Fresh re-install of Anaconda fails - remove all conflicts between Anaconda and the system

Question

After ending up breaking my Anaconda environmaent during an update process (issue described here), I decided to try to reinstall Anaconda. However, despite hours of research and error seeking, I failed to install Anaconda.

My question is how I could put my system back into a state such that Anaconda does not conflict with my system.

Find details below.

My steps were as follows:

I uninstalled Anaconda.
I downloaded the recent version of Anaconda and installed it. Unfortunately, no executable for the Anaconda prompt was installed, neither did Anaconda appear in the start menu. The issue is partly addressed here
I uninstalled Anaconda and installed Miniconda.
Miniconda installed successfully. I installed anaconda-clean as suggested here and ran it.
I uninstalled Miniconda and made sure no python installation appeared in PATH.
I deleted registry keys referring to Python
I removed all directories from PATH that included files belonging to Qt5
I checked that neither Python nor Anaconda appear in AppData
I tried to install Anaconda again, with the same failure as above.
I uninstalled Anaconda and installed Miniconda.
I installed anaconda-navigator
I tried to install Glueviz, but failed
I removed resulting inconsistencies and installed packages one after the other
I ran into an issue installing ipykernel, full output below.

(base) C:\Users\Me>conda install ipykernel -v
Collecting package metadata: ...working... done
Solving environment: ...working... done
initializing UnlinkLinkTransaction with
  target_prefix: D:\_Programme\Anaconda3
  unlink_precs:

  link_precs:
    defaults::libsodium-1.0.16-h9d3ae62_0
    defaults::zeromq-4.3.1-h33f27b4_3
    defaults::pyzmq-18.0.0-py37ha925a31_0
    defaults::jupyter_client-5.2.4-py37_0
    defaults::ipykernel-5.1.0-py37h39e3cac_0



## Package Plan ##

  environment location: D:\_Programme\Anaconda3

  added / updated specs:
    - ipykernel


The following NEW packages will be INSTALLED:

  ipykernel          pkgs/main/win-64::ipykernel-5.1.0-py37h39e3cac_0
  jupyter_client     pkgs/main/win-64::jupyter_client-5.2.4-py37_0
  libsodium          pkgs/main/win-64::libsodium-1.0.16-h9d3ae62_0
  pyzmq              pkgs/main/win-64::pyzmq-18.0.0-py37ha925a31_0
  zeromq             pkgs/main/win-64::zeromq-4.3.1-h33f27b4_3


Proceed ([y]/n)? y

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... ===> LINKING PACKAGE: defaults::libsodium-1.0.16-h9d3ae62_0 <===
  prefix=D:\_Programme\Anaconda3
  source=D:\_Programme\Anaconda3\pkgs\libsodium-1.0.16-h9d3ae62_0


===> LINKING PACKAGE: defaults::zeromq-4.3.1-h33f27b4_3 <===
  prefix=D:\_Programme\Anaconda3
  source=D:\_Programme\Anaconda3\pkgs\zeromq-4.3.1-h33f27b4_3


===> LINKING PACKAGE: defaults::pyzmq-18.0.0-py37ha925a31_0 <===
  prefix=D:\_Programme\Anaconda3
  source=D:\_Programme\Anaconda3\pkgs\pyzmq-18.0.0-py37ha925a31_0


===> LINKING PACKAGE: defaults::jupyter_client-5.2.4-py37_0 <===
  prefix=D:\_Programme\Anaconda3
  source=D:\_Programme\Anaconda3\pkgs\jupyter_client-5.2.4-py37_0


===> LINKING PACKAGE: defaults::ipykernel-5.1.0-py37h39e3cac_0 <===
  prefix=D:\_Programme\Anaconda3
  source=D:\_Programme\Anaconda3\pkgs\ipykernel-5.1.0-py37h39e3cac_0


$ C:\WINDOWS\system32\cmd.exe /d /c D:\_Programme\Anaconda3\.tmprx2boc11.bat
==> cwd: D:\_Programme\Anaconda3\Scripts <==
==> exit code: 1 <==
==> stdout <==

==> stderr <==
Das System kann den angegebenen Pfad nicht finden.
Parameterformat falsch - 65001.



An error occurred while installing package 'defaults::ipykernel-5.1.0-py37h39e3cac_0'.
LinkError: post-link script failed for package defaults::ipykernel-5.1.0-py37h39e3cac_0
running your command again with `-v` will provide additional information
location of failed script: D:\_Programme\Anaconda3\Scripts\.ipykernel-post-link.bat
==> script messages <==
<None>

Attempting to roll back.


===> REVERSING PACKAGE LINK: defaults::ipykernel-5.1.0-py37h39e3cac_0 <===
  prefix=D:\_Programme\Anaconda3


failed
An error occurred while installing package 'defaults::ipykernel-5.1.0-py37h39e3cac_0'.
LinkError: post-link script failed for package defaults::ipykernel-5.1.0-py37h39e3cac_0
running your command again with `-v` will provide additional information
location of failed script: D:\_Programme\Anaconda3\Scripts\.ipykernel-post-link.bat
==> script messages <==
<None>

Attempting to roll back.


Rolling back transaction: ...working... ===> REVERSING PACKAGE LINK: defaults::jupyter_client-5.2.4-py37_0 <===
  prefix=D:\_Programme\Anaconda3


===> REVERSING PACKAGE LINK: defaults::pyzmq-18.0.0-py37ha925a31_0 <===
  prefix=D:\_Programme\Anaconda3


===> REVERSING PACKAGE LINK: defaults::zeromq-4.3.1-h33f27b4_3 <===
  prefix=D:\_Programme\Anaconda3


===> REVERSING PACKAGE LINK: defaults::libsodium-1.0.16-h9d3ae62_0 <===
  prefix=D:\_Programme\Anaconda3


done
Traceback (most recent call last):
  File "D:\_Programme\Anaconda3\lib\site-packages\conda\core\link.py", line 1079, in run_script
    subprocess_call(command_args, env=env, path=dirname(path))
  File "D:\_Programme\Anaconda3\lib\site-packages\conda\gateways\subprocess.py", line 85, in subprocess_call
    output=formatted_output)
subprocess.CalledProcessError: Command '['C:\\WINDOWS\\system32\\cmd.exe', '/d', '/c', 'D:\\_Programme\\Anaconda3\\.tmprx2boc11.bat']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "D:\_Programme\Anaconda3\lib\site-packages\conda\core\link.py", line 649, in _execute_post_link_actions
    activate=True)
  File "D:\_Programme\Anaconda3\lib\site-packages\conda\core\link.py", line 1095, in run_script
    raise LinkError(message)
conda.exceptions.LinkError: post-link script failed for package defaults::ipykernel-5.1.0-py37h39e3cac_0
running your command again with `-v` will provide additional information
location of failed script: D:\_Programme\Anaconda3\Scripts\.ipykernel-post-link.bat
==> script messages <==
<None>


During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "D:\_Programme\Anaconda3\lib\site-packages\conda\core\link.py", line 558, in _execute
    cls._execute_post_link_actions(pkg_idx_tracked, axngroup)
  File "D:\_Programme\Anaconda3\lib\site-packages\conda\core\link.py", line 664, in _execute_post_link_actions
    reverse_excs,
conda.CondaMultiError: post-link script failed for package defaults::ipykernel-5.1.0-py37h39e3cac_0
running your command again with `-v` will provide additional information
location of failed script: D:\_Programme\Anaconda3\Scripts\.ipykernel-post-link.bat
==> script messages <==
<None>



During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "D:\_Programme\Anaconda3\lib\site-packages\conda\exceptions.py", line 1003, in __call__
    return func(*args, **kwargs)
  File "D:\_Programme\Anaconda3\lib\site-packages\conda\cli\main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "D:\_Programme\Anaconda3\lib\site-packages\conda\cli\conda_argparse.py", line 82, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "D:\_Programme\Anaconda3\lib\site-packages\conda\cli\main_install.py", line 20, in execute
    install(args, parser, 'install')
  File "D:\_Programme\Anaconda3\lib\site-packages\conda\cli\install.py", line 275, in install
    handle_txn(unlink_link_transaction, prefix, args, newenv)
  File "D:\_Programme\Anaconda3\lib\site-packages\conda\cli\install.py", line 304, in handle_txn
    unlink_link_transaction.execute()
  File "D:\_Programme\Anaconda3\lib\site-packages\conda\core\link.py", line 241, in execute
    self._execute(tuple(concat(interleave(itervalues(self.prefix_action_groups)))))
  File "D:\_Programme\Anaconda3\lib\site-packages\conda\core\link.py", line 587, in _execute
    rollback_excs,
conda.CondaMultiError: post-link script failed for package defaults::ipykernel-5.1.0-py37h39e3cac_0
running your command again with `-v` will provide additional information
location of failed script: D:\_Programme\Anaconda3\Scripts\.ipykernel-post-link.bat
==> script messages <==
<None>

The German part translated to English:

$ C:\WINDOWS\system32\cmd.exe /d /c D:\_Programme\Anaconda3\.tmprx2boc11.bat
==> cwd: D:\_Programme\Anaconda3\Scripts <==
==> exit code: 1 <==
==> stdout <==

==> stderr <==
Das System kann den angegebenen Pfad nicht finden.
Parameterformat falsch - 65001.

translates to

$ C:\WINDOWS\system32\cmd.exe /d /c D:\_Programme\Anaconda3\.tmprx2boc11.bat
==> cwd: D:\_Programme\Anaconda3\Scripts <==
==> exit code: 1 <==
==> stdout <==

==> stderr <==
The system cannot find the specified path
Parameter format is wrong - 65001.

Here is a long thread discussing this problem. A number of the steps that I undertook to finish my installation were inspired by posts in this thread, but I did not succeed. Note that I posted my question in the linked thread also. I will make sure the answer gets posted here as well, if I get help from the Anaconda developers.

I believe somehow my system must be in a state that hinders me from getting Anaconda installed. All described issues seam to be rather common, but none of the suggested solutions worked for me thus far. I ran out of ideas and would be interested in a list of steps that I (and other people with the same problem) can undertake to transfer my system in a state that is not conflicting with Anaconda.

Detailed info on conda:

(base) C:\Users\Me>conda info

     active environment : base
    active env location : D:\_Programme\Anaconda3
            shell level : 1
       user config file : C:\Users\Me\.condarc
 populated config files : C:\Users\Me\.condarc
          conda version : 4.6.9
    conda-build version : not installed
         python version : 3.7.1.final.0
       base environment : D:\_Programme\Anaconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/win-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/win-64
                          https://repo.anaconda.com/pkgs/free/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 : D:\_Programme\Anaconda3\pkgs
                          C:\Users\Me\.conda\pkgs
                          C:\Users\Me\AppData\Local\conda\conda\pkgs
       envs directories : D:\_Programme\Anaconda3\envs
                          C:\Users\Me\.conda\envs
                          C:\Users\Me\AppData\Local\conda\conda\envs
               platform : win-64
             user-agent : conda/4.6.9 requests/2.21.0 CPython/3.7.1 Windows/10 Windows/10.0.17134
          administrator : False
             netrc file : None
           offline mode : False

I am working on 64bit Windows 10.

score 1 · Accepted Answer · answered Apr 05 '19 at 06:31

Temporarily disabling my anti-virus program did the trick for me. I am using the anti-virus program built into Windows 10.

Open the Windows defender security centre and switch off real-time protection. Install the package ipykernel, switch on the real-time protection again.

After that I have not had any further issues so far.

Fresh re-install of Anaconda fails - remove all conflicts between Anaconda and the system

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