I just installed Anaconda for an online class and when I opened Spyder it said that a new version of Spyder was available so I thought I'd update through the Anaconda prompt. However when I type in
conda update spyder
it returns with
>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "C:\Users\sydne\OneDrive\Documents\PyMol\lib\site-packages\conda\exceptions.py", line 1074, in __call__
return func(*args, **kwargs)
File "C:\Users\sydne\OneDrive\Documents\PyMol\lib\site-packages\conda\cli\main.py", line 84, in _main
exit_code = do_call(args, p)
File "C:\Users\sydne\OneDrive\Documents\PyMol\lib\site-packages\conda\cli\conda_argparse.py", line 82, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "C:\Users\sydne\OneDrive\Documents\PyMol\lib\site-packages\conda\cli\main_update.py", line 20, in execute
install(args, parser, 'update')
File "C:\Users\sydne\OneDrive\Documents\PyMol\lib\site-packages\conda\cli\install.py", line 116, in install
if context.use_only_tar_bz2:
File "C:\Users\sydne\OneDrive\Documents\PyMol\lib\site-packages\conda\base\context.py", line 666, in use_only_tar_bz2
import conda_package_handling.api
File "C:\Users\sydne\OneDrive\Documents\PyMol\lib\site-packages\conda_package_handling\api.py", line 7, in <module>
import tqdm as _tqdm
ModuleNotFoundError: No module named 'tqdm'
$ C:\Users\sydne\OneDrive\Documents\PyMol\Scripts\conda-script.py update spyder
environment variables:
CIO_TEST=<not set>
CONDA_DEFAULT_ENV=base
CONDA_EXE=C:\Users\sydne\OneDrive\Documents\PyMol\condabin\..\Scripts\conda.exe
CONDA_EXES="C:\Users\sydne\OneDrive\Documents\PyMol\condabin\..\Scripts\conda.exe
"
CONDA_PREFIX=C:\Users\sydne\OneDrive\Documents\PyMol
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=C:\Users\sydne\OneDrive\Documents\PyMol\python.exe
CONDA_ROOT=C:\Users\sydne\OneDrive\Documents\PyMol
CONDA_SHLVL=1
HOMEPATH=\Users\sydne
PATH=C:\Users\sydne\OneDrive\Documents\PyMol;C:\Users\sydne\OneDrive\Docume
nts\PyMol\Library\mingw-w64\bin;C:\Users\sydne\OneDrive\Documents\PyMo
l\Library\usr\bin;C:\Users\sydne\OneDrive\Documents\PyMol\Library\bin;
C:\Users\sydne\OneDrive\Documents\PyMol\Scripts;C:\Users\sydne\OneDriv
e\Documents\PyMol\bin;C:\Users\sydne\OneDrive\Documents\PyMol;C:\Users
\sydne\OneDrive\Documents\PyMol\Library\mingw-w64\bin;C:\Users\sydne\O
neDrive\Documents\PyMol\Library\usr\bin;C:\Users\sydne\OneDrive\Docume
nts\PyMol\Library\bin;C:\Users\sydne\OneDrive\Documents\PyMol\Scripts;
C:\Users\sydne\OneDrive\Documents\PyMol\bin;C:\Users\sydne\OneDrive\Do
cuments\PyMol\condabin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\Syste
m32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0;C:\WINDOWS\System3
2\OpenSSH;C:\Program Files (x86)\Intel\Intel(R) Management Engine
Components\DAL;C:\Program Files\Intel\Intel(R) Management Engine Compo
nents\DAL;C:\Users\sydne\Anaconda3;C:\Users\sydne\Anaconda3\Library\mi
ngw-w64\bin;C:\Users\sydne\Anaconda3\Library\usr\bin;C:\Users\sydne\An
aconda3\Library\bin;C:\Users\sydne\Anaconda3\Scripts;C:\Users\sydne\Ap
pData\Local\Microsoft\WindowsApps
PSMODULEPATH=C:\Program Files\WindowsPowerShell\Modules;C:\WINDOWS\system32\Windows
PowerShell\v1.0\Modules
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
active environment : base
active env location : C:\Users\sydne\OneDrive\Documents\PyMol
shell level : 1
user config file : C:\Users\sydne\.condarc
populated config files : C:\Users\sydne\OneDrive\Documents\PyMol\.condarc
C:\Users\sydne\.condarc
conda version : 4.7.12
conda-build version : not installed
python version : 3.7.4.final.0
virtual packages :
base environment : C:\Users\sydne\OneDrive\Documents\PyMol (writable)
channel URLs : https://conda.anaconda.org/conda-forge/win-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/win-64
https://repo.anaconda.com/pkgs/main/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
https://conda.anaconda.org/conda_forge/win-64
https://conda.anaconda.org/conda_forge/noarch
https://conda.anaconda.org/schrodinger/win-64
https://conda.anaconda.org/schrodinger/noarch
https://repo.anaconda.com/pkgs/free/win-64
https://repo.anaconda.com/pkgs/free/noarch
package cache : C:\Users\sydne\OneDrive\Documents\PyMol\pkgs
C:\Users\sydne\.conda\pkgs
C:\Users\sydne\AppData\Local\conda\conda\pkgs
envs directories : C:\Users\sydne\OneDrive\Documents\PyMol\envs
C:\Users\sydne\.conda\envs
C:\Users\sydne\AppData\Local\conda\conda\envs
platform : win-64
user-agent : conda/4.7.12 requests/2.22.0 CPython/3.7.4 Windows/10 Windows/10.0.18362
administrator : False
netrc file : None
offline mode : False
It's a little bit overwhelming to look at for a first timer, so if anyone could give any advice as to whether I'm missing any packages or anything that would be helpful.
I don't know if this is relevant, but when I was installing it I was asked to both “Add Anaconda to my PATH environment variable”, and “Register Anaconda as my default Python 3.5.” for the purposes of the class. One of the options came up as 'not recommended'in the Setup Wizard, but it might have nothing to do with the problem at all.
Related
I just downloaded Spyder 5 using
conda upgrade anaconda
conda install spyder=5.0.0
However, after installation when I launch Spyder from the Windows menu, I see a pop up indicating that Spyder 5 is launching. However, after a few seconds the popup disappears and Spyder does not launch.
When I try to launch Spyder from the Anaconda Navigator, I get the following error:
C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\utils\image_path_manager.py:46: UserWarning: The icon located in C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\images\kite\kite_completions.png is overriding the existing kite_completions
f'The icon located in {complete_path} is overriding '
C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\utils\image_path_manager.py:46: UserWarning: The icon located in C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\images\old_svg\CloseButton.svg is overriding the existing CloseButton
f'The icon located in {complete_path} is overriding '
C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\utils\image_path_manager.py:46: UserWarning: The icon located in C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\images\spyder2_icon_theme\folding.arrow_down_off.png is overriding the existing folding.arrow_down_off
f'The icon located in {complete_path} is overriding '
C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\utils\image_path_manager.py:46: UserWarning: The icon located in C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\images\spyder2_icon_theme\folding.arrow_down_on.png is overriding the existing folding.arrow_down_on
f'The icon located in {complete_path} is overriding '
C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\utils\image_path_manager.py:46: UserWarning: The icon located in C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\images\spyder2_icon_theme\folding.arrow_right_off.png is overriding the existing folding.arrow_right_off
f'The icon located in {complete_path} is overriding '
C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\utils\image_path_manager.py:46: UserWarning: The icon located in C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\images\spyder2_icon_theme\folding.arrow_right_on.png is overriding the existing folding.arrow_right_on
f'The icon located in {complete_path} is overriding '
C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\utils\image_path_manager.py:46: UserWarning: The icon located in C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\images\tour\tour-spyder-logo.svg is overriding the existing tour-spyder-logo
f'The icon located in {complete_path} is overriding '
No QCoreApplication instance found. Application patches not applied. You have to call load_stylesheet function after instantiation of QApplication to take effect.
ipython_console: cannot import name 'secure_write' from 'jupyter_core.paths' (C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\jupyter_core\paths.py)
Traceback (most recent call last):
File "C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\app\solver.py", line 117, in find_external_plugins
mod = importlib.import_module(entry_point.module_name)
File "C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\importlib\__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1006, in _gcd_import
File "", line 983, in _find_and_load
File "", line 967, in _find_and_load_unlocked
File "", line 677, in _load_unlocked
File "", line 728, in exec_module
File "", line 219, in _call_with_frames_removed
File "C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\plugins\ipythonconsole\plugin.py", line 24, in
from jupyter_client.connect import find_connection_file
File "C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\jupyter_client\__init__.py", line 4, in
from .connect import *
File "C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\jupyter_client\connect.py", line 35, in
from jupyter_core.paths import jupyter_data_dir, jupyter_runtime_dir, secure_write
ImportError: cannot import name 'secure_write' from 'jupyter_core.paths' (C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\jupyter_core\paths.py)
Pruned plugin: variable_explorer
Pruned plugin: plots
Traceback (most recent call last):
File "C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\app\mainwindow.py", line 2146, in create_window
main.setup()
File "C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\app\mainwindow.py", line 836, in setup
plugin_deps = solve_plugin_dependencies(enabled_plugins.values())
File "C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\app\solver.py", line 210, in solve_plugin_dependencies
plugin_deps = [plugin_names[name] for name in deps]
File "C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\app\solver.py", line 210, in
plugin_deps = [plugin_names[name] for name in deps]
KeyError: 'plots'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\Scripts\spyder-script.py", line 10, in
sys.exit(main())
File "C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\app\start.py", line 214, in main
mainwindow.main(options, args)
File "C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\app\mainwindow.py", line 2293, in main
mainwindow = create_window(app, splash, options, args)
File "C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\app\mainwindow.py", line 2148, in create_window
if main.console is not None:
File "C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\app\mainwindow.py", line 1159, in __getattr__
return self.get_plugin(self._INTERNAL_PLUGINS_MAPPING[attr])
File "C:\Users\USERNAME\AppData\Local\Continuum\anaconda3\lib\site-packages\spyder\app\mainwindow.py", line 168, in get_plugin
raise SpyderAPIError('Plugin "{}" not found!'.format(plugin_name))
spyder.api.exceptions.SpyderAPIError: Plugin "internal_console" not found!
I have already tried the following things already (unsuccessfully):
Uninstalling (through Windows menu) Spyder and reinstalling it in the Anaconda prompt
Installing Spyder 4 again conda install spyder=4.0.0. However, this does not launch either anymore.
What can I do to launch Spyder again?
Try to use:
icon_theme = spyder 2
in the file C:\Users<user_name>.spyder-py3\config\spyder.ini
You need remove Spyder History.
rm ~/.config/spyder-py3
I was having the same problem and I just completely uninstalled anaconda 3 with the Uninstall-Anaconda.exe then I reinstalled and updated everything again. That may not really be a viable option for you but I did get it to work.
Below commands worked for me without breaking anything:
conda update anaconda
and then
conda install spyder=5
PermissionError: [WinError 5] Access is denied - running pytest after fresh conda install
Environment
# packages in environment at C:\Users\rick\miniconda3\envs\xml:
#
# Name Version Build Channel
pytest 6.2.2 py39haa95532_2
(xml) c:\Users\rick>conda info
active environment : xml
active env location : C:\Users\rick\miniconda3\envs\xml
shell level : 2
user config file : C:\Users\rick\.condarc
populated config files : C:\Users\rick\.condarc
conda version : 4.9.2
conda-build version : not installed
python version : 3.9.2.final.0
virtual packages : __win=0=0
__archspec=1=x86_64
base environment : C:\Users\rick\miniconda3 (writable)
channel URLs : https://repo.anaconda.com/pkgs/main/win-64
https://repo.anaconda.com/pkgs/main/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 : C:\Users\rick\miniconda3\pkgs
C:\Users\rick\.conda\pkgs
C:\Users\rick\AppData\Local\conda\conda\pkgs
envs directories : C:\Users\rick\miniconda3\envs
C:\Users\rick\.conda\envs
C:\Users\rick\AppData\Local\conda\conda\envs
platform : win-64
user-agent : conda/4.9.2 requests/2.25.1 CPython/3.9.2 Windows/10 Windows/10.0.18362
administrator : False
netrc file : None
offline mode : False
(xml) c:\Users\rick>pytest
=================================================== test session starts ===================================================
platform win32 -- Python 3.9.2, pytest-6.2.2, py-1.9.0, pluggy-0.13.1
rootdir: c:\Users\rick
collected 0 items / 1 error
========================================================= ERRORS ==========================================================
______________________________________________ ERROR collecting test session ______________________________________________
miniconda3\envs\xml\lib\site-packages\_pytest\runner.py:311: in from_call
result: Optional[TResult] = func()
miniconda3\envs\xml\lib\site-packages\_pytest\runner.py:341: in <lambda>
call = CallInfo.from_call(lambda: list(collector.collect()), "collect")
miniconda3\envs\xml\lib\site-packages\_pytest\main.py:690: in collect
for direntry in visit(str(argpath), self._recurse):
miniconda3\envs\xml\lib\site-packages\_pytest\pathlib.py:613: in visit
yield from visit(entry.path, recurse)
miniconda3\envs\xml\lib\site-packages\_pytest\pathlib.py:613: in visit
yield from visit(entry.path, recurse)
miniconda3\envs\xml\lib\site-packages\_pytest\pathlib.py:613: in visit
yield from visit(entry.path, recurse)
miniconda3\envs\xml\lib\site-packages\_pytest\pathlib.py:598: in visit
for entry in os.scandir(path):
E PermissionError: [WinError 5] Access is denied: 'c:\\Users\\rick\\AppData\\Local\\Application Data'
================================================= short test summary info =================================================
ERROR - PermissionError: [WinError 5] Access is denied: 'c:\\Users\\rick\\AppData\\Local\\Application Data'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
==================================================== 1 error in 2.35s =====================================================
From a Microsoft Technet post
The Application Data folder in that location is not a normal folder. It is a folder Junction and is normally hidden, by default. The only reason that the junction exists is to redirect legacy applications, that are hard coded to look for that folder, to the new location in Windows 7.
Seems odd that pytest would point to a deprecated "folder junction"? How to resolve?
pytest first tries to 'collect' tests - i.e. scans actual folder and its subfolders for python test files containing tests methods.
Looks like you've just installed (conda and) pytest and wanted to just try it, while being located at your os \users\rick folder, containing additional hidden\protected os folders which pytest lack permissions to access. I don't think pytest is deliberately trying to use this deprecated 'folder junction' ,it just happened to sit around your actual working folder at the moment. Running tests for real, you would know where to collect them, i.e. what folder to execute pytest from. For verify install only, run pytest from folder not containing any special os folders.
Collecting tests is also called 'test discovery' and can be parametrized and or configured, pytest docs touching the topic is here https://docs.pytest.org/en/7.0.x/explanation/goodpractices.html#test-discovery
)
Just run "pytest" from the directory you installed it or add it to the environmental variables.
In your example: >cd miniconda3\envs\xml\lib\site-packages_pytest
I have been working on creating custom environments using conda for new projects on my local machine (mac os). Within a project directory I created a new environment using yml file with:
$ conda env create --prefix ./env --file environment.yml
then:
$ conda activate ./env
I am now getting a conda error report every time I open a terminal and I do not understand what is going on. If anyone has any insight on what I broke and how to fix it would be greatly appreciated. I hope I have included enough information here to understand the problem. Here is the error output from terminal:
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/Users/jrudd/opt/anaconda3/lib/python3.8/site-packages/conda/cli/main.py", line 140, in main
return activator_main()
File "/Users/jrudd/opt/anaconda3/lib/python3.8/site-packages/conda/activate.py", line 1210, in main
print(activator.execute(), end='')
File "/Users/jrudd/opt/anaconda3/lib/python3.8/site-packages/conda/activate.py", line 178, in execute
return getattr(self, self.command)()
File "/Users/jrudd/opt/anaconda3/lib/python3.8/site-packages/conda/activate.py", line 152, in activate
builder_result = self.build_activate(self.env_name_or_prefix)
File "/Users/jrudd/opt/anaconda3/lib/python3.8/site-packages/conda/activate.py", line 300, in build_activate
return self._build_activate_stack(env_name_or_prefix, False)
File "/Users/jrudd/opt/anaconda3/lib/python3.8/site-packages/conda/activate.py", line 326, in _build_activate_stack
conda_prompt_modifier = self._prompt_modifier(prefix, conda_default_env)
File "/Users/jrudd/opt/anaconda3/lib/python3.8/site-packages/conda/activate.py", line 691, in _prompt_modifier
return context.env_prompt.format(
KeyError: 'ds-basic'
`$ /Users/jrudd/opt/anaconda3/bin/conda shell.posix activate base`
environment variables:
CIO_TEST=<not set>
CONDA_EXE=/Users/jrudd/opt/anaconda3/bin/conda
CONDA_PYTHON_EXE=/Users/jrudd/opt/anaconda3/bin/python
CONDA_ROOT=/Users/jrudd/opt/anaconda3
CONDA_SHLVL=0
CURL_CA_BUNDLE=<not set>
PATH=/Users/jrudd/opt/anaconda3/bin:/Users/jrudd/opt/anaconda3/condabin:/us
r/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
active environment : None
shell level : 0
user config file : /Users/jrudd/.condarc
populated config files : /Users/jrudd/.condarc
conda version : 4.9.2
conda-build version : 3.18.11
python version : 3.8.3.final.0
virtual packages : __osx=10.16=0
__unix=0=0
__archspec=1=x86_64
base environment : /Users/jrudd/opt/anaconda3 (writable)
channel URLs : 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 : /Users/jrudd/opt/anaconda3/pkgs
/Users/jrudd/.conda/pkgs
envs directories : /Users/jrudd/opt/anaconda3/envs
/Users/jrudd/.conda/envs
platform : osx-64
user-agent : conda/4.9.2 requests/2.24.0 CPython/3.8.3 Darwin/20.3.0 OSX/10.16
UID:GID : 501:20
netrc file : /Users/jrudd/.netrc
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers?
Thanks!
So, I found out that I had screwed up the .condarc config file by changing the base env_prompt to ({ds-basic}). For context, ds-basic is the name of this project environment. Don't ask me why or how I did this because I really have no idea. Was probably something I did during coffee induced haze. I found the .condarc file and edited out the offending code. It had actually broke conda completely and I couldn't even activate the base environment. Once I fixed the .condarc file all was well.
I just installed Anaconda3 and when I open the Anaconda command prompt, it shows me this error:
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "C:\Users\owner\Anaconda3\lib\site-packages\conda\cli\main.py", line 138, in main
return activator_main()
File "C:\Users\owner\Anaconda3\lib\site-packages\conda\activate.py", line 996, in main
print(activator.execute(), end='')
File "C:\Users\owner\Anaconda3\lib\site-packages\conda\activate.py", line 180, in execute
return getattr(self, self.command)()
File "C:\Users\owner\Anaconda3\lib\site-packages\conda\activate.py", line 154, in activate
builder_result = self.build_activate(self.env_name_or_prefix)
File "C:\Users\owner\Anaconda3\lib\site-packages\conda\activate.py", line 288, in build_activate
return self._build_activate_stack(env_name_or_prefix, False)
File "C:\Users\owner\Anaconda3\lib\site-packages\conda\activate.py", line 314, in _build_activate_stack
conda_prompt_modifier = self._prompt_modifier(prefix, conda_default_env)
File "C:\Users\owner\Anaconda3\lib\site-packages\conda\activate.py", line 639, in _prompt_modifier
name=basename(prefix),
KeyError: 'openSim'
`$ C:\Users\owner\Anaconda3\Scripts\conda-script.py shell.cmd.exe activate C:\Users\owner\Anaconda3`
environment variables:
CIO_TEST=<not set>
CONDA_BAT=C:\Users\owner\Anaconda3\condabin\conda.bat
CONDA_EXE=C:\Users\owner\Anaconda3\condabin\..\Scripts\conda.exe
CONDA_ROOT=C:\Users\owner\Anaconda3
CONDA_SHLVL=0
GIT_LFS_PATH=C:\Program Files\Git LFS
HOMEPATH=\Users\owner
PATH=C:\Users\owner\Anaconda3;C:\Users\owner\Anaconda3\Library\mingw-w64\bi
n;C:\Users\owner\Anaconda3\Library\usr\bin;C:\Users\owner\Anaconda3\Li
brary\bin;C:\Users\owner\Anaconda3\Scripts;C:\Users\owner\Anaconda3\bi
n;C:\Users\owner\Anaconda3\condabin;C:\Users\owner\Documents\R\win-
library\3.3\Rtools\bin;C:\Program Files (x86)\Common
Files\Oracle\Java\javapath;C:\Program Files
(x86)\STMicroelectronics\st_toolset\asm;C:\Program Files
(x86)\Intel\iCLS Client\;C:\Program Files\Intel\iCLS Client\;C:\WINDOW
S\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\Win
dowsPowerShell\v1.0\;C:\Program Files (x86)\Intel\Intel(R) Management
Engine Components\DAL;C:\Program Files\Intel\Intel(R) Management
Engine Components\DAL;C:\Program Files (x86)\Intel\Intel(R) Management
Engine Components\IPT;C:\Program Files\Intel\Intel(R) Management
Engine Components\IPT;C:\Program Files\Microsoft SQL
Server\110\Tools\Binn\;C:\Program Files (x86)\Microsoft
SDKs\TypeScript\1.0\;C:\Program Files\Microsoft SQL
Server\120\Tools\Binn\;C:\Users\owner\.dnx\bin;C:\Program
Files\Microsoft DNX\Dnvm\;C:\Program Files\Microsoft SQL
Server\130\Tools\Binn\;C:\Program Files\nodejs\;C:\Program
Files\doxygen\bin;C:\Program Files\PuTTY\;C:\Program Files\Git
LFS;C:\Program Files\Git\cmd;C:\Program
Files\Git\mingw64\bin;C:\Program Files\Git\usr\bin;C:\WINDOWS\System32
\OpenSSH\;C:\Users\owner\Documents\Libraries\gradle-4.10.2\bin;C:\Andr
oid;C:\Windows\System32;C:\Users\owner\Anaconda3;C:\Users\owner\Anacon
da3\Scripts;C:\Users\owner\Anaconda3\Library\bin;C:\OpenSim 3.3\bin;C:
\Users\owner\Anaconda3;C:\Users\owner\Anaconda3\Library\mingw-w64\bin;
C:\Users\owner\Anaconda3\Library\usr\bin;C:\Users\owner\Anaconda3\Libr
ary\bin;C:\Users\owner\Anaconda3\Scripts;C:\Users\owner\AppData\Local\
Microsoft\WindowsApps;C:\Program Files (x86)\FCIV;C:\Users\owner\AppDa
ta\Roaming\npm;C:\Users\owner\Downloads\swigwin-3.0.12\swigwin-3.0.12\
;C:\Users\owner\AppData\Local\Google\Cloud SDK\google-cloud-
sdk\bin;MSVCP140.DLL;C:\Users\owner\AppData\Local\Programs\Microsoft
VS Code\bin;C:\flutter\bin;C:\Users\owner\AppData\Local\Android\Sdk\to
ols;C:\Users\owner\AppData\Local\Android\Sdk\platform-
tools;C:\Users\owner\AppData\Local\Android\Sdk\build-
tools\28.0.3;C:\Users\owner\AppData\Roaming\Pub\Cache\bin;C:\Program
Files (x86)\Microsoft Visual Studio\Installer
PROTOC_PATH=C:\Users\owner\Documents\Libraries\protobuf-3.3.0\src\protoc\Debug\pro
toc.exe
PSMODULEPATH=;C:\Users\owner\AppData\Local\Google\Cloud SDK\google-cloud-
sdk\platform\PowerShell
PYTHONIOENCODING=UTF-8
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
active environment : None
shell level : 0
user config file : C:\Users\owner\.condarc
populated config files : C:\Users\owner\.condarc
conda version : 4.7.12
conda-build version : 3.18.9
python version : 3.7.4.final.0
virtual packages :
base environment : C:\Users\owner\Anaconda3 (writable)
channel URLs : https://repo.anaconda.com/pkgs/main/win-64
https://repo.anaconda.com/pkgs/main/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 : C:\Users\owner\Anaconda3\pkgs
C:\Users\owner\.conda\pkgs
C:\Users\owner\AppData\Local\conda\conda\pkgs
envs directories : C:\Users\owner\Anaconda3\envs
C:\Users\owner\.conda\envs
C:\Users\owner\AppData\Local\conda\conda\envs
platform : win-64
user-agent : conda/4.7.12 requests/2.22.0 CPython/3.7.4 Windows/10 Windows/10.0.18362
administrator : False
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
A similar error happens if I try to create a new environment and activate it. Any hint on what could be causing it? I see that that it's complaining about KeyError: 'openSim'. But I'm not sure what could be the root cause. The error message is not very explicit or at least I couldn't get anything from it.
I tried uninstalling Anaconda and OpenSim and installing them again with no luck in resolving the issue. Any hint is appreciated.
I found the solution to the problem which is so random that I thought I share it here. It's not easy (almost impossible) to figure out.
It looked like some configurations were cached and had to be manually deleted since even a fresh install of anaconda didn't resolve the issue.
I had to delete .condarc file in the anaconda directory to solve this issue.
For more info read this.
I am trying to create a conda environment from .yml file. I am using Miniconda3, python 3.7.3 on Windows. I receive the following error report. Any ideas what could cause such a problem?
PS. I apologise if the question is not appropriate.
Traceback (most recent call last):
File "C:\Users\mariyana\Miniconda3\lib\site-packages\conda\exceptions.py", line 1003, in __call__
return func(*args, **kwargs)
File "C:\Users\mariyana\Miniconda3\lib\site-packages\conda_env\cli\main.py", line 73, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "C:\Users\mariyana\Miniconda3\lib\site-packages\conda_env\cli\main_update.py", line 69, in execute
directory=os.getcwd())
File "C:\Users\mariyana\Miniconda3\lib\site-packages\conda_env\specs\__init__.py", line 40, in detect
if spec.can_handle():
File "C:\Users\mariyana\Miniconda3\lib\site-packages\conda_env\specs\yaml_file.py", line 18, in can_handle
self._environment = env.from_file(self.filename)
File "C:\Users\mariyana\Miniconda3\lib\site-packages\conda_env\env.py", line 143, in from_file
return from_yaml(yamlstr, filename=filename)
File "C:\Users\mariyana\Miniconda3\lib\site-packages\conda_env\env.py", line 129, in from_yaml
data = validate_keys(data, kwargs)
File "C:\Users\mariyana\Miniconda3\lib\site-packages\conda_env\env.py", line 34, in validate_keys
for key in data.keys():
AttributeError: 'NoneType' object has no attribute 'keys'
`$ C:\Users\mariyana\Miniconda3\Scripts\conda-env-script.py update --file spikesorting.yml`
environment variables:
CIO_TEST=<not set>
CONDA_AUTO_UPDATE_CONDA=false
CONDA_DEFAULT_ENV=spikesorting
CONDA_EXE=C:\Users\mariyana\Miniconda3\condabin\..\Scripts\conda.exe
CONDA_EXES="C:\Users\mariyana\Miniconda3\condabin\..\Scripts\conda.exe"
CONDA_PREFIX=C:\Users\mariyana\Miniconda3\envs\spikesorting
CONDA_PREFIX_1=C:\Users\mariyana\Miniconda3
CONDA_PROMPT_MODIFIER=(spikesorting)
CONDA_PYTHON_EXE=C:\Users\mariyana\Miniconda3\python.exe
CONDA_ROOT=C:\Users\mariyana\Miniconda3
CONDA_SHLVL=2
HOMEPATH=\Users\mariyana
PATH=C:\Users\mariyana\Miniconda3;C:\Users\mariyana\Miniconda3\Library\ming
w-w64\bin;C:\Users\mariyana\Miniconda3\Library\usr\bin;C:\Users\mariya
na\Miniconda3\Library\bin;C:\Users\mariyana\Miniconda3\Scripts;C:\User
s\mariyana\Miniconda3\bin;C:\Users\mariyana\Miniconda3\envs\spikesorti
ng;C:\Users\mariyana\Miniconda3\envs\spikesorting\Library\mingw-w64\bi
n;C:\Users\mariyana\Miniconda3\envs\spikesorting\Library\usr\bin;C:\Us
ers\mariyana\Miniconda3\envs\spikesorting\Library\bin;C:\Users\mariyan
a\Miniconda3\envs\spikesorting\Scripts;C:\Users\mariyana\Miniconda3\en
vs\spikesorting\bin;C:\Users\mariyana\Miniconda3\condabin;C:\ProgramDa
ta\Oracle\Java\javapath;C:\Program Files\Haskell\bin;C:\Program
Files\Haskell Platform\7.10.2-a\lib\extralibs\bin;C:\Program
Files\Haskell Platform\7.10.2-a\bin;C:\Program Files
(x86)\Lenovo\FusionEngine;C:\Program Files (x86)\Intel\iCLS
Client;C:\Program Files\Intel\iCLS Client;C:\WINDOWS\system32;C:\WINDO
WS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0
;C:\Program Files (x86)\ATI Technologies\ATI.ACE\Core-
Static;C:\Program Files\Intel\Intel(R) Management Engine
Components\DAL;C:\Program Files (x86)\Intel\Intel(R) Management Engine
Components\DAL;C:\Program Files\Intel\Intel(R) Management Engine
Components\IPT;C:\Program Files (x86)\Intel\Intel(R) Management Engine
Components\IPT;C:\Program Files\Intel\WiFi\bin;C:\Program Files\Common
Files\Intel\WirelessCommon;C:\Program Files (x86)\Common
Files\lenovo\easyplussdk\bin;C:\emacs-24.5\bin;C:\Program
Files\Haskell Platform\7.10.2-a\mingw\bin;C:\Program Files
(x86)\Windows Kits\8.1\Windows Performance Toolkit;C:\Program
Files\Microsoft SQL Server\130\Tools\Binn;C:\Program
Files\Git\cmd;C:\Program Files (x86)\Skype\Phone;C:\Program
Files\nodejs;C:\WINDOWS\System32\OpenSSH;C:\Program
Files\PuTTY;C:\Program Files (x86)\Heimdal\bin;C:\Program
Files\Heimdal\bin;C:\Program Files\Secure
Endpoints\NetIDMgr;C:\Program Files\MATLAB\R2018b\bin;C:\Users\mariyan
a\AppData\Local\Programs\Python\Python37-32\Scripts;C:\Users\mariyana\
AppData\Local\Programs\Python\Python37-32;C:\Users\mariyana\AppData\Lo
cal\Programs\Python\Python35\Scripts;C:\Users\mariyana\AppData\Local\P
rograms\Python\Python35;C:\Users\mariyana\AppData\Roaming\cabal\bin;C:
\Users\mariyana\AppData\Local\Microsoft\WindowsApps;C:\Users\mariyana\
AppData\Local\Google\Cloud SDK\google-cloud-
sdk\bin;C:\Users\mariyana\AppData\Roaming\npm;.
PSMODULEPATH=;C:\Users\mariyana\AppData\Local\Google\Cloud SDK\google-cloud-
sdk\platform\PowerShell
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
active environment : spikesorting
active env location : C:\Users\mariyana\Miniconda3\envs\spikesorting
shell level : 2
user config file : C:\home\.condarc
populated config files :
conda version : 4.6.14
conda-build version : not installed
python version : 3.7.3.final.0
base environment : C:\Users\mariyana\Miniconda3 (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 : C:\Users\mariyana\Miniconda3\pkgs
C:\home\.conda\pkgs
C:\Users\mariyana\AppData\Local\conda\conda\pkgs
envs directories : C:\Users\mariyana\Miniconda3\envs
C:\home\.conda\envs
C:\Users\mariyana\AppData\Local\conda\conda\envs
platform : win-64
user-agent : conda/4.6.14 requests/2.21.0 CPython/3.7.3 Windows/10 Windows/10.0.17134
administrator : False
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers?
This can happen when your environment yaml file is broken or empty. I ran into the same issue and noticed that while playing around with conda, the content of my environment.yml got deleted. Therefore, the for loop in env.py fails due to a None object.