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I am trying to update all conda packages.

Tried running these command

conda update anaconda

conda update --all

But getting this error after confirming on most of the packages.

How to solve and update all the packages ?

ClobberError: The package 'defaults::pip-10.0.1-py36_0' cannot be installed due to a
path collision for 'lib/python3.6/site-packages/pip/_vendor/urllib3/util/__pycache__/wait.cpython-36.pyc'.
This path already exists in the target prefix, and it won't be removed
by an uninstall action in this transaction. The path is one that conda
doesn't recognize. It may have been created by another package manager.


ClobberError: The package 'defaults::pip-10.0.1-py36_0' cannot be installed due to a
path collision for 'lib/python3.6/site-packages/pip/_vendor/urllib3/util/connection.py'.
This path already exists in the target prefix, and it won't be removed
by an uninstall action in this transaction. The path is one that conda
doesn't recognize. It may have been created by another package manager.


ClobberError: The package 'defaults::pip-10.0.1-py36_0' cannot be installed due to a
path collision for 'lib/python3.6/site-packages/pip/_vendor/urllib3/util/request.py'.
This path already exists in the target prefix, and it won't be removed
by an uninstall action in this transaction. The path is one that conda
doesn't recognize. It may have been created by another package manager.


ClobberError: The package 'defaults::pip-10.0.1-py36_0' cannot be installed due to a
path collision for 'lib/python3.6/site-packages/pip/_vendor/urllib3/util/response.py'.
This path already exists in the target prefix, and it won't be removed
by an uninstall action in this transaction. The path is one that conda
doesn't recognize. It may have been created by another package manager.


ClobberError: The package 'defaults::pip-10.0.1-py36_0' cannot be installed due to a
path collision for 'lib/python3.6/site-packages/pip/_vendor/urllib3/util/retry.py'.
This path already exists in the target prefix, and it won't be removed
by an uninstall action in this transaction. The path is one that conda
doesn't recognize. It may have been created by another package manager.


ClobberError: The package 'defaults::pip-10.0.1-py36_0' cannot be installed due to a
path collision for 'lib/python3.6/site-packages/pip/_vendor/urllib3/util/selectors.py'.
This path already exists in the target prefix, and it won't be removed
by an uninstall action in this transaction. The path is one that conda
doesn't recognize. It may have been created by another package manager.


ClobberError: The package 'defaults::pip-10.0.1-py36_0' cannot be installed due to a
path collision for 'lib/python3.6/site-packages/pip/_vendor/urllib3/util/ssl_.py'.
This path already exists in the target prefix, and it won't be removed
by an uninstall action in this transaction. The path is one that conda
doesn't recognize. It may have been created by another package manager.


ClobberError: The package 'defaults::pip-10.0.1-py36_0' cannot be installed due to a
path collision for 'lib/python3.6/site-packages/pip/_vendor/urllib3/util/timeout.py'.
This path already exists in the target prefix, and it won't be removed
by an uninstall action in this transaction. The path is one that conda
doesn't recognize. It may have been created by another package manager.


ClobberError: The package 'defaults::pip-10.0.1-py36_0' cannot be installed due to a
path collision for 'lib/python3.6/site-packages/pip/_vendor/urllib3/util/url.py'.
This path already exists in the target prefix, and it won't be removed
by an uninstall action in this transaction. The path is one that conda
doesn't recognize. It may have been created by another package manager.


ClobberError: The package 'defaults::pip-10.0.1-py36_0' cannot be installed due to a
path collision for 'lib/python3.6/site-packages/pip/_vendor/urllib3/util/wait.py'.
This path already exists in the target prefix, and it won't be removed
by an uninstall action in this transaction. The path is one that conda
doesn't recognize. It may have been created by another package manager.
Community
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Shan Khan
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  • Did you ever run `pip` commands? – darthbith Jul 07 '18 at 13:51
  • i have updated all pip packages , after updating when i try to update i get same error. – Shan Khan Jul 07 '18 at 21:27
  • Yeah, you should not use `pip` to update `pip` within conda. You should use conda to update everything. I'm afraid you'll probably have to uninstall pip and possibly urllib3 and reinstall them with conda. – darthbith Jul 07 '18 at 21:34
  • actually i did update `pip` after getting conda errors. Initially i wasnt getting errors while updating , my connection disconnect multiple times when after that upon updating i get these errors. After getting these error - I updated pip though. Is there any way to clean the corrupted packages using anaconda – Shan Khan Jul 07 '18 at 21:45

3 Answers3

22
conda clean --all
conda update --all

Worked for me. I needed to run update command multiple times to update all packages.

Shan Khan
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0

You don't need to update conda, particularly if you are using an HPC cluster conda so you don't have write permissions. You only need to clean any previously failed installations with

conda clean --all
Zhanwen Chen
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-1

If you need to update all packages, the command is:. 

conda update --all
cosmoscalibur
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