Rant: Miniconda blow-up during udpate
First and foremost, my life is miserable.
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environment variables:
CIO_TEST=<not set>
CONDA_BACKUP_AR=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-ar
CONDA_BACKUP_AS=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-as
CONDA_BACKUP_CC=x86_64-apple-darwin13.4.0-clang
CONDA_BACKUP_CC_FOR_BUILD=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-clang
CONDA_BACKUP_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE
-fstack-protector-strong -O2 -pipe -isystem
/opt/miniconda3/envs/econsa/include
CONDA_BACKUP_CHECKSYMS=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-checksyms
CONDA_BACKUP_CLANG=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-clang
CONDA_BACKUP_CLANGXX=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-clang++
CONDA_BACKUP_CMAKE_PREFIX_PATH=:/opt/miniconda3/envs/econsa
CONDA_BACKUP_CONDA_BUILD_SYSROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk
CONDA_BACKUP_CXX=x86_64-apple-darwin13.4.0-clang++
CONDA_BACKUP_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE
-fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-
inlines-hidden -std=c++14 -fmessage-length=0 -isystem
/opt/miniconda3/envs/econsa/include
CONDA_BACKUP_CXX_FOR_BUILD=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-clang++
CONDA_BACKUP_DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE
-fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem
/opt/miniconda3/envs/econsa/include
CONDA_BACKUP_DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE
-fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-
inlines-hidden -std=c++14 -fmessage-length=0 -Og -g -Wall -Wextra
-isystem /opt/miniconda3/envs/econsa/include
CONDA_BACKUP_DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector
-O2 -pipe -isystem /opt/miniconda3/envs/econsa/include
CONDA_BACKUP_DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector
-O2 -pipe -isystem /opt/miniconda3/envs/econsa/include
CONDA_BACKUP_F77=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-gfortran
CONDA_BACKUP_F90=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-gfortran
CONDA_BACKUP_F95=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-gfortran
CONDA_BACKUP_FC=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-gfortran
CONDA_BACKUP_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector
-O2 -pipe -isystem /opt/miniconda3/envs/econsa/include
CONDA_BACKUP_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector
-O2 -pipe -isystem /opt/miniconda3/envs/econsa/include
CONDA_BACKUP_GFORTRAN=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-gfortran
CONDA_BACKUP_HOST=x86_64-apple-darwin13.4.0
CONDA_BACKUP_INDR=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-indr
CONDA_BACKUP_INSTALL_NAME_TOOL=/opt/miniconda3/envs/econsa/bin/x86_64-apple-
darwin13.4.0-install_name_tool
CONDA_BACKUP_LD=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-ld
CONDA_BACKUP_LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath
/opt/miniconda3/envs/econsa/lib -L/opt/miniconda3/envs/econsa/lib
CONDA_BACKUP_LIBTOOL=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-libtool
CONDA_BACKUP_LIPO=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-lipo
CONDA_BACKUP_NM=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-nm
CONDA_BACKUP_NMEDIT=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-nmedit
CONDA_BACKUP_OTOOL=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-otool
CONDA_BACKUP_PAGESTUFF=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-pagestuff
CONDA_BACKUP_RANLIB=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-ranlib
CONDA_BACKUP_REDO_PREBINDING=/opt/miniconda3/envs/econsa/bin/x86_64-apple-
darwin13.4.0-redo_prebinding
CONDA_BACKUP_SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk
CONDA_BACKUP_SEGEDIT=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-segedit
CONDA_BACKUP_SEG_ADDR_TABLE=/opt/miniconda3/envs/econsa/bin/x86_64-apple-
darwin13.4.0-seg_addr_table
CONDA_BACKUP_SEG_HACK=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-seg_hack
CONDA_BACKUP_SIZE=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-size
CONDA_BACKUP_STRINGS=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-strings
CONDA_BACKUP_STRIP=/opt/miniconda3/envs/econsa/bin/x86_64-apple-darwin13.4.0-strip
CONDA_BACKUP__CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0
CONDA_BACKUP_host_alias=x86_64-apple-darwin13.4.0
CONDA_DEFAULT_ENV=base
CONDA_EXE=/opt/miniconda3/bin/conda
CONDA_PREFIX=/opt/miniconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/opt/miniconda3/bin/python
CONDA_ROOT=/opt/miniconda3
CONDA_SHLVL=1
CURL_CA_BUNDLE=<not set>
PATH=/opt/miniconda3/bin:/opt/miniconda3/bin:/opt/miniconda3/bin:/opt/minic
onda3/bin:/opt/miniconda3/bin:/Users/loikein/.rbenv/shims:/Users/
loikein/.gem/ruby/3.0.0/bin:/usr/local/lib/ruby/gems/3.0.0/bin:/usr
/local/lib/ruby/gems/2.7.0/bin:/usr/local/opt/ruby/bin:/Users/loikein
/.jenv/shims:/Users/loikein/Dakota/bin:/Users/loikein/Dakot
a/share/dakota/test:/usr/local/opt/python@3.9/bin:/usr/local/opt/opens
sl@1.1/bin:/opt/miniconda3/bin:/usr/local/opt/tcl-tk/bin:/usr/local/op
t/qt/bin:/Users/loikein/.jenv/bin:/Users/loikein/bin:/usr/loca
l/bin:/usr/local/sbin:/opt/miniconda3/condabin:/usr/bin:/bin:/usr/sbin
:/sbin:/Applications/VMware Fusion.app/Contents/Public:/Library/TeX/te
xbin:/usr/local/MacGPG2/bin:/Library/Apple/usr/bin:/usr/local/go/bin:/
usr/local/opt/fzf/bin:/Users/loikein/dotfiles/zsh/.antigen/bundles
/robbyrussell/oh-my-zsh/lib:/Users/loikein/dotfiles/zsh/.antigen/b
undles/robbyrussell/oh-my-zsh/plugins/colored-man-pages:/Users/loikein
/dotfiles/zsh/.antigen/bundles/robbyrussell/oh-my-zsh/plugins/fzf:
/Users/loikein/dotfiles/zsh/.antigen/bundles/robbyrussell/oh-my-zs
h/plugins/git:/Users/loikein/dotfiles/zsh/.antigen/bundles/robbyru
ssell/oh-my-zsh/plugins/vi-
mode:/Users/loikein/dotfiles/zsh/.antigen/bundles/robbyrussell/oh-
my-zsh/plugins/z:/Users/loikein/dotfiles/zsh/.antigen/bundles/zsh-
users/zsh-autosuggestions:/Users/loikein/dotfiles/zsh/.antigen/bun
dles/zdharma/fast-syntax-highlighting:/Users/loikein/dotfiles/zsh/
.antigen/bundles/romkatv/powerlevel10k
PKG_CONFIG_PATH=/usr/local/opt/ruby/lib/pkgconfig:/usr/local/opt/tcl-
tk/lib/pkgconfig:/usr/local/opt/openssl@1.1/lib/pkgconfig
PYTHONPATH=:/Users/loikein/Dakota/share/dakota/Python:/Users/loikein/Dako
ta/share/dakota/Python
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
active environment : base
active env location : /opt/miniconda3
shell level : 1
user config file : /Users/loikein/.condarc
populated config files : /Users/loikein/.condarc
conda version : 4.10.1
conda-build version : not installed
python version : 3.9.5.final.0
virtual packages : __osx=10.15.7=0
__unix=0=0
__archspec=1=x86_64
base environment : /opt/miniconda3 (writable)
conda av data dir : /opt/miniconda3/etc/conda
conda av metadata url : https://repo.anaconda.com/pkgs/main
channel URLs : https://conda.anaconda.org/conda-forge/osx-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/osx-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/osx-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /opt/miniconda3/pkgs
/Users/loikein/.conda/pkgs
envs directories : /opt/miniconda3/envs
/Users/loikein/.conda/envs
platform : osx-64
user-agent : conda/4.10.1 requests/2.24.0 CPython/3.9.5 Darwin/19.6.0 OSX/10.15.7
UID:GID : 502:20
netrc file : None
offline mode : False
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It all began with…
conda update -n base conda
doesn’t update · Issue #6941 · conda/conda
loikein commented 2021-06-10T17:34:17Z:
Any news on this issue?
Same problem here when trying to update from 4.8.4. I do automated regular upgrades on all the environments and packages on my computer, and thus did not even notice that it was not updating for a long while…
点击展开:$ conda update -n base conda
$ conda update -n base conda --yes
Collecting package metadata (current_repodata.json): done
Solving environment: /
==> WARNING: A newer version of conda exists. <==
current version: 4.8.4
latest version: 4.10.1
Please update conda by running
$ conda update -n base conda
# All requested packages already installed.
???
The meat part
I saw this question and think, oh, the answers look about right.
python - conda update -n base -c defaults conda won’t update to 4.6.x - Stack Overflow
Off we go…
点击展开:$ conda update python
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:
- conda-forge/noarch::requests==2.24.0=pyh9f0ad1d_0
- conda-forge/noarch::idna==2.10=pyh9f0ad1d_0
- conda-forge/osx-64::chardet==3.0.4=py37hc8dfbb8_1006
- conda-forge/osx-64::numpy==1.19.1=py37h7e69742_0
- conda-forge/osx-64::kiwisolver==1.2.0=py37ha1cc60f_0
- conda-forge/noarch::olefile==0.46=py_0
- conda-forge/noarch::pip==20.2.2=py_0
- conda-forge/noarch::tqdm==4.48.2=pyh9f0ad1d_0
- conda-forge/noarch::pycparser==2.20=pyh9f0ad1d_2
- conda-forge/osx-64::conda==4.8.4=py37hc8dfbb8_2
- conda-forge/osx-64::scipy==1.5.2=py37h2702c91_0
- conda-forge/osx-64::seaborn==0.10.1=1
- conda-forge/osx-64::pysocks==1.7.1=py37hc8dfbb8_1
- conda-forge/noarch::urllib3==1.25.10=py_0
- conda-forge/osx-64::brotlipy==0.7.0=py37h9bfed18_1000
- conda-forge/osx-64::statsmodels==0.11.1=py37h9bfed18_2
- conda-forge/osx-64::python.app==1.3=py37h9bfed18_1
- conda-forge/osx-64::pandas==1.1.0=py37hdadc0f0_0
- conda-forge/osx-64::sqlite==3.32.3=h93121df_1
- conda-forge/osx-64::matplotlib-base==3.3.0=py37h886f89f_1
- conda-forge/noarch::pyparsing==2.4.7=pyh9f0ad1d_0
- conda-forge/noarch::pyopenssl==19.1.0=py_1
- conda-forge/osx-64::setuptools==49.3.1=py37hc8dfbb8_0
- conda-forge/noarch::pytz==2020.1=pyh9f0ad1d_0
- conda-forge/osx-64::pycosat==0.6.3=py37h9bfed18_1004
- conda-forge/osx-64::cffi==1.14.1=py37hf5b7abd_0
- conda-forge/osx-64::pillow==7.2.0=py37hfd78ece_1
- conda-forge/osx-64::python_abi==3.7=1_cp37m
- conda-forge/osx-64::certifi==2020.6.20=py37hc8dfbb8_0
- conda-forge/noarch::cycler==0.10.0=py_2
- conda-forge/noarch::wheel==0.34.2=py_1
- conda-forge/noarch::patsy==0.5.1=py_0
- conda-forge/osx-64::ruamel_yaml==0.15.80=py37h9bfed18_1001
- conda-forge/osx-64::tornado==6.0.4=py37h9bfed18_1
- conda-forge/osx-64::python==3.7.6=cpython_h1fd5dd1_6
- conda-forge/noarch::python-dateutil==2.8.1=py_0
- conda-forge/noarch::six==1.15.0=pyh9f0ad1d_0
- conda-forge/noarch::seaborn-base==0.10.1=py_1
- conda-forge/osx-64::conda-package-handling==1.6.0=py37h9bfed18_2
- conda-forge/osx-64::cryptography==3.0=py37h94e4008_0
done
## Package Plan
environment location: /opt/miniconda3
added / updated specs:
- python
The following packages will be downloaded:
package | build
---------------------------|-----------------
certifi-2021.5.30 | py39h6e9494a_0 141 KB conda-forge
conda-4.10.1 | py39h6e9494a_0 3.0 MB conda-forge
libblas-3.9.0 | 9_openblas 11 KB conda-forge
libcblas-3.9.0 | 9_openblas 11 KB conda-forge
libgfortran-5.0.0 |9_3_0_h6c81a4c_22 19 KB conda-forge
libgfortran5-9.3.0 | h6c81a4c_22 1.7 MB conda-forge
liblapack-3.9.0 | 9_openblas 11 KB conda-forge
libopenblas-0.3.15 |openmp_h5e1b9a4_1 8.7 MB conda-forge
olefile-0.46 | py_0 31 KB conda-forge
openjpeg-2.4.0 | h6e7aa92_1 374 KB conda-forge
pyopenssl-19.1.0 | py_1 47 KB conda-forge
python-3.9.5 | h88f2d9e_3 9.9 MB
python.app-3 | py39h9ed2024_0 20 KB
urllib3-1.25.10 | py_0 92 KB conda-forge
------------------------------------------------------------
Total: 24.1 MB
The following NEW packages will be INSTALLED:
libgfortran5 conda-forge/osx-64::libgfortran5-9.3.0-h6c81a4c_22
openjpeg conda-forge/osx-64::openjpeg-2.4.0-h6e7aa92_1
tzdata conda-forge/noarch::tzdata-2021a-he74cb21_0
The following packages will be UPDATED:
certifi 2020.6.20-py37hc8dfbb8_0 --> 2021.5.30-py39h6e9494a_0
conda 4.8.4-py37hc8dfbb8_2 --> 4.10.1-py39h6e9494a_0
libblas 3.8.0-17_openblas --> 3.9.0-9_openblas
libcblas 3.8.0-17_openblas --> 3.9.0-9_openblas
libffi 3.2.1-hb1e8313_1007 --> 3.3-h046ec9c_2
libgfortran 4.0.0-7_5_0_h1a10cd1_22 --> 5.0.0-9_3_0_h6c81a4c_22
liblapack 3.8.0-17_openblas --> 3.9.0-9_openblas
libopenblas 0.3.10-openmp_h63d9170_4 --> 0.3.15-openmp_h5e1b9a4_1
python conda-forge::python-3.7.6-cpython_h1f~ --> pkgs/main::python-3.9.5-h88f2d9e_3
python.app conda-forge::python.app-1.3-py37h9bfe~ --> pkgs/main::python.app-3-py39h9ed2024_0
Proceed ([y]/n)? y
Downloading and Extracting Packages
olefile-0.46 | 31 KB | ####################################################################################### | 100%
libgfortran-5.0.0 | 19 KB | ####################################################################################### | 100%
libgfortran5-9.3.0 | 1.7 MB | ####################################################################################### | 100%
openjpeg-2.4.0 | 374 KB | ####################################################################################### | 100%
liblapack-3.9.0 | 11 KB | ####################################################################################### | 100%
python-3.9.5 | 9.9 MB | ####################################################################################### | 100%
libopenblas-0.3.15 | 8.7 MB | ####################################################################################### | 100%
python.app-3 | 20 KB | ####################################################################################### | 100%
urllib3-1.25.10 | 92 KB | ####################################################################################### | 100%
conda-4.10.1 | 3.0 MB | ####################################################################################### | 100%
libblas-3.9.0 | 11 KB | ####################################################################################### | 100%
pyopenssl-19.1.0 | 47 KB | ####################################################################################### | 100%
certifi-2021.5.30 | 141 KB | ####################################################################################### | 100%
libcblas-3.9.0 | 11 KB | ####################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Traceback (most recent call last):
File "/opt/miniconda3/lib/python3.9/site-packages/conda/common/serialize.py", line 19, in get_yaml
import ruamel_yaml as yaml
ModuleNotFoundError: No module named 'ruamel_yaml'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/miniconda3/lib/python3.9/site-packages/conda/common/serialize.py", line 22, in get_yaml
import ruamel.yaml as yaml
ModuleNotFoundError: No module named 'ruamel'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/miniconda3/lib/python3.9/site-packages/conda/cli/main.py", line 139, in main
from ..activate import main as activator_main
File "/opt/miniconda3/lib/python3.9/site-packages/conda/activate.py", line 22, in <module>
from .base.context import ROOT_ENV_NAME, context, locate_prefix_by_name
File "/opt/miniconda3/lib/python3.9/site-packages/conda/base/context.py", line 29, in <module>
from ..common.configuration import (Configuration, ConfigurationLoadError, MapParameter,
File "/opt/miniconda3/lib/python3.9/site-packages/conda/common/configuration.py", line 37, in <module>
from .serialize import yaml_round_trip_load
File "/opt/miniconda3/lib/python3.9/site-packages/conda/common/serialize.py", line 30, in <module>
yaml = get_yaml()
File "/opt/miniconda3/lib/python3.9/site-packages/conda/_vendor/auxlib/decorators.py", line 59, in _memoized_func
result = func(*args, **kwargs)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/common/serialize.py", line 24, in get_yaml
raise ImportError("No yaml library available.\n"
ImportError: No yaml library available.
To proceed, conda install ruamel_yaml
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/miniconda3/lib/python3.9/site-packages/conda/common/serialize.py", line 19, in get_yaml
import ruamel_yaml as yaml
ModuleNotFoundError: No module named 'ruamel_yaml'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/miniconda3/lib/python3.9/site-packages/conda/common/serialize.py", line 22, in get_yaml
import ruamel.yaml as yaml
ModuleNotFoundError: No module named 'ruamel'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/miniconda3/bin/conda", line 13, in <module>
sys.exit(main())
File "/opt/miniconda3/lib/python3.9/site-packages/conda/cli/main.py", line 149, in main
return ExceptionHandler().handle_exception(exc_val, exc_tb)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1126, in handle_exception
return self.handle_unexpected_exception(exc_val, exc_tb)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1137, in handle_unexpected_exception
self.print_unexpected_error_report(error_report)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1192, in print_unexpected_error_report
from .base.context import context
File "/opt/miniconda3/lib/python3.9/site-packages/conda/base/context.py", line 29, in <module>
from ..common.configuration import (Configuration, ConfigurationLoadError, MapParameter,
File "/opt/miniconda3/lib/python3.9/site-packages/conda/common/configuration.py", line 37, in <module>
from .serialize import yaml_round_trip_load
File "/opt/miniconda3/lib/python3.9/site-packages/conda/common/serialize.py", line 30, in <module>
yaml = get_yaml()
File "/opt/miniconda3/lib/python3.9/site-packages/conda/_vendor/auxlib/decorators.py", line 59, in _memoized_func
result = func(*args, **kwargs)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/common/serialize.py", line 24, in get_yaml
raise ImportError("No yaml library available.\n"
ImportError: No yaml library available.
To proceed, conda install ruamel_yaml
点击展开:$ conda install ruamel_yaml
Traceback (most recent call last):
File "/opt/miniconda3/lib/python3.9/site-packages/conda/common/serialize.py", line 19, in get_yaml
import ruamel_yaml as yaml
ModuleNotFoundError: No module named 'ruamel_yaml'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/miniconda3/lib/python3.9/site-packages/conda/common/serialize.py", line 22, in get_yaml
import ruamel.yaml as yaml
ModuleNotFoundError: No module named 'ruamel'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1079, in __call__
return func(*args, **kwargs)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/cli/main.py", line 74, in _main
from ..base.context import context
File "/opt/miniconda3/lib/python3.9/site-packages/conda/base/context.py", line 29, in <module>
from ..common.configuration import (Configuration, ConfigurationLoadError, MapParameter,
File "/opt/miniconda3/lib/python3.9/site-packages/conda/common/configuration.py", line 37, in <module>
from .serialize import yaml_round_trip_load
File "/opt/miniconda3/lib/python3.9/site-packages/conda/common/serialize.py", line 30, in <module>
yaml = get_yaml()
File "/opt/miniconda3/lib/python3.9/site-packages/conda/_vendor/auxlib/decorators.py", line 59, in _memoized_func
result = func(*args, **kwargs)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/common/serialize.py", line 24, in get_yaml
raise ImportError("No yaml library available.\n"
ImportError: No yaml library available.
To proceed, conda install ruamel_yaml
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/miniconda3/lib/python3.9/site-packages/conda/common/serialize.py", line 19, in get_yaml
import ruamel_yaml as yaml
ModuleNotFoundError: No module named 'ruamel_yaml'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/miniconda3/lib/python3.9/site-packages/conda/common/serialize.py", line 22, in get_yaml
import ruamel.yaml as yaml
ModuleNotFoundError: No module named 'ruamel'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/miniconda3/bin/conda", line 13, in <module>
sys.exit(main())
File "/opt/miniconda3/lib/python3.9/site-packages/conda/cli/main.py", line 152, in main
return conda_exception_handler(_main, *args, **kwargs)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1371, in conda_exception_handler
return_value = exception_handler(func, *args, **kwargs)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1082, in __call__
return self.handle_exception(exc_val, exc_tb)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1126, in handle_exception
return self.handle_unexpected_exception(exc_val, exc_tb)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1137, in handle_unexpected_exception
self.print_unexpected_error_report(error_report)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1192, in print_unexpected_error_report
from .base.context import context
File "/opt/miniconda3/lib/python3.9/site-packages/conda/base/context.py", line 29, in <module>
from ..common.configuration import (Configuration, ConfigurationLoadError, MapParameter,
File "/opt/miniconda3/lib/python3.9/site-packages/conda/common/configuration.py", line 37, in <module>
from .serialize import yaml_round_trip_load
File "/opt/miniconda3/lib/python3.9/site-packages/conda/common/serialize.py", line 30, in <module>
yaml = get_yaml()
File "/opt/miniconda3/lib/python3.9/site-packages/conda/_vendor/auxlib/decorators.py", line 59, in _memoized_func
result = func(*args, **kwargs)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/common/serialize.py", line 24, in get_yaml
raise ImportError("No yaml library available.\n"
ImportError: No yaml library available.
To proceed, conda install ruamel_yaml
Turns out this ruamel thing is quite a drama on its own, but no, I will not go down this particular rabbit hole at this point: ModuleNotFoundError: No module named ‘ruamel’ · Issue #106 · fair-workflows/nanopub
At this point, I almost gave up but saw this:
$ which pip
/opt/miniconda3/bin/pip
$ which python
/opt/miniconda3/bin/python
$ python --version
Python 3.9.5
$ conda --version
conda 4.10.1
Shit, might as well give pip a try. (Reference: ModuleNotFoundError: No module named ‘ruamel’ - AMSET - Materials Science Community Discourse)
点击展开:$ pip install ruamel.yaml
Collecting ruamel.yaml
Downloading ruamel.yaml-0.17.9-py3-none-any.whl (108 kB)
|████████████████████████████████| 108 kB 5.1 MB/s
Collecting ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.10"
Downloading ruamel.yaml.clib-0.2.2-cp39-cp39-macosx_10_9_x86_64.whl (156 kB)
|████████████████████████████████| 156 kB 5.6 MB/s
Installing collected packages: ruamel.yaml.clib, ruamel.yaml
Successfully installed ruamel.yaml-0.17.9 ruamel.yaml.clib-0.2.2
And try again…
点击展开:$ conda install ruamel_yaml
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1079, in __call__
return func(*args, **kwargs)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/cli/main.py", line 84, in _main
exit_code = do_call(args, p)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
return getattr(module, func_name)(args, parser)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/cli/main_install.py", line 20, in execute
install(args, parser, 'install')
File "/opt/miniconda3/lib/python3.9/site-packages/conda/cli/install.py", line 116, in install
if context.use_only_tar_bz2:
File "/opt/miniconda3/lib/python3.9/site-packages/conda/base/context.py", line 734, in use_only_tar_bz2
import conda_package_handling.api
ModuleNotFoundError: No module named 'conda_package_handling'
…well, what about…
点击展开:$ conda install conda_package_handling
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1079, in __call__
return func(*args, **kwargs)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/cli/main.py", line 84, in _main
exit_code = do_call(args, p)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
return getattr(module, func_name)(args, parser)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/cli/main_install.py", line 20, in execute
install(args, parser, 'install')
File "/opt/miniconda3/lib/python3.9/site-packages/conda/cli/install.py", line 116, in install
if context.use_only_tar_bz2:
File "/opt/miniconda3/lib/python3.9/site-packages/conda/base/context.py", line 734, in use_only_tar_bz2
import conda_package_handling.api
ModuleNotFoundError: No module named 'conda_package_handling'
or…
点击展开:$ conda update -n base
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/opt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1079, in __call__
return func(*args, **kwargs)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/cli/main.py", line 84, in _main
exit_code = do_call(args, p)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
return getattr(module, func_name)(args, parser)
File "/opt/miniconda3/lib/python3.9/site-packages/conda/cli/main_update.py", line 20, in execute
install(args, parser, 'update')
File "/opt/miniconda3/lib/python3.9/site-packages/conda/cli/install.py", line 116, in install
if context.use_only_tar_bz2:
File "/opt/miniconda3/lib/python3.9/site-packages/conda/base/context.py", line 734, in use_only_tar_bz2
import conda_package_handling.api
ModuleNotFoundError: No module named 'conda_package_handling'
Shit.
Have you heard of the good news of copy-and-paste?
I almost did how to reinstall miniconda - Google Search, but then found this Samaritan who opened an issue and actually solved it afterwords: Conda is broken after update. No module named conda_package_handling
· Issue #8920 · conda/conda
sbushmanov commented 2019-07-12T16:35:32Z:
After I copied old version of
conda_package_handling
from another machine and doconda install conda-package-handling
conda became functional again, includingconda update --all
to correct for conflicting packages.
And, thank Archons, there are two folders called conda_package_handling
and conda_package_handling-1.6.0.dist-info
under /opt/miniconda3/lib/python3.7/site-packages/conda/
. I copied them to /opt/miniconda3/lib/python3.9/site-packages/conda/
, and…
$ conda install conda-package-handling
Collecting package metadata (repodata.json): done
Solving environment: | WARNING conda.resolve:_get_sat_solver_cls(57): Could not run SAT solver through interface 'pycosat'.
failed with initial frozen solve. Retrying with flexible solve.
CondaDependencyError: Cannot run solver. No functioning SAT implementations available.
Tried the find, copy & paste for this pycosat
, but nothing changes. At this point I’m just so done with it.
Pip, my superman
You thought that was the end? No, I still have one last $ pip install pycosat --force-reinstall
up my sleeve.
点击展开:First try…
Collecting pycosat
Downloading pycosat-0.6.3.zip (66 kB)
|████████████████████████████████| 66 kB 4.2 MB/s
ERROR: Command errored out with exit status 1:
command: /opt/miniconda3/bin/python3.9 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/c2/2fxscjk958993tlvdbw2fxt80000gp/T/pip-install-gqudjxke/pycosat/setup.py'"'"'; __file__='"'"'/private/var/folders/c2/2fxscjk958993tlvdbw2fxt80000gp/T/pip-install-gqudjxke/pycosat/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/c2/2fxscjk958993tlvdbw2fxt80000gp/T/pip-pip-egg-info-hodcfrgl
cwd: /private/var/folders/c2/2fxscjk958993tlvdbw2fxt80000gp/T/pip-install-gqudjxke/pycosat/
Complete output (3 lines):
Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'setuptools'
----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
(…find-copy-paste…)
点击展开:Second try…
Collecting pycosat
Using cached pycosat-0.6.3.zip (66 kB)
ERROR: Command errored out with exit status 1:
command: /opt/miniconda3/bin/python3.9 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/c2/2fxscjk958993tlvdbw2fxt80000gp/T/pip-install-5u4hi3jp/pycosat/setup.py'"'"'; __file__='"'"'/private/var/folders/c2/2fxscjk958993tlvdbw2fxt80000gp/T/pip-install-5u4hi3jp/pycosat/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/c2/2fxscjk958993tlvdbw2fxt80000gp/T/pip-pip-egg-info-bhrehjnm
cwd: /private/var/folders/c2/2fxscjk958993tlvdbw2fxt80000gp/T/pip-install-5u4hi3jp/pycosat/
Complete output (5 lines):
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/opt/miniconda3/lib/python3.9/site-packages/setuptools/__init__.py", line 8, in <module>
import _distutils_hack.override # noqa: F401
ModuleNotFoundError: No module named '_distutils_hack'
----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
(…find-copy-paste…)
点击展开:Third try…
Collecting pycosat
Using cached pycosat-0.6.3.zip (66 kB)
ERROR: Command errored out with exit status 1:
command: /opt/miniconda3/bin/python3.9 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/c2/2fxscjk958993tlvdbw2fxt80000gp/T/pip-install-whln8cm1/pycosat/setup.py'"'"'; __file__='"'"'/private/var/folders/c2/2fxscjk958993tlvdbw2fxt80000gp/T/pip-install-whln8cm1/pycosat/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/c2/2fxscjk958993tlvdbw2fxt80000gp/T/pip-pip-egg-info-r6zrlb0u
cwd: /private/var/folders/c2/2fxscjk958993tlvdbw2fxt80000gp/T/pip-install-whln8cm1/pycosat/
Complete output (7 lines):
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/opt/miniconda3/lib/python3.9/site-packages/setuptools/__init__.py", line 19, in <module>
import setuptools.version
File "/opt/miniconda3/lib/python3.9/site-packages/setuptools/version.py", line 1, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
(…find-copy-paste…)
点击展开:Forth try…
Collecting pycosat
Using cached pycosat-0.6.3.zip (66 kB)
Building wheels for collected packages: pycosat
Building wheel for pycosat (setup.py) ... done
Created wheel for pycosat: filename=pycosat-0.6.3-cp39-cp39-macosx_10_9_x86_64.whl size=57667 sha256=3a4f96d9a02ca9076f358a6868443ef85be7cdc700e54834c4ae67e61ba6d802
Stored in directory: /Users/loikein/Library/Caches/pip/wheels/8c/c4/34/9ccbaac74c64deb727e916d00905158b6941b006bc829fa7fe
Successfully built pycosat
Installing collected packages: pycosat
Attempting uninstall: pycosat
Found existing installation: pycosat 0.6.3
Uninstalling pycosat-0.6.3:
Successfully uninstalled pycosat-0.6.3
ERROR: After October 2020 you may experience errors when installing or updating packages. This is because pip will change the way that it resolves dependency conflicts.
We recommend you use --use-feature=2020-resolver to test your packages with the new resolver before it becomes the default.
conda 4.10.1 requires ruamel_yaml_conda>=0.11.14, which is not installed.
Successfully installed pycosat-0.6.3
Oh. My. Word. And indeed…
点击展开:$ conda update 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:
............
done
## Package Plan
environment location: /opt/miniconda3
added / updated specs:
- conda
The following packages will be downloaded:
package | build
---------------------------|-----------------
libblas-3.9.0 | 8_openblas 11 KB conda-forge
libcblas-3.9.0 | 8_openblas 11 KB conda-forge
libgfortran-4.0.0 |7_5_0_h1a10cd1_22 19 KB conda-forge
liblapack-3.9.0 | 8_openblas 11 KB conda-forge
libopenblas-0.3.12 |openmp_h63d9170_1 8.7 MB conda-forge
------------------------------------------------------------
Total: 8.7 MB
The following packages will be UPDATED:
sqlite 3.32.3-h93121df_1 --> 3.35.5-h44b9ce1_0
The following packages will be DOWNGRADED:
libblas 3.9.0-9_openblas --> 3.9.0-8_openblas
libcblas 3.9.0-9_openblas --> 3.9.0-8_openblas
libgfortran 5.0.0-9_3_0_h6c81a4c_22 --> 4.0.0-7_5_0_h1a10cd1_22
liblapack 3.9.0-9_openblas --> 3.9.0-8_openblas
libopenblas 0.3.15-openmp_h5e1b9a4_1 --> 0.3.12-openmp_h63d9170_1
Proceed ([y]/n)? y
Voilà!
And of course, $ conda update --all
after this. All it actually did was downgrading five packages, which I found peculiar, but hey, would I ever be surprised at Python for anything after today? Probably not.
Side note: conda revision
Reference: conda update后出现的问题及conda回滚,回到历史版本_生如的博客-CSDN博客
What a handy function, maybe someone has experienced precisely what I did and invented this.
点击展开:$ conda list --revision
2020-03-09 12:32:13 (rev 0)
+asn1crypto-1.3.0
+ca-certificates-2020.1.1
+certifi-2019.11.28
+cffi-1.14.0
+chardet-3.0.4
+conda-4.8.2
+conda-package-handling-1.6.0
+cryptography-2.8
+idna-2.8
+libcxx-4.0.1
+libcxxabi-4.0.1
+libedit-3.1.20181209
+libffi-3.2.1
+ncurses-6.2
+openssl-1.1.1d
+pip-20.0.2
+pycosat-0.6.3
+pycparser-2.19
+pyopenssl-19.1.0
+pysocks-1.7.1
+python-3.7.6
+python.app-2
+readline-7.0
+requests-2.22.0
+ruamel_yaml-0.15.87
+setuptools-45.2.0
+six-1.14.0
+sqlite-3.31.1
+tk-8.6.8
+tqdm-4.42.1
+urllib3-1.25.8
+wheel-0.34.2
+xz-5.2.4
+yaml-0.1.7
+zlib-1.2.11
............
2021-06-10 19:28:33 (rev 37)
freetype {2.10.4 (defaults/osx-64) -> 2.10.4 (conda-forge/osx-64)}
jbig {2.1 (defaults/osx-64) -> 2.1 (conda-forge/osx-64)}
lcms2 {2.12 (defaults/osx-64) -> 2.12 (conda-forge/osx-64)}
lerc {2.2.1 (defaults/osx-64) -> 2.2.1 (conda-forge/osx-64)}
libdeflate {1.7 (defaults/osx-64) -> 1.7 (conda-forge/osx-64)}
libffi {3.2.1 (defaults/osx-64) -> 3.2.1 (conda-forge/osx-64)}
libpng {1.6.37 (defaults/osx-64) -> 1.6.37 (conda-forge/osx-64)}
libwebp-base {1.2.0 (defaults/osx-64) -> 1.2.0 (conda-forge/osx-64)}
lz4-c {1.9.3 (defaults/osx-64) -> 1.9.3 (conda-forge/osx-64)}
ncurses {6.2 (defaults/osx-64) -> 6.2 (conda-forge/osx-64)}
openssl {1.1.1k (defaults/osx-64) -> 1.1.1k (conda-forge/osx-64)}
readline {8.1 (defaults/osx-64) -> 8.1 (conda-forge/osx-64)}
tk {8.6.10 (defaults/osx-64) -> 8.6.10 (conda-forge/osx-64)}
xz {5.2.5 (defaults/osx-64) -> 5.2.5 (conda-forge/osx-64)}
yaml {0.2.5 (defaults/osx-64) -> 0.2.5 (conda-forge/osx-64)}
zlib {1.2.11 (defaults/osx-64) -> 1.2.11 (conda-forge/osx-64)}
2021-06-10 19:35:15 (rev 38)
certifi {2020.6.20 (conda-forge/osx-64) -> 2021.5.30 (conda-forge/osx-64)}
conda {4.8.4 (conda-forge/osx-64) -> 4.10.1 (conda-forge/osx-64)}
libblas {3.8.0 (conda-forge/osx-64) -> 3.9.0 (conda-forge/osx-64)}
libcblas {3.8.0 (conda-forge/osx-64) -> 3.9.0 (conda-forge/osx-64)}
libffi {3.2.1 (conda-forge/osx-64) -> 3.3 (conda-forge/osx-64)}
libgfortran {4.0.0 (conda-forge/osx-64) -> 5.0.0 (conda-forge/osx-64)}
liblapack {3.8.0 (conda-forge/osx-64) -> 3.9.0 (conda-forge/osx-64)}
libopenblas {0.3.10 (conda-forge/osx-64) -> 0.3.15 (conda-forge/osx-64)}
python {3.7.6 (conda-forge/osx-64) -> 3.9.5 (defaults/osx-64)}
python.app {1.3 (conda-forge/osx-64) -> 3 (defaults/osx-64)}
+libgfortran5-9.3.0 (conda-forge/osx-64)
+openjpeg-2.4.0 (conda-forge/osx-64)
+tzdata-2021a (conda-forge/noarch)
So in theory, I will then just have to do $ conda install --revision=37
to revert to the previous working version of conda. Good to know.
Doc: Restoring an environment - Managing environments — conda 4.10.1.post26+e14d58909 documentation
Closing thoughts
Everything I have to go through to day, and gone through by many across the Internet, is all very confusing and disappointing.
Given also how slow conda devs on GitHub response to their issues (you can do sort by most commented and see for yourself how many of these issues’ comment sections are just users helping each other without any useful actions or even a thank-you from the devs), I guess the lesson here is don’t use conda.
Or better yet, don’t use Python. Actually, you know what, don’t ever get into this programming business, if you are not mentally ready to sit down and debug a single environment line for two hour and a half just like I did.