anaconda 基础环境（版本 2022.05）克隆期间的安全和 Clobber 错误

Question

我在 windows 10（64 位）机器上安装了 anaconda 发行版（版本 2022.05）。在安装过程中，我遵循了 here 给出的建议（仅为我自己安装，没有将 anaconda 添加到 PATH 变量）。我没有更改任何设置，因此您可以假设使用默认设置的原始水蟒。

我需要安装一些不属于发行版的附加包。因此，我想使用基础环境的克隆作为起点来创建一个新环境。但是，当我尝试通过

克隆基地时

conda create --clone base --name base_clone

我收到奇怪的错误消息：

Source:      C:\Users\john.smith\Anaconda3
Destination: C:\Users\john.smith\Anaconda3\envs\base_clone
The following packages cannot be cloned out of the root environment:
 - defaults/win-64::conda-4.12.0-py39haa95532_0
 - defaults/win-64::conda-build-3.21.8-py39haa95532_2
 - defaults/win-64::conda-env-2.6.0-haa95532_1
 - defaults/noarch::conda-token-0.3.0-pyhd3eb1b0_0
 - defaults/win-64::anaconda-2022.05-py39_0
 - defaults/win-64::anaconda-navigator-2.1.4-py39haa95532_0
 - defaults/win-64::console_shortcut-0.1.1-4
 - defaults/win-64::powershell_shortcut-0.0.1-3
Packages: 397
Files: 6
Preparing transaction: done
Verifying transaction: |
SafetyError: The package for _ipyw_jlab_nb_ext_conf located at C:\Users\john.smith\Anaconda3\pkgs\_ipyw_jlab_nb_ext_conf-0.1.0-py39haa95532_0
appears to be corrupted. The path 'Scripts/jupyter-labhub-script.py'
has an incorrect size.
  reported size: 962 bytes
  actual size: 203 bytes

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::pycparser-2.21-pyhd3eb1b0_0, defaults/win-64::brotlipy-0.7.0-py39h2bbff1b_1003, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/pycparser/__pycache__/__init__.cpython-39.pyc'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::pycparser-2.21-pyhd3eb1b0_0, defaults/win-64::brotlipy-0.7.0-py39h2bbff1b_1003, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/pycparser/__pycache__/ast_transforms.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::pycparser-2.21-pyhd3eb1b0_0, defaults/win-64::brotlipy-0.7.0-py39h2bbff1b_1003, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/pycparser/__pycache__/c_ast.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::pycparser-2.21-pyhd3eb1b0_0, defaults/win-64::brotlipy-0.7.0-py39h2bbff1b_1003, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/pycparser/__pycache__/c_lexer.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::pycparser-2.21-pyhd3eb1b0_0, defaults/win-64::brotlipy-0.7.0-py39h2bbff1b_1003, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/pycparser/__pycache__/c_parser.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::pycparser-2.21-pyhd3eb1b0_0, defaults/win-64::brotlipy-0.7.0-py39h2bbff1b_1003, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/pycparser/__pycache__/lextab.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::pycparser-2.21-pyhd3eb1b0_0, defaults/win-64::brotlipy-0.7.0-py39h2bbff1b_1003, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/pycparser/ply/__pycache__/__init__.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::pycparser-2.21-pyhd3eb1b0_0, defaults/win-64::brotlipy-0.7.0-py39h2bbff1b_1003, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/pycparser/ply/__pycache__/lex.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::pycparser-2.21-pyhd3eb1b0_0, defaults/win-64::brotlipy-0.7.0-py39h2bbff1b_1003, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/pycparser/ply/__pycache__/yacc.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::pycparser-2.21-pyhd3eb1b0_0, defaults/win-64::brotlipy-0.7.0-py39h2bbff1b_1003, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/pycparser/__pycache__/plyparser.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::pycparser-2.21-pyhd3eb1b0_0, defaults/win-64::brotlipy-0.7.0-py39h2bbff1b_1003, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/pycparser/__pycache__/yacctab.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::wheel-0.37.1-pyhd3eb1b0_0, defaults/win-64::win_inet_pton-1.1.0-py39haa95532_0, defaults/win-64::wrapt-1.12.1-py39h196d8e1_1, defaults/win-64::pysocks-1.7.1-py39haa95532_0, defaults/win-64::yarl-1.6.3-py39h2bbff1b_0, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/wheel/__pycache__/__init__.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::wheel-0.37.1-pyhd3eb1b0_0, defaults/win-64::win_inet_pton-1.1.0-py39haa95532_0, defaults/win-64::wrapt-1.12.1-py39h196d8e1_1, defaults/win-64::pysocks-1.7.1-py39haa95532_0, defaults/win-64::yarl-1.6.3-py39h2bbff1b_0, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/wheel/__pycache__/bdist_wheel.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::wheel-0.37.1-pyhd3eb1b0_0, defaults/win-64::win_inet_pton-1.1.0-py39haa95532_0, defaults/win-64::wrapt-1.12.1-py39h196d8e1_1, defaults/win-64::pysocks-1.7.1-py39haa95532_0, defaults/win-64::yarl-1.6.3-py39h2bbff1b_0, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/wheel/cli/__pycache__/__init__.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::wheel-0.37.1-pyhd3eb1b0_0, defaults/win-64::win_inet_pton-1.1.0-py39haa95532_0, defaults/win-64::wrapt-1.12.1-py39h196d8e1_1, defaults/win-64::pysocks-1.7.1-py39haa95532_0, defaults/win-64::yarl-1.6.3-py39h2bbff1b_0, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/wheel/__pycache__/macosx_libfile.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::wheel-0.37.1-pyhd3eb1b0_0, defaults/win-64::win_inet_pton-1.1.0-py39haa95532_0, defaults/win-64::wrapt-1.12.1-py39h196d8e1_1, defaults/win-64::pysocks-1.7.1-py39haa95532_0, defaults/win-64::yarl-1.6.3-py39h2bbff1b_0, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/wheel/__pycache__/metadata.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::wheel-0.37.1-pyhd3eb1b0_0, defaults/win-64::win_inet_pton-1.1.0-py39haa95532_0, defaults/win-64::wrapt-1.12.1-py39h196d8e1_1, defaults/win-64::pysocks-1.7.1-py39haa95532_0, defaults/win-64::yarl-1.6.3-py39h2bbff1b_0, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/wheel/__pycache__/pkginfo.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::wheel-0.37.1-pyhd3eb1b0_0, defaults/win-64::win_inet_pton-1.1.0-py39haa95532_0, defaults/win-64::wrapt-1.12.1-py39h196d8e1_1, defaults/win-64::pysocks-1.7.1-py39haa95532_0, defaults/win-64::yarl-1.6.3-py39h2bbff1b_0, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/wheel/__pycache__/util.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::wheel-0.37.1-pyhd3eb1b0_0, defaults/win-64::win_inet_pton-1.1.0-py39haa95532_0, defaults/win-64::wrapt-1.12.1-py39h196d8e1_1, defaults/win-64::pysocks-1.7.1-py39haa95532_0, defaults/win-64::yarl-1.6.3-py39h2bbff1b_0, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/wheel/vendored/__pycache__/__init__.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::wheel-0.37.1-pyhd3eb1b0_0, defaults/win-64::win_inet_pton-1.1.0-py39haa95532_0, defaults/win-64::wrapt-1.12.1-py39h196d8e1_1, defaults/win-64::pysocks-1.7.1-py39haa95532_0, defaults/win-64::yarl-1.6.3-py39h2bbff1b_0, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/wheel/vendored/packaging/__pycache__/__init__.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::wheel-0.37.1-pyhd3eb1b0_0, defaults/win-64::win_inet_pton-1.1.0-py39haa95532_0, defaults/win-64::wrapt-1.12.1-py39h196d8e1_1, defaults/win-64::pysocks-1.7.1-py39haa95532_0, defaults/win-64::yarl-1.6.3-py39h2bbff1b_0, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/wheel/vendored/packaging/__pycache__/_typing.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::wheel-0.37.1-pyhd3eb1b0_0, defaults/win-64::win_inet_pton-1.1.0-py39haa95532_0, defaults/win-64::wrapt-1.12.1-py39h196d8e1_1, defaults/win-64::pysocks-1.7.1-py39haa95532_0, defaults/win-64::yarl-1.6.3-py39h2bbff1b_0, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/wheel/vendored/packaging/__pycache__/tags.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::wheel-0.37.1-pyhd3eb1b0_0, defaults/win-64::win_inet_pton-1.1.0-py39haa95532_0, defaults/win-64::wrapt-1.12.1-py39h196d8e1_1, defaults/win-64::pysocks-1.7.1-py39haa95532_0, defaults/win-64::yarl-1.6.3-py39h2bbff1b_0, defaults/win-64::pynacl-1.4.0-py39hbd8134f_1, defaults/win-64::bcrypt-3.2.0-py39h196d8e1_0
  path: 'lib/site-packages/wheel/__pycache__/wheelfile.cpython-39.pyc'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/win-64::notebook-6.4.8-py39haa95532_0, defaults/win-64::notebook-6.4.8-py39haa95532_0
  path: 'menu/notebook.json'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::jupyterlab-3.3.2-pyhd3eb1b0_0, defaults/win-64::_ipyw_jlab_nb_ext_conf-0.1.0-py39haa95532_0
  path: 'scripts/jupyter-labhub-script.py'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/noarch::jupyterlab-3.3.2-pyhd3eb1b0_0, defaults/win-64::_ipyw_jlab_nb_ext_conf-0.1.0-py39haa95532_0
  path: 'scripts/jupyter-labhub.exe'


ClobberError: This transaction has incompatible packages due to a shared path.
  packages: defaults/win-64::spyder-5.1.5-py39haa95532_1, defaults/win-64::spyder-5.1.5-py39haa95532_1
  path: 'menu/spyder_shortcut.json'



done
Executing transaction: -

    Windows 64-bit packages of scikit-learn can be accelerated using scikit-learn-intelex.
    More details are available here: https://intel.github.io/scikit-learn-intelex

    For example:

        $ conda install scikit-learn-intelex
        $ python -m sklearnex my_application.py


done
#
# To activate this environment, use
#
#     $ conda activate base_clone
#
# To deactivate an active environment, use
#
#     $ conda deactivate

消息的第一部分（“无法从根环境中克隆以下包”）在问题中进行了解释，我猜这可能与安全和破坏错误有关？在做了一些研究后，我发现 this 问题表明我不能克隆基础环境，因为它很特殊。这让我有点困惑，因为据我所知，anaconda 文档中的任何地方都没有说明。编辑 1：但是，在 anaconda 导航器中，支持此概念的基本环境禁用了“克隆”按钮。

因此，为了我的目的，复制基础环境的正确方法是什么？

附带说明：我也尝试了yml方法（我在yml的第一行更改了环境名称）

(base) PS D:-05-2022_PythonDeployment> conda env export  --name base > base2305.yml
(base) PS D:-05-2022_PythonDeployment> conda env create --file .\base2305.yml

产生了同样的错误。我在 windows 10 VM 以及物理 windows 10 安装上对此进行了测试。编辑 2：我忘了提到克隆过程有些成功，因为执行后确实存在一个新环境“base_clone”。但是，我不愿意在克隆过程中忽略错误消息。

Answer 1

我找到了一个解决方案，可以在克隆过程中生成几乎相同的基本环境副本，并且没有任何错误消息：

将基础环境导出到yaml文件：

conda env export  --name base > base.yml

打开yaml文件。在第一行中，将第一行 name: base 中的环境名称更改为任何其他名称。在依赖项列表中，删除以下九个包：

anaconda=2022.05=py39_0
anaconda-navigator=2.1.4=py39haa95532_0
conda=4.12.0=py39haa95532_0
conda-build=3.21.8=py39haa95532_2
conda-env=2.6.0=haa95532_1
conda-token=0.3.0=pyhd3eb1b0_0
console_shortcut=0.1.1=4
powershell_shortcut=0.0.1=3
_ipyw_jlab_nb_ext_conf=0.1.0=py39haa95532_0

conda 提到前八个包不可克隆（请参阅相关代码部分）。最后一个包裹似乎是违规者，需要另外删除。

以新名称保存修改后的yaml文件，例如base_mod.yml

使用修改后的yaml文件生成与基础环境几乎一致的环境：

conda env create --file base_mod.yml

据我所知，Conda、anaconda navigator、jupyter ……在特此创建的环境中运行良好。尽管像克隆（原始）基础环境这样的基本功能需要一些尝试和错误才能使其正常工作，但这有点令人沮丧。

anaconda 基础环境（版本 2022.05）克隆期间的安全和 Clobber 错误

Safety and Clobber errors during clone of anaconda base environment (Version 2022.05)

python

windows

anaconda

clone

environment