I installed the anaconda distribution (version 2022.05) on a windows 10 (64 bit) machine. During installation I followed the recommendations given here (installed it only for myself and didn’t add anaconda to the PATH variable). I didn’t change any setting, so you can assume a virgin anaconda with default settings.
I need to install some additional packages which aren’t part of the distribution. Hence, I wanted to create a new environment using a clone of the base environment as a starting point. However, when I tried to clone base via
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conda create --clone base --name base_clone2
I got weird error messages:
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Source: C:Usersjohn.smithAnaconda32
Destination: C:Usersjohn.smithAnaconda3envsbase_clone3
The following packages cannot be cloned out of the root environment:4
- defaults/win-64::conda-4.12.0-py39haa95532_05
- defaults/win-64::conda-build-3.21.8-py39haa95532_26
- defaults/win-64::conda-env-2.6.0-haa95532_17
- defaults/noarch::conda-token-0.3.0-pyhd3eb1b0_08
- defaults/win-64::anaconda-2022.05-py39_09
- defaults/win-64::anaconda-navigator-2.1.4-py39haa95532_010
- defaults/win-64::console_shortcut-0.1.1-411
- defaults/win-64::powershell_shortcut-0.0.1-312
Packages: 39713
Files: 614
Preparing transaction: done15
Verifying transaction: |16
SafetyError: The package for _ipyw_jlab_nb_ext_conf located at C:Usersjohn.smithAnaconda3pkgs_ipyw_jlab_nb_ext_conf-0.1.0-py39haa95532_017
appears to be corrupted. The path 'Scripts/jupyter-labhub-script.py'18
has an incorrect size.19
reported size: 962 bytes20
actual size: 203 bytes21
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ClobberError: This transaction has incompatible packages due to a shared path.23
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_024
path: 'lib/site-packages/pycparser/__pycache__/__init__.cpython-39.pyc'25
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ClobberError: This transaction has incompatible packages due to a shared path.27
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_028
path: 'lib/site-packages/pycparser/__pycache__/ast_transforms.cpython-39.pyc'29
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ClobberError: This transaction has incompatible packages due to a shared path.32
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_033
path: 'lib/site-packages/pycparser/__pycache__/c_ast.cpython-39.pyc'34
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ClobberError: This transaction has incompatible packages due to a shared path.37
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_038
path: 'lib/site-packages/pycparser/__pycache__/c_lexer.cpython-39.pyc'39
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ClobberError: This transaction has incompatible packages due to a shared path.42
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_043
path: 'lib/site-packages/pycparser/__pycache__/c_parser.cpython-39.pyc'44
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ClobberError: This transaction has incompatible packages due to a shared path.47
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_048
path: 'lib/site-packages/pycparser/__pycache__/lextab.cpython-39.pyc'49
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ClobberError: This transaction has incompatible packages due to a shared path.52
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_053
path: 'lib/site-packages/pycparser/ply/__pycache__/__init__.cpython-39.pyc'54
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ClobberError: This transaction has incompatible packages due to a shared path.57
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_058
path: 'lib/site-packages/pycparser/ply/__pycache__/lex.cpython-39.pyc'59
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ClobberError: This transaction has incompatible packages due to a shared path.62
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_063
path: 'lib/site-packages/pycparser/ply/__pycache__/yacc.cpython-39.pyc'64
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ClobberError: This transaction has incompatible packages due to a shared path.67
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_068
path: 'lib/site-packages/pycparser/__pycache__/plyparser.cpython-39.pyc'69
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ClobberError: This transaction has incompatible packages due to a shared path.72
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_073
path: 'lib/site-packages/pycparser/__pycache__/yacctab.cpython-39.pyc'74
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ClobberError: This transaction has incompatible packages due to a shared path.77
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_078
path: 'lib/site-packages/wheel/__pycache__/__init__.cpython-39.pyc'79
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ClobberError: This transaction has incompatible packages due to a shared path.82
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_083
path: 'lib/site-packages/wheel/__pycache__/bdist_wheel.cpython-39.pyc'84
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ClobberError: This transaction has incompatible packages due to a shared path.87
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_088
path: 'lib/site-packages/wheel/cli/__pycache__/__init__.cpython-39.pyc'89
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ClobberError: This transaction has incompatible packages due to a shared path.92
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_093
path: 'lib/site-packages/wheel/__pycache__/macosx_libfile.cpython-39.pyc'94
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ClobberError: This transaction has incompatible packages due to a shared path.97
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_098
path: 'lib/site-packages/wheel/__pycache__/metadata.cpython-39.pyc'99
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ClobberError: This transaction has incompatible packages due to a shared path.102
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_0103
path: 'lib/site-packages/wheel/__pycache__/pkginfo.cpython-39.pyc'104
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ClobberError: This transaction has incompatible packages due to a shared path.107
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_0108
path: 'lib/site-packages/wheel/__pycache__/util.cpython-39.pyc'109
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ClobberError: This transaction has incompatible packages due to a shared path.112
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_0113
path: 'lib/site-packages/wheel/vendored/__pycache__/__init__.cpython-39.pyc'114
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ClobberError: This transaction has incompatible packages due to a shared path.117
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_0118
path: 'lib/site-packages/wheel/vendored/packaging/__pycache__/__init__.cpython-39.pyc'119
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ClobberError: This transaction has incompatible packages due to a shared path.122
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_0123
path: 'lib/site-packages/wheel/vendored/packaging/__pycache__/_typing.cpython-39.pyc'124
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ClobberError: This transaction has incompatible packages due to a shared path.127
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_0128
path: 'lib/site-packages/wheel/vendored/packaging/__pycache__/tags.cpython-39.pyc'129
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ClobberError: This transaction has incompatible packages due to a shared path.132
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_0133
path: 'lib/site-packages/wheel/__pycache__/wheelfile.cpython-39.pyc'134
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ClobberError: This transaction has incompatible packages due to a shared path.137
packages: defaults/win-64::notebook-6.4.8-py39haa95532_0, defaults/win-64::notebook-6.4.8-py39haa95532_0138
path: 'menu/notebook.json'139
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ClobberError: This transaction has incompatible packages due to a shared path.142
packages: defaults/noarch::jupyterlab-3.3.2-pyhd3eb1b0_0, defaults/win-64::_ipyw_jlab_nb_ext_conf-0.1.0-py39haa95532_0143
path: 'scripts/jupyter-labhub-script.py'144
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ClobberError: This transaction has incompatible packages due to a shared path.147
packages: defaults/noarch::jupyterlab-3.3.2-pyhd3eb1b0_0, defaults/win-64::_ipyw_jlab_nb_ext_conf-0.1.0-py39haa95532_0148
path: 'scripts/jupyter-labhub.exe'149
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ClobberError: This transaction has incompatible packages due to a shared path.152
packages: defaults/win-64::spyder-5.1.5-py39haa95532_1, defaults/win-64::spyder-5.1.5-py39haa95532_1153
path: 'menu/spyder_shortcut.json'154
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done158
Executing transaction: -159
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Windows 64-bit packages of scikit-learn can be accelerated using scikit-learn-intelex.161
More details are available here: https://intel.github.io/scikit-learn-intelex162
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For example:164
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$ conda install scikit-learn-intelex166
$ python -m sklearnex my_application.py167
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done170
#171
# To activate this environment, use172
#173
# $ conda activate base_clone174
#175
# To deactivate an active environment, use176
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# $ conda deactivate178
The first part of the message (“The following packages cannot be cloned out of the root environment”) is explained in this question which could be related to the safety and clobber errors, I guess? After doing some research I found this issue which suggests that I must not clone the base environment as it is special. This is a bit confusing to me as this is, to my best knowledge, not stated anywhere in the anaconda documentation. EDIT 1: However, in anaconda navigator the “clone” button is disabled for the base environment which supports this notion.
Hence, what is the proper way of copying the base environment for my purpose?
On a side note: I tried the yml approach as well (I changed the name of the environment in the first line of the yml)
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(base) PS D:19-05-2022_PythonDeployment> conda env export --name base > base2305.yml2
(base) PS D:19-05-2022_PythonDeployment> conda env create --file .base2305.yml3
which yielded the same errors. I tested this on a windows 10 VM as well as a physical windows 10 installation. EDIT 2: I forgot to mention that the cloning process somewhat succeeds as there exists indeed a new environment “base_clone” after execution. However, I don’t feel comfortable ignoring the error messages during the cloning process.
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Answer
I found a solution which results in an almost identical copy of the base environment without any error messages during the cloning process:
- Export the base environment to a yaml file:
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conda env export --name base > base.yml2
- Open the yaml file. In the first line, change name of the environment in the first line
name: baseto any other name. In the dependencies list, remove the following nine packages:
- 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
The first eight packages are mentioned by conda to be not clonable (see code section in question). The last package appears to be the offender which needs to be removed additionally.
Save the modified yaml file under a new name, e.g. base_mod.yml
- Use the modified yaml file to generate an environment almost identical to the base environment:
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conda env create --file base_mod.yml2
Conda, anaconda navigator, jupyter, … work fine with the hereby created environment as far as I can tell. It’s a bit frustrating though that such a basic functionality as cloning the (virgin) base environment required a bit of try and error to get it working.