) and it recognizes already Python 3.7.3:

(base) C:\windows\system32>conda info

     active environment : base
    active env location : C:\ProgramData\Anaconda3
            shell level : 1
       user config file : C:\Users\AMo1809.43853\.condarc
 populated config files : C:\Users\AMo1809.43853\.condarc
          conda version : 4.7.10
    conda-build version : 3.18.8
         python version : 3.7.3.final.0
       virtual packages :
       base environment : C:\ProgramData\Anaconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/win-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/win-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/msys2/win-64
                          https://repo.anaconda.com/pkgs/msys2/noarch
          package cache : C:\ProgramData\Anaconda3\pkgs
                          C:\Users\AMo1809.43853\.conda\pkgs
                          C:\Users\AMo1809.43853\AppData\Local\conda\conda\pkgs
       envs directories : C:\ProgramData\Anaconda3\envs
                          C:\Users\AMo1809.43853\.conda\envs
                          C:\Users\AMo1809.43853\AppData\Local\conda\conda\envs
               platform : win-64
             user-agent : conda/4.7.10 requests/2.22.0 CPython/3.7.3 Windows/10 Windows/10.0.17134
          administrator : True
             netrc file : None
           offline mode : False

I know this isn't the ideal solution, but it gets the job done

arturomoncadatorres on 29 Jul 2019

yes, this was the only way that worked for me, too. Remove miniconda3 folder completely, clear anything loaded automatically in home and then reinstall + immediate conda update conda. I did manually reinstall my environments by prior looking up the history file in meta folder of each env - there its possible to extract the main dependencies that have been installed.

Sieboldianus on 30 Jul 2019

I had to follow the same procedure of uninstalling the anaconda and reinstalling it to make it work again. Every conda command was basically failing!!

Alan-Rusty24 on 3 Aug 2019

having the same issue here.
I wanted to update my Anaconda installation, and uninstalled it, downloaded the newest version, installed it w/o any problem.
When I try to open Anaconda navigator it opens and suddenly disappears 2 cmd windows and does nothing. no navigator, no nothing.

When I try to run Anaconda navigator from cmd I get the below:

`C:\Users\FK\Anaconda3>anaconda-navigator
Traceback (most recent call last):
  File "C:\Users\FK\Anaconda3\lib\site-packages\qtpy\__init__.py", line 202, in <module>
    from PySide import __version__ as PYSIDE_VERSION  # analysis:ignore
ModuleNotFoundError: No module named 'PySide'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\FK\Anaconda3\Scripts\anaconda-navigator-script.py", line 6, in <module>
    from anaconda_navigator.app.main import main
  File "C:\Users\FK\Anaconda3\lib\site-packages\anaconda_navigator\app\main.py", line 22, in <module>
    from anaconda_navigator.utils.conda import is_conda_available
  File "C:\Users\FK\Anaconda3\lib\site-packages\anaconda_navigator\utils\__init__.py", line 15, in <module>
    from qtpy.QtGui import QIcon
  File "C:\Users\FK\Anaconda3\lib\site-packages\qtpy\__init__.py", line 208, in <module>
    raise PythonQtError('No Qt bindings could be found')
qtpy.PythonQtError: No Qt bindings could be found

K-Fatih on 4 Aug 2019

finally solved my problem by updating OpenSSL from the link.

You just download OpenSSL and install it.
Then run Anaconda-Navigator or process the update.

K-Fatih on 5 Aug 2019

Having the same issue on more than one machine conda update conda

conda list --revisions results in ...
`Traceback (most recent call last):
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1062, in __call__
return func(args, *kwargs)
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/conda/cli/main.py", line 84, in _main
exit_code = do_call(args, p)
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/conda/cli/conda_argparse.py", line 80, in do_call
module = import_module(relative_mod, __name__.rsplit('.', 1)[0])
File "/home/adamvs/anaconda3/lib/python3.7/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1006, in _gcd_import
File "", line 983, in _find_and_load
File "", line 967, in _find_and_load_unlocked
File "", line 677, in _load_unlocked
File "", line 728, in exec_module
File "", line 219, in _call_with_frames_removed
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/conda/cli/main_list.py", line 14, in
from ..core.prefix_data import PrefixData
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/conda/core/prefix_data.py", line 24, in
from ..gateways.disk.create import write_as_json_to_file
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/conda/gateways/disk/create.py", line 17, in
import conda_package_handling.api
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/conda_package_handling/api.py", line 3, in
from libarchive.exception import ArchiveError as _LibarchiveArchiveError
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/libarchive/__init__.py", line 1, in
from .entry import ArchiveEntry
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/libarchive/entry.py", line 6, in
from . import ffi
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/libarchive/ffi.py", line 48, in
libarchive = ctypes.cdll.LoadLibrary(libarchive_path)
File "/home/adamvs/anaconda3/lib/python3.7/ctypes/__init__.py", line 434, in LoadLibrary
return self._dlltype(name)
File "/home/adamvs/anaconda3/lib/python3.7/ctypes/__init__.py", line 356, in __init__
self._handle = _dlopen(self._name, mode)
OSError: libiconv.so.2: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/adamvs/anaconda3/bin/conda", line 13, in
sys.exit(main())
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/conda/cli/main.py", line 150, in main
return conda_exception_handler(_main, args, *kwargs)
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1354, in conda_exception_handler
return_value = exception_handler(func, args, *kwargs)
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1065, in __call__
return self.handle_exception(exc_val, exc_tb)
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1109, in handle_exception
return self.handle_unexpected_exception(exc_val, exc_tb)
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1120, in handle_unexpected_exception
self.print_unexpected_error_report(error_report)
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1190, in print_unexpected_error_report
from .cli.main_info import get_env_vars_str, get_main_info_str
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/conda/cli/main_info.py", line 19, in
from ..core.index import _supplement_index_with_system
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/conda/core/index.py", line 9, in
from .package_cache_data import PackageCacheData
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/conda/core/package_cache_data.py", line 15, in
from conda_package_handling.api import InvalidArchiveError
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/conda_package_handling/api.py", line 7, in
from .tarball import CondaTarBZ2 as _CondaTarBZ2
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/conda_package_handling/tarball.py", line 7, in
import libarchive
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/libarchive/__init__.py", line 1, in
from .entry import ArchiveEntry
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/libarchive/entry.py", line 6, in
from . import ffi
File "/home/adamvs/anaconda3/lib/python3.7/site-packages/libarchive/ffi.py", line 48, in
libarchive = ctypes.cdll.LoadLibrary(libarchive_path)
File "/home/adamvs/anaconda3/lib/python3.7/ctypes/__init__.py", line 434, in LoadLibrary
return self._dlltype(name)
File "/home/adamvs/anaconda3/lib/python3.7/ctypes/__init__.py", line 356, in __init__
self._handle = _dlopen(self._name, mode)
conda infois also broken, butconda config` is not

on another machine - conda update conda
conda automatically attempted to roll back but failed, resulting in the same error above. Will try to post that data

AdamVS on 7 Aug 2019

The libiconv error is indicative of a mix of incompatible packages, centered around libiconv. There was a bit of discussion at https://github.com/conda-forge/libxml2-feedstock/pull/48#issuecomment-518331253

Long story short: you should try to have purely defaults or purely conda-forge as much as possible. Using the "strict" channel priority setting will help.

conda config --set channel_priority strict

We believe the correct solution here is for conda-forge to rebuild their stack without the explicit libiconv dependency on linux, because libiconv is included with the glibc in our compilers (which conda-forge uses).

Openssl errors are most often on Windows, and we've had a few similar reports. We suspect bad interaction from packages across multiple channels here as well. see https://github.com/conda/conda/issues/9003#issuecomment-518703672

msarahan on 7 Aug 2019

I'm also experiencing this issue (on Windows 7). A few days ago conda told me I needed to update conda. I dutifully did so and everything broke. I couldn't even do conda info. Based on some posts here and in other issues I installed another miniconda on the side and used conda install -p to install various things that seemed to be missing. (Basically I would run conda info and look at the error to see what module it wasn't finding, and then use miniconda to install that.) For some reason the broken conda upgrade also removed libbz2.dll from my conda Lib directory; I copied it over from miniconda.

At first this seemed to get it working again, but I'm still getting sporadic errors when I try to do stuff, and sometimes it breaks conda completely again. Now when I try to conda install anything, it shows me multiple "possible package resolutions" and just hangs (with no indicator of any operation in progress, e.g., no "Solving" spinner or anything). This time there aren't even any error messages; it just hangs.

Any ideas how I can debug this?

Also, one thing I haven't really seen on any of these issues is an explanation of how we initially got into the position where it was even possible for conda upgrade conda to so completely hose the whole install. I'm always leery of upgrading almost anything for exactly this reason, and I'm going to be even more leery of upgrading conda after this. How did it happen that such a "bomb" was released in the main channel?

BrenBarn on 10 Aug 2019

Faced the same issue. @andystevens91 's fix worked !

My issue also started out exactly like this with inconsistencies.

shubhvachher on 16 Aug 2019

I experienced the same issue, when upgrading from conda 4.7.10 to 4.7.11

I managed to fix it with a fresh reinstall, as @andystevens91 suggested.

ljorda on 6 Sep 2019

same here! So annoying!

diegoscarabelli on 10 Sep 2019

👍4

Still broken update path.

I ran conda update conda, which left me with a broken system. I had to install miniconda elsewhere, get it to the same conda & python version, then tar-gzip & copy over conda_package_handling and libbz2. Then I uninstalled all parts of jupyter to get conda to update to the latest version, and reinstalled the removed packages and updated everything. A faff, but fortunately (with the pointers from above) it only wasted an hour of my time.

itsallonetome on 11 Sep 2019

Did this just happen? I don't understand how it is possible that, two months after the initial bug report, we're still in a situation where conda update conda is destroying people's setups. When is it going to be actually fixed?

BrenBarn on 11 Sep 2019

👍15

Would be nice to have a pinned solution for this issue. Disruptive!

raeidsaqur on 11 Sep 2019

👍3

ooops +1 on this. same issue running mac. may have to rebuild from scratch (fresh miniconda install) as i can't do anything conda related now.

lwasser on 16 Sep 2019

This just happened to me, and my workflow is broken. :-1:

osjerick on 24 Sep 2019

👍1

Also happened to me today on a conda update --all call. Python crippled on machine (Mac).

SiccarPoint on 1 Oct 2019

FWIW I also experienced this issue today. I came upon it while doing conda update conda trying to resolve the issue described in https://github.com/conda/conda/issues/8149. I also received the AssertionError() described by others above, as seen below:

$ conda update conda
Collecting package metadata (current_repodata.json): done
Solving environment: | 
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:

  - defaults/osx-64::conda==4.7.5=py36_0
done

...

Executing transaction: done
ERROR conda.core.link:_execute(637): An error occurred while installing package 'None'.
AssertionError()
Attempting to roll back.

Rolling back transaction: done

AssertionError()
()
AssertionError()
AssertionError()
AssertionError()
$

JLHasson on 2 Oct 2019

👍1

I ran into the same problem. Now my Python is broken and I can't seem to fix it with usual conda commands.
I tried to update conda and it resulted in AssertionError() and anything after that has resulted in No module named 'package-handling'

(base) PS C:\> conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): done
Solving environment: -
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:

  - defaults/win-64::anaconda==2019.07=py37_0
done

## Package Plan ##

  environment location: C:\Users\username\AppData\Local\Continuum\anaconda3

  added / updated specs:
    - conda


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _anaconda_depends-2019.03  |           py37_0           6 KB
    anaconda-custom            |           py37_1           3 KB
    astroid-2.3.1              |           py37_0         286 KB
    beautifulsoup4-4.8.0       |           py37_0         153 KB
    bitarray-1.0.1             |   py37he774522_0          60 KB
    bokeh-1.3.4                |           py37_0         4.9 MB
    ca-certificates-2019.8.28  |                0         165 KB
    certifi-2019.9.11          |           py37_0         155 KB
    chardet-3.0.4              |        py37_1003         193 KB
    cloudpickle-1.2.2          |             py_0          29 KB
    conda-4.7.12               |           py37_0         3.0 MB
    conda-package-handling-1.6.0|   py37h62dcd97_0         611 KB
    contextlib2-0.6.0          |             py_0          16 KB
    curl-7.65.3                |       h2a8f88b_0         118 KB
    cython-0.29.13             |   py37ha925a31_0         1.8 MB
    dask-2.5.0                 |             py_0          12 KB
    dask-core-2.5.0            |             py_0         578 KB
    distributed-2.5.1          |             py_0         386 KB
    docutils-0.15.2            |           py37_0         671 KB
    fsspec-0.5.1               |             py_0          45 KB
    heapdict-1.0.1             |             py_0           9 KB
    importlib_metadata-0.23    |           py37_0          44 KB
    intelpython-2019.5         |                0           3 KB  intel
    ipykernel-5.1.2            |   py37h39e3cac_0         173 KB
    ipython-7.8.0              |   py37h39e3cac_0        1001 KB
    ipywidgets-7.5.1           |             py_0         107 KB
    jedi-0.15.1                |           py37_0         704 KB
    json5-0.8.5                |             py_0          25 KB
    jsonschema-3.0.2           |           py37_0         109 KB
    jupyter_client-5.3.3       |           py37_1         162 KB
    jupyterlab-1.1.4           |     pyhf63ae98_0         4.4 MB
    jupyterlab_server-1.0.6    |             py_0          26 KB
    lazy-object-proxy-1.4.2    |   py37he774522_0          30 KB
    libcurl-7.65.3             |       h2a8f88b_0         268 KB
    libpng-1.6.36              |           vc14_2         571 KB  intel
    lxml-4.4.1                 |   py37h1350720_0         1.1 MB
    matplotlib-2.2.3           |   py37hd159220_0         4.7 MB
    mkl-service-2.3.0          |   py37hb782905_0         210 KB
    mkl_fft-1.0.14             |   py37h14836fe_0         118 KB
    mkl_random-1.1.0           |   py37h675688f_0         232 KB
    more-itertools-7.2.0       |           py37_0         101 KB
    nbconvert-5.6.0            |           py37_1         509 KB
    nltk-3.4.5                 |           py37_0         1.7 MB
    notebook-6.0.1             |           py37_0         7.4 MB
    numba-0.45.1               |   py37hf9181ef_0         2.7 MB
    numexpr-2.7.0              |   py37hdce8814_0         124 KB
    numpy-1.16.5               |   py37h19fb1c0_0          50 KB
    numpy-base-1.16.5          |   py37hc3f5095_0         4.1 MB
    openpyxl-3.0.0             |             py_0         157 KB
    openssl-1.1.1d             |       he774522_2         4.8 MB
    packaging-19.2             |             py_0          30 KB
    pandas-0.25.1              |   py37ha925a31_0         7.6 MB
    parso-0.5.1                |             py_0          68 KB
    pathlib2-2.3.5             |           py37_0          37 KB
    pip-19.2.3                 |           py37_0         1.9 MB
    pluggy-0.13.0              |           py37_0          32 KB
    pylint-2.4.2               |           py37_0         449 KB
    pyodbc-4.0.27              |   py37ha925a31_0          66 KB
    pyparsing-2.4.2            |             py_0          61 KB
    pyrsistent-0.15.4          |   py37he774522_0          95 KB
    pysocks-1.7.1              |           py37_0          30 KB
    pytest-5.2.0               |           py37_0         389 KB
    pytest-doctestplus-0.4.0   |             py_0          18 KB
    pytest-openfiles-0.4.0     |             py_0          10 KB
    pytest-remotedata-0.3.2    |           py37_0          15 KB
    python-libarchive-c-2.8    |          py37_13          24 KB
    pytz-2019.2                |             py_0         245 KB
    pyyaml-5.1.2               |   py37he774522_0         152 KB
    pyzmq-18.1.0               |   py37ha925a31_0         400 KB
    qtawesome-0.6.0            |             py_0         671 KB
    qtconsole-4.5.5            |             py_0          94 KB
    qtpy-1.9.0                 |             py_0          39 KB
    scikit-learn-0.21.3        |   py37h6288b17_0         4.4 MB
    scipy-1.3.1                |   py37h29ff71c_0        11.2 MB
    setuptools-41.2.0          |           py37_0         665 KB
    snowballstemmer-1.9.1      |             py_0          59 KB
    soupsieve-1.9.3            |           py37_0          60 KB
    sphinx-2.2.0               |             py_0         1.5 MB
    spyder-kernels-0.5.2       |           py37_0          70 KB
    sqlalchemy-1.3.8           |   py37he774522_0         1.8 MB
    statsmodels-0.10.1         |   py37h8c2d366_0         7.1 MB
    werkzeug-0.16.0            |             py_0         255 KB
    wheel-0.33.6               |           py37_0          58 KB
    widgetsnbextension-3.5.1   |           py37_0         868 KB
    xlsxwriter-1.2.1           |             py_0         106 KB
    xlwings-0.15.10            |           py37_0         810 KB
    zipp-0.6.0                 |             py_0           9 KB
    ------------------------------------------------------------
                                           Total:        89.8 MB

The following NEW packages will be INSTALLED:

  _anaconda_depends  pkgs/main/win-64::_anaconda_depends-2019.03-py37_0
  astroid            pkgs/main/win-64::astroid-2.3.1-py37_0
  beautifulsoup4     pkgs/main/win-64::beautifulsoup4-4.8.0-py37_0
  bitarray           pkgs/main/win-64::bitarray-1.0.1-py37he774522_0
  bokeh              pkgs/main/win-64::bokeh-1.3.4-py37_0
  chardet            pkgs/main/win-64::chardet-3.0.4-py37_1003
  cloudpickle        pkgs/main/noarch::cloudpickle-1.2.2-py_0
  conda-package-han~ pkgs/main/win-64::conda-package-handling-1.6.0-py37h62dcd97_0
  contextlib2        pkgs/main/noarch::contextlib2-0.6.0-py_0
  curl               pkgs/main/win-64::curl-7.65.3-h2a8f88b_0
  cython             pkgs/main/win-64::cython-0.29.13-py37ha925a31_0
  dask               pkgs/main/noarch::dask-2.5.0-py_0
  dask-core          pkgs/main/noarch::dask-core-2.5.0-py_0
  distributed        pkgs/main/noarch::distributed-2.5.1-py_0
  docutils           pkgs/main/win-64::docutils-0.15.2-py37_0
  fsspec             pkgs/main/noarch::fsspec-0.5.1-py_0
  heapdict           pkgs/main/noarch::heapdict-1.0.1-py_0
  importlib_metadata pkgs/main/win-64::importlib_metadata-0.23-py37_0
  intelpython        intel/win-64::intelpython-2019.5-0
  ipykernel          pkgs/main/win-64::ipykernel-5.1.2-py37h39e3cac_0
  ipython            pkgs/main/win-64::ipython-7.8.0-py37h39e3cac_0
  ipywidgets         pkgs/main/noarch::ipywidgets-7.5.1-py_0
  jedi               pkgs/main/win-64::jedi-0.15.1-py37_0
  json5              pkgs/main/noarch::json5-0.8.5-py_0
  jsonschema         pkgs/main/win-64::jsonschema-3.0.2-py37_0
  jupyter_client     pkgs/main/win-64::jupyter_client-5.3.3-py37_1
  jupyterlab         pkgs/main/noarch::jupyterlab-1.1.4-pyhf63ae98_0
  jupyterlab_server  pkgs/main/noarch::jupyterlab_server-1.0.6-py_0
  lazy-object-proxy  pkgs/main/win-64::lazy-object-proxy-1.4.2-py37he774522_0
  libcurl            pkgs/main/win-64::libcurl-7.65.3-h2a8f88b_0
  libpng             intel/win-64::libpng-1.6.36-vc14_2
  lxml               pkgs/main/win-64::lxml-4.4.1-py37h1350720_0
  matplotlib         pkgs/main/win-64::matplotlib-2.2.3-py37hd159220_0
  mkl-service        pkgs/main/win-64::mkl-service-2.3.0-py37hb782905_0
  mkl_fft            pkgs/main/win-64::mkl_fft-1.0.14-py37h14836fe_0
  mkl_random         pkgs/main/win-64::mkl_random-1.1.0-py37h675688f_0
  more-itertools     pkgs/main/win-64::more-itertools-7.2.0-py37_0
  nbconvert          pkgs/main/win-64::nbconvert-5.6.0-py37_1
  nltk               pkgs/main/win-64::nltk-3.4.5-py37_0
  notebook           pkgs/main/win-64::notebook-6.0.1-py37_0
  numba              pkgs/main/win-64::numba-0.45.1-py37hf9181ef_0
  numexpr            pkgs/main/win-64::numexpr-2.7.0-py37hdce8814_0
  numpy              pkgs/main/win-64::numpy-1.16.5-py37h19fb1c0_0
  numpy-base         pkgs/main/win-64::numpy-base-1.16.5-py37hc3f5095_0
  openpyxl           pkgs/main/noarch::openpyxl-3.0.0-py_0
  packaging          pkgs/main/noarch::packaging-19.2-py_0
  pandas             pkgs/main/win-64::pandas-0.25.1-py37ha925a31_0
  parso              pkgs/main/noarch::parso-0.5.1-py_0
  pathlib2           pkgs/main/win-64::pathlib2-2.3.5-py37_0
  pip                pkgs/main/win-64::pip-19.2.3-py37_0
  pluggy             pkgs/main/win-64::pluggy-0.13.0-py37_0
  pylint             pkgs/main/win-64::pylint-2.4.2-py37_0
  pyodbc             pkgs/main/win-64::pyodbc-4.0.27-py37ha925a31_0
  pyparsing          pkgs/main/noarch::pyparsing-2.4.2-py_0
  pyrsistent         pkgs/main/win-64::pyrsistent-0.15.4-py37he774522_0
  pysocks            pkgs/main/win-64::pysocks-1.7.1-py37_0
  pytest             pkgs/main/win-64::pytest-5.2.0-py37_0
  pytest-doctestplus pkgs/main/noarch::pytest-doctestplus-0.4.0-py_0
  pytest-openfiles   pkgs/main/noarch::pytest-openfiles-0.4.0-py_0
  pytest-remotedata  pkgs/main/win-64::pytest-remotedata-0.3.2-py37_0
  python-libarchive~ pkgs/main/win-64::python-libarchive-c-2.8-py37_13
  pytz               pkgs/main/noarch::pytz-2019.2-py_0
  pyyaml             pkgs/main/win-64::pyyaml-5.1.2-py37he774522_0
  pyzmq              pkgs/main/win-64::pyzmq-18.1.0-py37ha925a31_0
  qtawesome          pkgs/main/noarch::qtawesome-0.6.0-py_0
  qtconsole          pkgs/main/noarch::qtconsole-4.5.5-py_0
  qtpy               pkgs/main/noarch::qtpy-1.9.0-py_0
  scikit-learn       pkgs/main/win-64::scikit-learn-0.21.3-py37h6288b17_0
  scipy              pkgs/main/win-64::scipy-1.3.1-py37h29ff71c_0
  setuptools         pkgs/main/win-64::setuptools-41.2.0-py37_0
  snowballstemmer    pkgs/main/noarch::snowballstemmer-1.9.1-py_0
  soupsieve          pkgs/main/win-64::soupsieve-1.9.3-py37_0
  sphinx             pkgs/main/noarch::sphinx-2.2.0-py_0
  spyder-kernels     pkgs/main/win-64::spyder-kernels-0.5.2-py37_0
  sqlalchemy         pkgs/main/win-64::sqlalchemy-1.3.8-py37he774522_0
  statsmodels        pkgs/main/win-64::statsmodels-0.10.1-py37h8c2d366_0
  tqdm               pkgs/main/noarch::tqdm-4.36.1-py_0
  vs2015_runtime     pkgs/main/win-64::vs2015_runtime-14.16.27012-hf0eaf9b_0
  werkzeug           pkgs/main/noarch::werkzeug-0.16.0-py_0
  wheel              pkgs/main/win-64::wheel-0.33.6-py37_0
  widgetsnbextension pkgs/main/win-64::widgetsnbextension-3.5.1-py37_0
  xlsxwriter         pkgs/main/noarch::xlsxwriter-1.2.1-py_0
  xlwings            pkgs/main/win-64::xlwings-0.15.10-py37_0
  zipp               pkgs/main/noarch::zipp-0.6.0-py_0
  zlib               intel/win-64::zlib-1.2.11-vc14h21ff451_5

The following packages will be UPDATED:

  ca-certificates                               2019.5.15-0 --> 2019.8.28-0
  certifi                                  2019.6.16-py37_0 --> 2019.9.11-py37_0
  conda                                       4.7.10-py37_0 --> 4.7.12-py37_0
  openssl                                 1.1.1c-he774522_1 --> 1.1.1d-he774522_2

The following packages will be DOWNGRADED:

  anaconda                                   2019.07-py37_0 --> custom-py37_1


Proceed ([y]/n)? y


Downloading and Extracting Packages
scikit-learn-0.21.3  | 4.4 MB    | ############################################################################ | 100%
soupsieve-1.9.3      | 60 KB     | ############################################################################ | 100%
pyodbc-4.0.27        | 66 KB     | ############################################################################ | 100%
certifi-2019.9.11    | 155 KB    | ############################################################################ | 100%
wheel-0.33.6         | 58 KB     | ############################################################################ | 100%
jupyterlab-1.1.4     | 4.4 MB    | ############################################################################ | 100%
docutils-0.15.2      | 671 KB    | ############################################################################ | 100%
pyyaml-5.1.2         | 152 KB    | ############################################################################ | 100%
dask-2.5.0           | 12 KB     | ############################################################################ | 100%
libpng-1.6.36        | 571 KB    | ############################################################################ | 100%
pip-19.2.3           | 1.9 MB    | ############################################################################ | 100%
intelpython-2019.5   | 3 KB      | ############################################################################ | 100%
xlwings-0.15.10      | 810 KB    | ############################################################################ | 100%
cloudpickle-1.2.2    | 29 KB     | ############################################################################ | 100%
ipykernel-5.1.2      | 173 KB    | ############################################################################ | 100%
chardet-3.0.4        | 193 KB    | ############################################################################ | 100%
pytest-5.2.0         | 389 KB    | ############################################################################ | 100%
pyrsistent-0.15.4    | 95 KB     | ############################################################################ | 100%
nltk-3.4.5           | 1.7 MB    | ############################################################################ | 100%
ipywidgets-7.5.1     | 107 KB    | ############################################################################ | 100%
nbconvert-5.6.0      | 509 KB    | ############################################################################ | 100%
pyparsing-2.4.2      | 61 KB     | ############################################################################ | 100%
conda-4.7.12         | 3.0 MB    | ############################################################################ | 100%
mkl_fft-1.0.14       | 118 KB    | ############################################################################ | 100%
astroid-2.3.1        | 286 KB    | ############################################################################ | 100%
lazy-object-proxy-1. | 30 KB     | ############################################################################ | 100%
sphinx-2.2.0         | 1.5 MB    | ############################################################################ | 100%
pandas-0.25.1        | 7.6 MB    | ############################################################################ | 100%
packaging-19.2       | 30 KB     | ############################################################################ | 100%
conda-package-handli | 611 KB    | ############################################################################ | 100%
beautifulsoup4-4.8.0 | 153 KB    | ############################################################################ | 100%
json5-0.8.5          | 25 KB     | ############################################################################ | 100%
pytest-remotedata-0. | 15 KB     | ############################################################################ | 100%
openssl-1.1.1d       | 4.8 MB    | ############################################################################ | 100%
_anaconda_depends-20 | 6 KB      | ############################################################################ | 100%
ipython-7.8.0        | 1001 KB   | ############################################################################ | 100%
pylint-2.4.2         | 449 KB    | ############################################################################ | 100%
numpy-base-1.16.5    | 4.1 MB    | ############################################################################ | 100%
matplotlib-2.2.3     | 4.7 MB    | ############################################################################ | 100%
jupyterlab_server-1. | 26 KB     | ############################################################################ | 100%
lxml-4.4.1           | 1.1 MB    | ############################################################################ | 100%
jedi-0.15.1          | 704 KB    | ############################################################################ | 100%
pyzmq-18.1.0         | 400 KB    | ############################################################################ | 100%
heapdict-1.0.1       | 9 KB      | ############################################################################ | 100%
werkzeug-0.16.0      | 255 KB    | ############################################################################ | 100%
zipp-0.6.0           | 9 KB      | ############################################################################ | 100%
jupyter_client-5.3.3 | 162 KB    | ############################################################################ | 100%
jsonschema-3.0.2     | 109 KB    | ############################################################################ | 100%
qtconsole-4.5.5      | 94 KB     | ############################################################################ | 100%
curl-7.65.3          | 118 KB    | ############################################################################ | 100%
pathlib2-2.3.5       | 37 KB     | ############################################################################ | 100%
contextlib2-0.6.0    | 16 KB     | ############################################################################ | 100%
notebook-6.0.1       | 7.4 MB    | ############################################################################ | 100%
dask-core-2.5.0      | 578 KB    | ############################################################################ | 100%
bitarray-1.0.1       | 60 KB     | ############################################################################ | 100%
mkl-service-2.3.0    | 210 KB    | ############################################################################ | 100%
setuptools-41.2.0    | 665 KB    | ############################################################################ | 100%
importlib_metadata-0 | 44 KB     | ############################################################################ | 100%
distributed-2.5.1    | 386 KB    | ############################################################################ | 100%
openpyxl-3.0.0       | 157 KB    | ############################################################################ | 100%
numexpr-2.7.0        | 124 KB    | ############################################################################ | 100%
snowballstemmer-1.9. | 59 KB     | ############################################################################ | 100%
fsspec-0.5.1         | 45 KB     | ############################################################################ | 100%
numba-0.45.1         | 2.7 MB    | ############################################################################ | 100%
qtpy-1.9.0           | 39 KB     | ############################################################################ | 100%
xlsxwriter-1.2.1     | 106 KB    | ############################################################################ | 100%
anaconda-custom      | 3 KB      | ############################################################################ | 100%
sqlalchemy-1.3.8     | 1.8 MB    | ############################################################################ | 100%
bokeh-1.3.4          | 4.9 MB    | ############################################################################ | 100%
statsmodels-0.10.1   | 7.1 MB    | ############################################################################ | 100%
pytest-doctestplus-0 | 18 KB     | ############################################################################ | 100%
spyder-kernels-0.5.2 | 70 KB     | ############################################################################ | 100%
libcurl-7.65.3       | 268 KB    | ############################################################################ | 100%
pytz-2019.2          | 245 KB    | ############################################################################ | 100%
ca-certificates-2019 | 165 KB    | ############################################################################ | 100%
pluggy-0.13.0        | 32 KB     | ############################################################################ | 100%
scipy-1.3.1          | 11.2 MB   | ############################################################################ | 100%
more-itertools-7.2.0 | 101 KB    | ############################################################################ | 100%
widgetsnbextension-3 | 868 KB    | ############################################################################ | 100%
pytest-openfiles-0.4 | 10 KB     | ############################################################################ | 100%
pysocks-1.7.1        | 30 KB     | ############################################################################ | 100%
parso-0.5.1          | 68 KB     | ############################################################################ | 100%
python-libarchive-c- | 24 KB     | ############################################################################ | 100%
qtawesome-0.6.0      | 671 KB    | ############################################################################ | 100%
cython-0.29.13       | 1.8 MB    | ############################################################################ | 100%
mkl_random-1.1.0     | 232 KB    | ############################################################################ | 100%
numpy-1.16.5         | 50 KB     | ############################################################################ | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: - DEBUG menuinst_win32:__init__(199): Menu: name: 'Anaconda${PY_VER} ${PLATFORM}', prefix: 'C:\Users\username\AppData\Local\Continuum\anaconda3', env_name: 'None', mode: 'user', used_mode: 'user'
DEBUG menuinst_win32:create(323): Shortcut cmd is C:\Users\username\AppData\Local\Continuum\anaconda3\python.exe, args are ['C:\\Users\\username\\AppData\\Local\\Continuum\\anaconda3\\cwp.py', 'C:\\Users\\username\\AppData\\Local\\Continuum\\anaconda3', 'C:\\Users\\username\\AppData\\Local\\Continuum\\anaconda3\\python.exe', 'C:\\Users\\username\\AppData\\Local\\Continuum\\anaconda3\\Scripts\\jupyter-notebook-script.py', '"%USERPROFILE%/"']
done
Rolling back transaction: done

AssertionError()
()
AssertionError()
AssertionError()

(base) PS C:\> conda list
Error processing line 1 of C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\matplotlib-3.1.0-py3.7-nspkg.pth:

  Traceback (most recent call last):
    File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site.py", line 168, in addpackage
      exec(line)
    File "<string>", line 1, in <module>
    File "<frozen importlib._bootstrap>", line 580, in module_from_spec
  AttributeError: 'NoneType' object has no attribute 'loader'

Remainder of file ignored
Traceback (most recent call last):
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1062, in __call__
    return func(*args, **kwargs)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\conda_argparse.py", line 80, in do_call
    module = import_module(relative_mod, __name__.rsplit('.', 1)[0])
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\importlib\__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\main_list.py", line 14, in <module>
    from ..core.prefix_data import PrefixData
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\prefix_data.py", line 24, in <module>
    from ..gateways.disk.create import write_as_json_to_file
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\gateways\disk\create.py", line 17, in <module>
    import conda_package_handling.api
ModuleNotFoundError: No module named 'conda_package_handling'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\Scripts\conda-script.py", line 12, in <module>
    sys.exit(main())
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\main.py", line 150, in main
    return conda_exception_handler(_main, *args, **kwargs)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1354, in conda_exception_handler
    return_value = exception_handler(func, *args, **kwargs)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1065, in __call__
    return self.handle_exception(exc_val, exc_tb)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1109, in handle_exception
    return self.handle_unexpected_exception(exc_val, exc_tb)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1120, in handle_unexpected_exception
    self.print_unexpected_error_report(error_report)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1190, in print_unexpected_error_report
    from .cli.main_info import get_env_vars_str, get_main_info_str
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\main_info.py", line 19, in <module>
    from ..core.index import _supplement_index_with_system
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\index.py", line 9, in <module>
    from .package_cache_data import PackageCacheData
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\package_cache_data.py", line 15, in <module>
    from conda_package_handling.api import InvalidArchiveError
ModuleNotFoundError: No module named 'conda_package_handling'
(base) PS C:\> conda update conda
Error processing line 1 of C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\matplotlib-3.1.0-py3.7-nspkg.pth:

  Traceback (most recent call last):
    File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site.py", line 168, in addpackage
      exec(line)
    File "<string>", line 1, in <module>
    File "<frozen importlib._bootstrap>", line 580, in module_from_spec
  AttributeError: 'NoneType' object has no attribute 'loader'

Remainder of file ignored
Traceback (most recent call last):
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1062, in __call__
    return func(*args, **kwargs)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\conda_argparse.py", line 80, in do_call
    module = import_module(relative_mod, __name__.rsplit('.', 1)[0])
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\importlib\__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\main_update.py", line 8, in <module>
    from .install import install
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\install.py", line 19, in <module>
    from ..core.index import calculate_channel_urls, get_index
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\index.py", line 9, in <module>
    from .package_cache_data import PackageCacheData
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\package_cache_data.py", line 15, in <module>
    from conda_package_handling.api import InvalidArchiveError
ModuleNotFoundError: No module named 'conda_package_handling'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\Scripts\conda-script.py", line 12, in <module>
    sys.exit(main())
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\main.py", line 150, in main
    return conda_exception_handler(_main, *args, **kwargs)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1354, in conda_exception_handler
    return_value = exception_handler(func, *args, **kwargs)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1065, in __call__
    return self.handle_exception(exc_val, exc_tb)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1109, in handle_exception
    return self.handle_unexpected_exception(exc_val, exc_tb)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1120, in handle_unexpected_exception
    self.print_unexpected_error_report(error_report)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1190, in print_unexpected_error_report
    from .cli.main_info import get_env_vars_str, get_main_info_str
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\main_info.py", line 19, in <module>
    from ..core.index import _supplement_index_with_system
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\index.py", line 9, in <module>
    from .package_cache_data import PackageCacheData
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\package_cache_data.py", line 15, in <module>
    from conda_package_handling.api import InvalidArchiveError
ModuleNotFoundError: No module named 'conda_package_handling'
(base) PS C:\> conda env list
Error processing line 1 of C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\matplotlib-3.1.0-py3.7-nspkg.pth:

  Traceback (most recent call last):
    File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site.py", line 168, in addpackage
      exec(line)
    File "<string>", line 1, in <module>
    File "<frozen importlib._bootstrap>", line 580, in module_from_spec
  AttributeError: 'NoneType' object has no attribute 'loader'

Remainder of file ignored
Error processing line 1 of C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\matplotlib-3.1.0-py3.7-nspkg.pth:

  Traceback (most recent call last):
    File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site.py", line 168, in addpackage
      exec(line)
    File "<string>", line 1, in <module>
    File "<frozen importlib._bootstrap>", line 580, in module_from_spec
  AttributeError: 'NoneType' object has no attribute 'loader'

Remainder of file ignored
Traceback (most recent call last):
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\Scripts\conda-env-script.py", line 5, in <module>
    from conda_env.cli.main import main
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda_env\cli\main.py", line 39, in <module>
    from . import main_create
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda_env\cli\main_create.py", line 12, in <module>
    from conda.cli import install as cli_install
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\install.py", line 19, in <module>
    from ..core.index import calculate_channel_urls, get_index
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\index.py", line 9, in <module>
    from .package_cache_data import PackageCacheData
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\package_cache_data.py", line 15, in <module>
    from conda_package_handling.api import InvalidArchiveError
ModuleNotFoundError: No module named 'conda_package_handling'
(base) PS C:\> conda install anaconda
Error processing line 1 of C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\matplotlib-3.1.0-py3.7-nspkg.pth:

  Traceback (most recent call last):
    File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site.py", line 168, in addpackage
      exec(line)
    File "<string>", line 1, in <module>
    File "<frozen importlib._bootstrap>", line 580, in module_from_spec
  AttributeError: 'NoneType' object has no attribute 'loader'

Remainder of file ignored
Traceback (most recent call last):
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1062, in __call__
    return func(*args, **kwargs)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\conda_argparse.py", line 80, in do_call
    module = import_module(relative_mod, __name__.rsplit('.', 1)[0])
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\importlib\__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\main_install.py", line 8, in <module>
    from .install import install
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\install.py", line 19, in <module>
    from ..core.index import calculate_channel_urls, get_index
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\index.py", line 9, in <module>
    from .package_cache_data import PackageCacheData
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\package_cache_data.py", line 15, in <module>
    from conda_package_handling.api import InvalidArchiveError
ModuleNotFoundError: No module named 'conda_package_handling'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\Scripts\conda-script.py", line 12, in <module>
    sys.exit(main())
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\main.py", line 150, in main
    return conda_exception_handler(_main, *args, **kwargs)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1354, in conda_exception_handler
    return_value = exception_handler(func, *args, **kwargs)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1065, in __call__
    return self.handle_exception(exc_val, exc_tb)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1109, in handle_exception
    return self.handle_unexpected_exception(exc_val, exc_tb)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1120, in handle_unexpected_exception
    self.print_unexpected_error_report(error_report)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1190, in print_unexpected_error_report
    from .cli.main_info import get_env_vars_str, get_main_info_str
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\main_info.py", line 19, in <module>
    from ..core.index import _supplement_index_with_system
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\index.py", line 9, in <module>
    from .package_cache_data import PackageCacheData
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\package_cache_data.py", line 15, in <module>
    from conda_package_handling.api import InvalidArchiveError
ModuleNotFoundError: No module named 'conda_package_handling'
(base) PS C:\> conda update --all
Error processing line 1 of C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\matplotlib-3.1.0-py3.7-nspkg.pth:

  Traceback (most recent call last):
    File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site.py", line 168, in addpackage
      exec(line)
    File "<string>", line 1, in <module>
    File "<frozen importlib._bootstrap>", line 580, in module_from_spec
  AttributeError: 'NoneType' object has no attribute 'loader'

Remainder of file ignored
Traceback (most recent call last):
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1062, in __call__
    return func(*args, **kwargs)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\conda_argparse.py", line 80, in do_call
    module = import_module(relative_mod, __name__.rsplit('.', 1)[0])
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\importlib\__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\main_update.py", line 8, in <module>
    from .install import install
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\install.py", line 19, in <module>
    from ..core.index import calculate_channel_urls, get_index
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\index.py", line 9, in <module>
    from .package_cache_data import PackageCacheData
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\package_cache_data.py", line 15, in <module>
    from conda_package_handling.api import InvalidArchiveError
ModuleNotFoundError: No module named 'conda_package_handling'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\Scripts\conda-script.py", line 12, in <module>
    sys.exit(main())
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\main.py", line 150, in main
    return conda_exception_handler(_main, *args, **kwargs)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1354, in conda_exception_handler
    return_value = exception_handler(func, *args, **kwargs)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1065, in __call__
    return self.handle_exception(exc_val, exc_tb)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1109, in handle_exception
    return self.handle_unexpected_exception(exc_val, exc_tb)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1120, in handle_unexpected_exception
    self.print_unexpected_error_report(error_report)
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\exceptions.py", line 1190, in print_unexpected_error_report
    from .cli.main_info import get_env_vars_str, get_main_info_str
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\cli\main_info.py", line 19, in <module>
    from ..core.index import _supplement_index_with_system
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\index.py", line 9, in <module>
    from .package_cache_data import PackageCacheData
  File "C:\Users\username\AppData\Local\Continuum\anaconda3\lib\site-packages\conda\core\package_cache_data.py", line 15, in <module>
    from conda_package_handling.api import InvalidArchiveError
ModuleNotFoundError: No module named 'conda_package_handling'

(base) PS C:\>
(base) PS C:\>

asukumari on 3 Oct 2019

👍3

I've also run into this problem...

pjohno on 15 Oct 2019

I just ran into the same problem on Ubuntu 18.04.3 LTS after updating with conda update -n root conda. The core python installation still seems to work, but conda is currently unusable.

gbrookshire on 28 Oct 2019

I have the same problem

theSekyi on 31 Oct 2019

I also just had this happen

sandormatyi on 31 Oct 2019

Me too

Roverzed on 2 Nov 2019

@asukumari

I had exact same issue. Below is something working on my end:

Download a replacement package here:
https://anaconda.org/anaconda/conda-package-handling/files
Uncompress conda_package_handling and conda_package_handling-1.6.0.dist-info to ../anaconda/lib/python3.6/site-package
type: conda install anaconda
type: conda update conda

kikoland on 6 Nov 2019

👍1

your workaround worked partially, @kikoland - thank you!

step 2 needs explanation and the listed target directory is incorrect, should be "site-packages".

To make it easier to others, with python 3.6 on linux-64 and anaconda located at ~/anaconda3, this is what I had to do:

cd /tmp
wget https://anaconda.org/anaconda/conda-package-handling/1.6.0/download/linux-64/conda-package-handling-1.6.0-py37h7b6447c_0.tar.bz2
tar -xvjf conda-package-handling-1.6.0-py37h7b6447c_0.tar.bz2
cp -r lib/python3.6/site-packages/* ~/anaconda3/lib/python3.6/site-packages
conda install anaconda
conda update conda

you will have to adjust things for a different python, os, etc.

except afterwards, it is still broken:

conda update -n base -c defaults conda
[...]
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(637): An error occurred while installing package 'None'.
AssertionError()
Attempting to roll back.

Rolling back transaction: done

AssertionError()
()
AssertionError()
AssertionError()

bummer :( had to wipe out anaconda and reinstall from scratch.

it is nuts that 5 months after the report the package is still broken.

stas00 on 16 Nov 2019

👍2

Broken for me as well. Unfortunately, it has been my experience for several years that updating the base environment is extremely dangerous and more frequently than not, it results in a broken conda and requires full reinstallation.

isarandi on 21 Nov 2019

😕1 👍1

Another report for a broken conda environment after: conda update -n base -c defaults conda

Wanted to create a new environment on my Ubuntu 18.04 system, and got this information:

Collecting package metadata (repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.7.10
  latest version: 4.7.12

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /home/*user*/anaconda3/envs/hdf5access



Proceed ([y]/n)? n

So I cancelled my env creation and ran: conda update -n base -c defaults conda
This broke whole Anaconda for me. Below the full output log.

Full install log (CLICK ME)

conda update -n base -c defaults conda
Collecting package metadata (repodata.json): done
Solving environment: \ 
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:

  - defaults/linux-64::mkl_random==1.0.1=py37h4414c95_1
  - defaults/linux-64::odo==0.5.1=py37_0
  - defaults/linux-64::widgetsnbextension==3.4.1=py37_0
  - defaults/linux-64::sphinx==1.7.9=py37_0
  - defaults/linux-64::blaze==0.11.3=py37_0
  - defaults/linux-64::_ipyw_jlab_nb_ext_conf==0.1.0=py37_0
  - defaults/linux-64::scipy==1.1.0=py37hfa4b5c9_1
  - defaults/linux-64::pandas==0.23.4=py37h04863e7_0
  - defaults/linux-64::numba==0.39.0=py37h04863e7_0
  - defaults/linux-64::numexpr==2.6.8=py37hd89afb7_0
  - defaults/linux-64::pytables==3.4.4=py37ha205bf6_0
  - defaults/linux-64::statsmodels==0.9.0=py37h035aef0_0
  - defaults/linux-64::scikit-image==0.14.0=py37hf484d3e_1
  - defaults/linux-64::datashape==0.5.4=py37_1
  - defaults/linux-64::astropy==3.0.4=py37h14c3975_0
  - defaults/linux-64::pytest-astropy==0.4.0=py37_0
  - defaults/linux-64::patsy==0.5.0=py37_0
  - defaults/linux-64::pywavelets==1.0.0=py37hdd07704_0
  - defaults/linux-64::bottleneck==1.2.1=py37h035aef0_1
  - defaults/linux-64::mkl-service==1.1.2=py37h90e4bf4_5
  - defaults/linux-64::numpy-base==1.15.1=py37h81de0dd_0
  - defaults/linux-64::dask==0.19.1=py37_0
  - defaults/linux-64::matplotlib==2.2.3=py37hb69df0a_0
  - defaults/linux-64::jupyter==1.0.0=py37_7
  - defaults/linux-64::nbformat==4.4.0=py37_0
  - defaults/linux-64::anaconda-navigator==1.9.2=py37_0
  - defaults/linux-64::spyder==3.3.1=py37_1
  - defaults/linux-64::pytest-arraydiff==0.2=py37h39e3cac_0
  - defaults/linux-64::anaconda==5.3.0=py37_0
  - defaults/linux-64::numpy==1.15.1=py37h1d66e8a_0
  - defaults/linux-64::seaborn==0.9.0=py37_0
  - defaults/linux-64::mkl_fft==1.0.4=py37h4414c95_1
  - defaults/linux-64::anaconda-project==0.8.2=py37_0
  - defaults/linux-64::jupyterlab==0.34.9=py37_0
  - defaults/linux-64::bokeh==0.13.0=py37_0
  - defaults/linux-64::anaconda-client==1.7.2=py37_0
  - defaults/linux-64::ipywidgets==7.4.1=py37_0
  - defaults/linux-64::jupyterlab_launcher==0.13.1=py37_0
  - defaults/linux-64::h5py==2.8.0=py37h989c5e5_3
  - defaults/linux-64::numpydoc==0.8.0=py37_0
  - defaults/linux-64::scikit-learn==0.19.2=py37h4989274_0
  - defaults/linux-64::conda-build==3.15.1=py37_0
  - defaults/linux-64::bkcharts==0.2=py37_0
  - defaults/linux-64::nbconvert==5.4.0=py37_1
  - defaults/linux-64::imageio==2.4.1=py37_0
  - defaults/linux-64::pytest-doctestplus==0.1.3=py37_0
  - defaults/linux-64::flask-cors==3.0.6=py37_0
  - defaults/linux-64::notebook==5.6.0=py37_0
done

## Package Plan ##

  environment location: /home/*user*/anaconda3

  added / updated specs:
    - conda


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _anaconda_depends-2019.03  |           py37_0           5 KB
    anaconda-custom            |           py37_1           3 KB
    asn1crypto-1.2.0           |           py37_0         162 KB
    astroid-2.3.3              |           py37_0         292 KB
    atomicwrites-1.3.0         |           py37_1          13 KB
    attrs-19.3.0               |             py_0          39 KB
    babel-2.7.0                |             py_0         5.8 MB
    backports-1.0              |             py_2         139 KB
    backports.os-0.1.1         |           py37_0          15 KB
    beautifulsoup4-4.8.1       |           py37_0         153 KB
    bitarray-1.1.0             |   py37h7b6447c_0          67 KB
    blosc-1.16.3               |       hd408876_0          82 KB
    certifi-2019.9.11          |           py37_0         154 KB
    cffi-1.13.2                |   py37h2e261b9_0         225 KB
    click-7.0                  |           py37_0         118 KB
    cloudpickle-1.2.2          |             py_0          29 KB
    colorama-0.4.1             |           py37_0          24 KB
    conda-4.7.12               |           py37_0         3.0 MB
    conda-package-handling-1.6.0|   py37h7b6447c_0         872 KB
    contextlib2-0.6.0.post1    |             py_0          16 KB
    cryptography-2.8           |   py37h1ba5d50_0         612 KB
    curl-7.67.0                |       hbc83047_0         145 KB
    cython-0.29.14             |   py37he6710b0_0         2.2 MB
    cytoolz-0.10.1             |   py37h7b6447c_0         437 KB
    dbus-1.13.12               |       h746ee38_0         611 KB
    decorator-4.4.1            |             py_0          13 KB
    distributed-1.28.1         |           py37_0         861 KB
    docutils-0.15.2            |           py37_0         736 KB
    fastcache-1.1.0            |   py37h7b6447c_0          31 KB
    filelock-3.0.12            |             py_0          12 KB
    flask-1.1.1                |             py_0          73 KB
    gevent-1.4.0               |   py37h7b6447c_0         2.5 MB
    glib-2.63.1                |       h5a9c865_0         3.4 MB
    glob2-0.7                  |             py_0          14 KB
    heapdict-1.0.1             |             py_0           9 KB
    importlib_metadata-0.23    |           py37_0          43 KB
    ipykernel-5.1.3            |   py37h39e3cac_0         167 KB
    ipython-7.9.0              |   py37h39e3cac_0         1.1 MB
    isort-4.3.21               |           py37_0          68 KB
    itsdangerous-1.1.0         |           py37_0          27 KB
    jdcal-1.4.1                |             py_0          11 KB
    jedi-0.15.1                |           py37_0         713 KB
    jeepney-0.4.1              |             py_0          21 KB
    jinja2-2.10.3              |             py_0          95 KB
    json5-0.8.5                |             py_0          25 KB
    jsonschema-3.2.0           |           py37_0          93 KB
    jupyter_client-5.3.4       |           py37_0         136 KB
    jupyter_console-6.0.0      |           py37_0          35 KB
    jupyter_core-4.6.1         |           py37_0          74 KB
    jupyterlab_server-1.0.6    |             py_0          26 KB
    keyring-19.2.0             |           py37_0          56 KB
    lazy-object-proxy-1.4.3    |   py37h7b6447c_0          31 KB
    libcurl-7.67.0             |       h20c2e04_0         576 KB
    liblief-0.9.0              |       h7725739_2         4.4 MB
    libssh2-1.8.2              |       h1ba5d50_0         250 KB
    libtiff-4.1.0              |       h2733197_0         589 KB
    libtool-2.4.6              |       h7b6447c_5         513 KB
    lxml-4.4.1                 |   py37hefd8a0e_0         1.6 MB
    more-itertools-7.2.0       |           py37_0          99 KB
    mpmath-1.1.0               |           py37_0         957 KB
    networkx-2.4               |             py_0         1.2 MB
    nltk-3.4.5                 |           py37_0         2.1 MB
    openpyxl-3.0.1             |             py_0         158 KB
    packaging-19.2             |             py_0          30 KB
    parso-0.5.1                |             py_0          68 KB
    partd-1.1.0                |             py_0          20 KB
    patchelf-0.10              |       he6710b0_0          78 KB
    path.py-12.0.2             |             py_0          23 KB
    pathlib2-2.3.5             |           py37_0          37 KB
    pillow-6.2.1               |   py37h34e0f95_0         643 KB
    pip-19.3.1                 |           py37_0         1.9 MB
    pkginfo-1.5.0.1            |           py37_0          43 KB
    pluggy-0.13.1              |           py37_0          32 KB
    prometheus_client-0.7.1    |             py_0          42 KB
    prompt_toolkit-2.0.10      |             py_0         227 KB
    psutil-5.6.5               |   py37h7b6447c_0         328 KB
    py-1.8.0                   |           py37_0         140 KB
    py-lief-0.9.0              |   py37h7725739_2         1.5 MB
    pycodestyle-2.5.0          |           py37_0          60 KB
    pycurl-7.43.0.3            |   py37h1ba5d50_0          70 KB
    pyflakes-2.1.1             |           py37_0         105 KB
    pygments-2.4.2             |             py_0         664 KB
    pylint-2.4.4               |           py37_0         432 KB
    pyodbc-4.0.27              |   py37he6710b0_0          70 KB
    pyopenssl-19.1.0           |           py37_0          87 KB
    pyparsing-2.4.5            |             py_0          62 KB
    pyrsistent-0.15.6          |   py37h7b6447c_0          93 KB
    pysocks-1.7.1              |           py37_0          30 KB
    pytest-5.3.0               |           py37_0         379 KB
    pytest-openfiles-0.4.0     |             py_0          10 KB
    pytest-remotedata-0.3.2    |           py37_0          15 KB
    python-dateutil-2.8.1      |             py_0         224 KB
    pytz-2019.3                |             py_0         231 KB
    pyyaml-5.1.2               |   py37h7b6447c_0         189 KB
    pyzmq-18.1.0               |   py37he6710b0_0         498 KB
    qtawesome-0.6.0            |             py_0         671 KB
    qtconsole-4.6.0            |             py_0          95 KB
    qtpy-1.9.0                 |             py_0          39 KB
    rope-0.14.0                |             py_0         113 KB
    secretstorage-3.1.1        |           py37_0          24 KB
    setuptools-42.0.1          |           py37_0         670 KB
    six-1.13.0                 |           py37_0          27 KB
    snowballstemmer-2.0.0      |             py_0          58 KB
    sortedcollections-1.1.2    |           py37_0          18 KB
    sortedcontainers-2.1.0     |           py37_0          45 KB
    soupsieve-1.9.5            |           py37_0          61 KB
    sphinxcontrib-websupport-1.1.2|             py_0          35 KB
    spyder-kernels-0.5.2       |           py37_0          69 KB
    sqlalchemy-1.3.11          |   py37h7b6447c_0         1.8 MB
    sympy-1.4                  |           py37_0         9.7 MB
    tbb-2019.8                 |       hfd86e86_0         1.4 MB
    tbb4py-2019.8              |   py37hfd86e86_0         253 KB
    tblib-1.5.0                |             py_0          14 KB
    terminado-0.8.3            |           py37_0          25 KB
    testpath-0.4.4             |             py_0          88 KB
    toolz-0.10.0               |             py_0          50 KB
    tqdm-4.39.0                |             py_0          52 KB
    traitlets-4.3.3            |           py37_0         138 KB
    werkzeug-0.16.0            |             py_0         255 KB
    wheel-0.33.6               |           py37_0          40 KB
    wrapt-1.11.2               |   py37h7b6447c_0          49 KB
    wurlitzer-2.0.0            |           py37_0          14 KB
    xlrd-1.2.0                 |           py37_0         186 KB
    xlsxwriter-1.2.6           |             py_0         107 KB
    zict-1.0.0                 |             py_0          12 KB
    zipp-0.6.0                 |             py_0           9 KB
    ------------------------------------------------------------
                                           Total:        62.0 MB

The following NEW packages will be INSTALLED:

  _anaconda_depends  pkgs/main/linux-64::_anaconda_depends-2019.03-py37_0
  alabaster          pkgs/main/linux-64::alabaster-0.7.12-py37_0
  asn1crypto         pkgs/main/linux-64::asn1crypto-1.2.0-py37_0
  astroid            pkgs/main/linux-64::astroid-2.3.3-py37_0
  atomicwrites       pkgs/main/linux-64::atomicwrites-1.3.0-py37_1
  attrs              pkgs/main/noarch::attrs-19.3.0-py_0
  babel              pkgs/main/noarch::babel-2.7.0-py_0
  backports          pkgs/main/noarch::backports-1.0-py_2
  backports.os       pkgs/main/linux-64::backports.os-0.1.1-py37_0
  beautifulsoup4     pkgs/main/linux-64::beautifulsoup4-4.8.1-py37_0
  bitarray           pkgs/main/linux-64::bitarray-1.1.0-py37h7b6447c_0
  bleach             pkgs/main/linux-64::bleach-3.1.0-py37_0
  blosc              pkgs/main/linux-64::blosc-1.16.3-hd408876_0
  cffi               pkgs/main/linux-64::cffi-1.13.2-py37h2e261b9_0
  click              pkgs/main/linux-64::click-7.0-py37_0
  cloudpickle        pkgs/main/noarch::cloudpickle-1.2.2-py_0
  colorama           pkgs/main/linux-64::colorama-0.4.1-py37_0
  conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.0-py37h7b6447c_0
  contextlib2        pkgs/main/noarch::contextlib2-0.6.0.post1-py_0
  cryptography       pkgs/main/linux-64::cryptography-2.8-py37h1ba5d50_0
  curl               pkgs/main/linux-64::curl-7.67.0-hbc83047_0
  cython             pkgs/main/linux-64::cython-0.29.14-py37he6710b0_0
  cytoolz            pkgs/main/linux-64::cytoolz-0.10.1-py37h7b6447c_0
  dbus               pkgs/main/linux-64::dbus-1.13.12-h746ee38_0
  decorator          pkgs/main/noarch::decorator-4.4.1-py_0
  defusedxml         pkgs/main/noarch::defusedxml-0.6.0-py_0
  distributed        pkgs/main/linux-64::distributed-1.28.1-py37_0
  docutils           pkgs/main/linux-64::docutils-0.15.2-py37_0
  entrypoints        pkgs/main/linux-64::entrypoints-0.3-py37_0
  fastcache          pkgs/main/linux-64::fastcache-1.1.0-py37h7b6447c_0
  filelock           pkgs/main/noarch::filelock-3.0.12-py_0
  flask              pkgs/main/noarch::flask-1.1.1-py_0
  gevent             pkgs/main/linux-64::gevent-1.4.0-py37h7b6447c_0
  glib               pkgs/main/linux-64::glib-2.63.1-h5a9c865_0
  glob2              pkgs/main/noarch::glob2-0.7-py_0
  graphite2          pkgs/main/linux-64::graphite2-1.3.13-h23475e2_0
  heapdict           pkgs/main/noarch::heapdict-1.0.1-py_0
  importlib_metadata pkgs/main/linux-64::importlib_metadata-0.23-py37_0
  intel-openmp       pkgs/main/linux-64::intel-openmp-2019.4-243
  ipykernel          pkgs/main/linux-64::ipykernel-5.1.3-py37h39e3cac_0
  ipython            pkgs/main/linux-64::ipython-7.9.0-py37h39e3cac_0
  isort              pkgs/main/linux-64::isort-4.3.21-py37_0
  itsdangerous       pkgs/main/linux-64::itsdangerous-1.1.0-py37_0
  jdcal              pkgs/main/noarch::jdcal-1.4.1-py_0
  jedi               pkgs/main/linux-64::jedi-0.15.1-py37_0
  jeepney            pkgs/main/noarch::jeepney-0.4.1-py_0
  jinja2             pkgs/main/noarch::jinja2-2.10.3-py_0
  json5              pkgs/main/noarch::json5-0.8.5-py_0
  jsonschema         pkgs/main/linux-64::jsonschema-3.2.0-py37_0
  jupyter_client     pkgs/main/linux-64::jupyter_client-5.3.4-py37_0
  jupyter_console    pkgs/main/linux-64::jupyter_console-6.0.0-py37_0
  jupyter_core       pkgs/main/linux-64::jupyter_core-4.6.1-py37_0
  jupyterlab_server  pkgs/main/noarch::jupyterlab_server-1.0.6-py_0
  keyring            pkgs/main/linux-64::keyring-19.2.0-py37_0
  kiwisolver         pkgs/main/linux-64::kiwisolver-1.1.0-py37he6710b0_0
  lazy-object-proxy  pkgs/main/linux-64::lazy-object-proxy-1.4.3-py37h7b6447c_0
  libcurl            pkgs/main/linux-64::libcurl-7.67.0-h20c2e04_0
  liblief            pkgs/main/linux-64::liblief-0.9.0-h7725739_2
  libpng             pkgs/main/linux-64::libpng-1.6.37-hbc83047_0
  libssh2            pkgs/main/linux-64::libssh2-1.8.2-h1ba5d50_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  libtiff            pkgs/main/linux-64::libtiff-4.1.0-h2733197_0
  libtool            pkgs/main/linux-64::libtool-2.4.6-h7b6447c_5
  libxslt            pkgs/main/linux-64::libxslt-1.1.33-h7d1a2b0_0
  lxml               pkgs/main/linux-64::lxml-4.4.1-py37hefd8a0e_0
  markupsafe         pkgs/main/linux-64::markupsafe-1.1.1-py37h7b6447c_0
  mistune            pkgs/main/linux-64::mistune-0.8.4-py37h7b6447c_0
  mkl                pkgs/main/linux-64::mkl-2018.0.3-1
  more-itertools     pkgs/main/linux-64::more-itertools-7.2.0-py37_0
  mpmath             pkgs/main/linux-64::mpmath-1.1.0-py37_0
  msgpack-python     pkgs/main/linux-64::msgpack-python-0.6.1-py37hfd86e86_1
  networkx           pkgs/main/noarch::networkx-2.4-py_0
  nltk               pkgs/main/linux-64::nltk-3.4.5-py37_0
  openpyxl           pkgs/main/noarch::openpyxl-3.0.1-py_0
  packaging          pkgs/main/noarch::packaging-19.2-py_0
  parso              pkgs/main/noarch::parso-0.5.1-py_0
  partd              pkgs/main/noarch::partd-1.1.0-py_0
  patchelf           pkgs/main/linux-64::patchelf-0.10-he6710b0_0
  path.py            pkgs/main/noarch::path.py-12.0.2-py_0
  pathlib2           pkgs/main/linux-64::pathlib2-2.3.5-py37_0
  pcre               pkgs/main/linux-64::pcre-8.43-he6710b0_0
  pexpect            pkgs/main/linux-64::pexpect-4.7.0-py37_0
  pickleshare        pkgs/main/linux-64::pickleshare-0.7.5-py37_0
  pillow             pkgs/main/linux-64::pillow-6.2.1-py37h34e0f95_0
  pip                pkgs/main/linux-64::pip-19.3.1-py37_0
  pixman             pkgs/main/linux-64::pixman-0.38.0-h7b6447c_0
  pkginfo            pkgs/main/linux-64::pkginfo-1.5.0.1-py37_0
  pluggy             pkgs/main/linux-64::pluggy-0.13.1-py37_0
  prometheus_client  pkgs/main/noarch::prometheus_client-0.7.1-py_0
  prompt_toolkit     pkgs/main/noarch::prompt_toolkit-2.0.10-py_0
  psutil             pkgs/main/linux-64::psutil-5.6.5-py37h7b6447c_0
  py                 pkgs/main/linux-64::py-1.8.0-py37_0
  py-lief            pkgs/main/linux-64::py-lief-0.9.0-py37h7725739_2
  pycodestyle        pkgs/main/linux-64::pycodestyle-2.5.0-py37_0
  pycurl             pkgs/main/linux-64::pycurl-7.43.0.3-py37h1ba5d50_0
  pyflakes           pkgs/main/linux-64::pyflakes-2.1.1-py37_0
  pygments           pkgs/main/noarch::pygments-2.4.2-py_0
  pylint             pkgs/main/linux-64::pylint-2.4.4-py37_0
  pyodbc             pkgs/main/linux-64::pyodbc-4.0.27-py37he6710b0_0
  pyopenssl          pkgs/main/linux-64::pyopenssl-19.1.0-py37_0
  pyparsing          pkgs/main/noarch::pyparsing-2.4.5-py_0
  pyrsistent         pkgs/main/linux-64::pyrsistent-0.15.6-py37h7b6447c_0
  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py37_0
  pytest             pkgs/main/linux-64::pytest-5.3.0-py37_0
  pytest-openfiles   pkgs/main/noarch::pytest-openfiles-0.4.0-py_0
  pytest-remotedata  pkgs/main/linux-64::pytest-remotedata-0.3.2-py37_0
  python-dateutil    pkgs/main/noarch::python-dateutil-2.8.1-py_0
  pytz               pkgs/main/noarch::pytz-2019.3-py_0
  pyyaml             pkgs/main/linux-64::pyyaml-5.1.2-py37h7b6447c_0
  pyzmq              pkgs/main/linux-64::pyzmq-18.1.0-py37he6710b0_0
  qtawesome          pkgs/main/noarch::qtawesome-0.6.0-py_0
  qtconsole          pkgs/main/noarch::qtconsole-4.6.0-py_0
  qtpy               pkgs/main/noarch::qtpy-1.9.0-py_0
  rope               pkgs/main/noarch::rope-0.14.0-py_0
  secretstorage      pkgs/main/linux-64::secretstorage-3.1.1-py37_0
  setuptools         pkgs/main/linux-64::setuptools-42.0.1-py37_0
  six                pkgs/main/linux-64::six-1.13.0-py37_0
  snowballstemmer    pkgs/main/noarch::snowballstemmer-2.0.0-py_0
  sortedcollections  pkgs/main/linux-64::sortedcollections-1.1.2-py37_0
  sortedcontainers   pkgs/main/linux-64::sortedcontainers-2.1.0-py37_0
  soupsieve          pkgs/main/linux-64::soupsieve-1.9.5-py37_0
  sphinxcontrib-web~ pkgs/main/noarch::sphinxcontrib-websupport-1.1.2-py_0
  spyder-kernels     pkgs/main/linux-64::spyder-kernels-0.5.2-py37_0
  sqlalchemy         pkgs/main/linux-64::sqlalchemy-1.3.11-py37h7b6447c_0
  sqlite             pkgs/main/linux-64::sqlite-3.30.1-h7b6447c_0
  sympy              pkgs/main/linux-64::sympy-1.4-py37_0
  tbb                pkgs/main/linux-64::tbb-2019.8-hfd86e86_0
  tbb4py             pkgs/main/linux-64::tbb4py-2019.8-py37hfd86e86_0
  tblib              pkgs/main/noarch::tblib-1.5.0-py_0
  terminado          pkgs/main/linux-64::terminado-0.8.3-py37_0
  testpath           pkgs/main/noarch::testpath-0.4.4-py_0
  toolz              pkgs/main/noarch::toolz-0.10.0-py_0
  tornado            pkgs/main/linux-64::tornado-5.1.1-py37h7b6447c_0
  tqdm               pkgs/main/noarch::tqdm-4.39.0-py_0
  traitlets          pkgs/main/linux-64::traitlets-4.3.3-py37_0
  werkzeug           pkgs/main/noarch::werkzeug-0.16.0-py_0
  wheel              pkgs/main/linux-64::wheel-0.33.6-py37_0
  wrapt              pkgs/main/linux-64::wrapt-1.11.2-py37h7b6447c_0
  wurlitzer          pkgs/main/linux-64::wurlitzer-2.0.0-py37_0
  xlrd               pkgs/main/linux-64::xlrd-1.2.0-py37_0
  xlsxwriter         pkgs/main/noarch::xlsxwriter-1.2.6-py_0
  zeromq             pkgs/main/linux-64::zeromq-4.3.1-he6710b0_3
  zict               pkgs/main/noarch::zict-1.0.0-py_0
  zipp               pkgs/main/noarch::zipp-0.6.0-py_0

The following packages will be UPDATED:

  ca-certificates                               2019.5.15-0 --> 2019.10.16-0
  certifi                                  2019.6.16-py37_1 --> 2019.9.11-py37_0
  conda                                       4.7.10-py37_0 --> 4.7.12-py37_0
  openssl                                 1.1.1c-h7b6447c_1 --> 1.1.1d-h7b6447c_3

The following packages will be DOWNGRADED:

  anaconda                                     5.3.0-py37_0 --> custom-py37_1


Proceed ([y]/n)? y


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importlib_metadata-0 | 43 KB     | ################################################################################################# | 100% 
pyopenssl-19.1.0     | 87 KB     | ################################################################################################# | 100% 
xlsxwriter-1.2.6     | 107 KB    | ################################################################################################# | 100% 
pysocks-1.7.1        | 30 KB     | ################################################################################################# | 100% 
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werkzeug-0.16.0      | 255 KB    | ################################################################################################# | 100% 
pytest-openfiles-0.4 | 10 KB     | ################################################################################################# | 100% 
psutil-5.6.5         | 328 KB    | ################################################################################################# | 100% 
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dbus-1.13.12         | 611 KB    | ################################################################################################# | 100% 
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partd-1.1.0          | 20 KB     | ################################################################################################# | 100% 
pylint-2.4.4         | 432 KB    | ################################################################################################# | 100% 
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pyflakes-2.1.1       | 105 KB    | ################################################################################################# | 100% 
jupyter_core-4.6.1   | 74 KB     | ################################################################################################# | 100% 
setuptools-42.0.1    | 670 KB    | ################################################################################################# | 100% 
rope-0.14.0          | 113 KB    | ################################################################################################# | 100% 
heapdict-1.0.1       | 9 KB      | ################################################################################################# | 100% 
networkx-2.4         | 1.2 MB    | ################################################################################################# | 100% 
lxml-4.4.1           | 1.6 MB    | ################################################################################################# | 100% 
libcurl-7.67.0       | 576 KB    | ################################################################################################# | 100% 
atomicwrites-1.3.0   | 13 KB     | ################################################################################################# | 100% 
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lazy-object-proxy-1. | 31 KB     | ################################################################################################# | 100% 
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conda-4.7.12         | 3.0 MB    | ################################################################################################# | 100% 
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contextlib2-0.6.0.po | 16 KB     | ################################################################################################# | 100% 
pyparsing-2.4.5      | 62 KB     | ################################################################################################# | 100% 
cffi-1.13.2          | 225 KB    | ################################################################################################# | 100% 
liblief-0.9.0        | 4.4 MB    | ################################################################################################# | 100% 
colorama-0.4.1       | 24 KB     | ################################################################################################# | 100% 
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prompt_toolkit-2.0.1 | 227 KB    | ################################################################################################# | 100% 
pytz-2019.3          | 231 KB    | ################################################################################################# | 100% 
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ipykernel-5.1.3      | 167 KB    | ################################################################################################# | 100% 
packaging-19.2       | 30 KB     | ################################################################################################# | 100% 
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libtool-2.4.6        | 513 KB    | ################################################################################################# | 100% 
qtpy-1.9.0           | 39 KB     | ################################################################################################# | 100% 
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isort-4.3.21         | 68 KB     | ################################################################################################# | 100% 
tblib-1.5.0          | 14 KB     | ################################################################################################# | 100% 
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json5-0.8.5          | 25 KB     | ################################################################################################# | 100% 
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Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Rolling back transaction: done

AssertionError()
()
AssertionError()

Calling any conda command, like conda list now gives me:

conda list
Traceback (most recent call last):
  File "/home/*user*/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1062, in __call__
    return func(*args, **kwargs)
  File "/home/*user*/anaconda3/lib/python3.7/site-packages/conda/cli/main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "/home/*user*/anaconda3/lib/python3.7/site-packages/conda/cli/conda_argparse.py", line 80, in do_call
    module = import_module(relative_mod, __name__.rsplit('.', 1)[0])
  File "/home/*user*/anaconda3/lib/python3.7/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/home/*user*/anaconda3/lib/python3.7/site-packages/conda/cli/main_list.py", line 14, in <module>
    from ..core.prefix_data import PrefixData
  File "/home/*user*/anaconda3/lib/python3.7/site-packages/conda/core/prefix_data.py", line 24, in <module>
    from ..gateways.disk.create import write_as_json_to_file
  File "/home/*user*/anaconda3/lib/python3.7/site-packages/conda/gateways/disk/create.py", line 17, in <module>
    import conda_package_handling.api
ModuleNotFoundError: No module named 'conda_package_handling'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/*user*/anaconda3/bin/conda", line 13, in <module>
    sys.exit(main())
  File "/home/*user*/anaconda3/lib/python3.7/site-packages/conda/cli/main.py", line 150, in main
    return conda_exception_handler(_main, *args, **kwargs)
  File "/home/*user*/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1354, in conda_exception_handler
    return_value = exception_handler(func, *args, **kwargs)
  File "/home/*user*/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1065, in __call__
    return self.handle_exception(exc_val, exc_tb)
  File "/home/*user*/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1109, in handle_exception
    return self.handle_unexpected_exception(exc_val, exc_tb)
  File "/home/*user*/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1120, in handle_unexpected_exception
    self.print_unexpected_error_report(error_report)
  File "/home/*user*/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1190, in print_unexpected_error_report
    from .cli.main_info import get_env_vars_str, get_main_info_str
  File "/home/*user*/anaconda3/lib/python3.7/site-packages/conda/cli/main_info.py", line 19, in <module>
    from ..core.index import _supplement_index_with_system
  File "/home/*user*/anaconda3/lib/python3.7/site-packages/conda/core/index.py", line 9, in <module>
    from .package_cache_data import PackageCacheData
  File "/home/*user*/anaconda3/lib/python3.7/site-packages/conda/core/package_cache_data.py", line 15, in <module>
    from conda_package_handling.api import InvalidArchiveError
ModuleNotFoundError: No module named 'conda_package_handling'

NumesSanguis on 29 Nov 2019

I followed rgommers' comments (#8172 (comment)) which is slightly different from @Sieboldianus :

1. downloaded `Miniconda3-latest-Linux-x86_64.sh` from https://repo.continuum.io/miniconda/

2. `bash Miniconda3-latest-Linux-x86_64.sh`

3. "Do you wish the installer to initialize Miniconda3 by running conda init?"  **NO** If you choose this, I think the default environment when startup should be in miniconda3 but not the original anaconda3.

4. `cd ~/miniconda3/bin` This conda from miniconda3 should work perfectly without bugs.

5. Use the conda from miniconda3 to 'heal' your anaconda3. Like this:
   `./conda install --prefix ~/anaconda3/ ~/anaconda3/pkgs/conda_package_handling_XXX.tar.bz2`
   This should allow you to reinstall the packages that are missing in the error output of anaconda3.
   In my case, I reinstall `conda_package_handling`, `requests`, and `urllib3`.

6. Try your anaconda3 conda using `conda info` or `conda install PACKAGE`.

7. If you can get a normal output from `conda info`, you should be able to revert to previous version of conda using `conda install --revision`. Please see: http://blog.rtwilson.com/conda-revisions-letting-you-rollback-to-a-previous-version-of-your-environment/

Now everything is reverted back to the previous version. Hope this can be of any help!

This solution worked for me! Thank you @YichaoCaiDBS .

Additional info:

_1. Instead of Miniconda3-latest-Linux-x86_64.sh I downloaded Miniconda3-4.7.10-Linux-x86_64.sh, because that was my version of Anaconda before it broke.
_5. To find out what your XXX is, open a folder and navigate to ~/anaconda3/pkgs/. See there which *.tar.bz2 are available. I had to repeat this command twice, once for conda-package-handling (conda-package-handling-1.3.11-py37_0.tar.bz2) and once for six (six-1.13.0-py37_0.tar.bz2).
_7. In my case revision 9 was before my attempted base attempt, so I did: conda install --revision 9. Then the following output appeared:

conda install --revision 9

## Package Plan ##

  environment location: /home/*user*/anaconda3

  added / updated specs:
    - _ipyw_jlab_nb_ext_conf
    - anaconda-navigator
    - anaconda==5.3.0=py37_0
    - conda
    - conda-build
    - conda-package-handling[url=file:///home/*user*/anaconda3/pkgs/conda-package-handling-1.3.11-py37_0.tar.bz2]
    - navigator-updater
    - python=3
    - six[url=file:///home/*user*/anaconda3/pkgs/six-1.13.0-py37_0.tar.bz2]


The following packages will be SUPERSEDED by a higher-priority channel:

  conda-package-han~                              <unknown> --> pkgs/main
  six                          <unknown>::six-1.13.0-py37_0 --> pkgs/main::six-1.12.0-py37_0


Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

It seems like it is working again.

NumesSanguis on 29 Nov 2019

for my case after updating conda, my conda all env has been broken. my all module is couldn't be found, and tried conda clean / update other shit solutions but my modules are still unseen by conda. wow

sinramyeon on 18 Feb 2020

I uninstalled numpy in conda and now the whole environment is broken. Even running "conda" alone yields an error message.
AttributeError: module 'colorama' has no attribute 'init'.

This is why I avoid conda at all costs... Breaks year after year.

bscully27 on 9 Mar 2020

👍2

How long will it take for this issue to be solved?
I installed modules and after working for a while the modules are no longer installed. Now I can no longer install the module because of conflict with existing module which conda does not even recognize as installed

skmaingi on 24 Mar 2020

👍6

Also ran into these issues. It's been half a year now. I really think that this issue requires a higher priority...

Zethson on 16 Apr 2020

👍8 ❤2 👀1

sadly, it is 20/04/2020 and i just got the SAME PROBLEM. is it really something unsolvable? i really appreciate conda, super helpful. but the stability is quite weak point. i am always very afraid of installing some new package.. and here we go, again J

i use only conda-forge as a channel. i did update --all because there were 'inconsistencies' (i do not understand why there are again 'defaults' packages listed...) and now conda got into the 'conda_package_handling' problem.

perhaps i should keep 'defaults' as possible channel? thanks for updates on this 'forever issue'

espiritocz on 20 Apr 2020

👍1

I imported an old enviroment.yaml to start my new enviroment, this install gave me a message on pip but installed it anyways. When launching Jupiter notebook it resulted in errors described above. When I did a good old conda update --all it runs as expected. This might help some people out.

bglnelissen on 23 Apr 2020

Same problem here. I was installing pytorch and I ended up with the issue of a installation of the latest version of conda. And it tooked all my packages away. I think I will reinstall everything again.

danistenia on 28 Apr 2020

Updating failed for my case. Downgrading worked for me.

skmaingi on 28 Apr 2020

Okay, so I found the issue fix (at least for me - comment if it works for you).

How to fix it:

Download Colorama
Copy the "Colorama" from the download then replace the folder named "colorama" in C:\Program Files\Anaconda3\Libsite-packages

For all those that have issues with _"libarchive"_ try using the above steps but for that specific module instead.

I suspect this issue occurs because of (issue 8842)

TSH-Simon on 14 May 2020

This did not resolve the issue for me, giving any command in anaconda prompt results the same issue

Tharunmandadi on 17 Aug 2020

This did not resolve the issue for me, giving any command in anaconda prompt results the same issue

Try using pip to install rather than conda. If it helps, personally I've moved to pip as my manager and python directly without Anaconda. I haven't looked back since.

TSH-Simon on 19 Aug 2020

Conda: Conda is broken after update. No module named `conda_package_handling`

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