Error message
Traceback (most recent call last):
File "/home/djan/anaconda3/lib/python3.7/site-packages/tornado/web.py", line 1699, in _execute
result = await result
File "/home/djan/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/home/djan/anaconda3/lib/python3.7/site-packages/notebook/services/sessions/handlers.py", line 72, in post
type=mtype))
File "/home/djan/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/home/djan/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/home/djan/anaconda3/lib/python3.7/site-packages/notebook/services/sessions/sessionmanager.py", line 88, in create_session
kernel_id = yield self.start_kernel_for_session(session_id, path, name, type, kernel_name)
File "/home/djan/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/home/djan/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/home/djan/anaconda3/lib/python3.7/site-packages/notebook/services/sessions/sessionmanager.py", line 101, in start_kernel_for_session
self.kernel_manager.start_kernel(path=kernel_path, kernel_name=kernel_name)
File "/home/djan/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/home/djan/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 209, in wrapper
yielded = next(result)
File "/home/djan/anaconda3/lib/python3.7/site-packages/notebook/services/kernels/kernelmanager.py", line 168, in start_kernel
super(MappingKernelManager, self).start_kernel(**kwargs)
File "/home/djan/anaconda3/lib/python3.7/site-packages/jupyter_client/multikernelmanager.py", line 110, in start_kernel
km.start_kernel(**kwargs)
File "/home/djan/anaconda3/lib/python3.7/site-packages/jupyter_client/manager.py", line 240, in start_kernel
self.write_connection_file()
File "/home/djan/anaconda3/lib/python3.7/site-packages/jupyter_client/connect.py", line 547, in write_connection_file
kernel_name=self.kernel_name
File "/home/djan/anaconda3/lib/python3.7/site-packages/jupyter_client/connect.py", line 212, in write_connection_file
with secure_write(fname) as f:
File "/home/djan/anaconda3/lib/python3.7/contextlib.py", line 112, in __enter__
return next(self.gen)
File "/home/djan/anaconda3/lib/python3.7/site-packages/jupyter_client/connect.py", line 105, in secure_write
assert '0600' == oct(stat.S_IMODE(os.stat(fname).st_mode)).replace('0o', '0')
AssertionError
System information
Running Jupyter (v. 1.0.0) on a Linux server, with anaconda3 (v. 2019.07) 64-bit.
Available Kernels
Available kernels:
python3 /home/djan/.local/share/jupyter/kernels/python3
nn /home/djan/.local/share/jupyter/kernels/nn
Reproducing the issue
Install the newest anaconda3 version.
Run Jupyter notebook in the base version --> Kernel runs fine
Create a new environment with python: conda create -n test python=3.7
After activating the environment, Jupyter notebook is not available, thus I must install it via Conda: conda install -c anaconda jupyter
Run Jupyter notebook in the test environment --> Kernel breaks down as explained above
What I tried so far
There seems to be an issue with file permissions when running Jupyter on a server inside a Conda environment. I tried to give all files inside my anaconda3 folder the requested permissions (0600), but this did not help.
Update
It turns out that the newest version of jupyter_client, available under anaconda as version 5.3.3, breaks the Jupyter environment on a server.
Installing the previous version of jupyter_client via following command fixes this issue:
conda install -c anaconda jupyter_client=5.3.1
nice
Update
It turns out that the newest version of jupyter_client, available under anaconda as version 5.3.3, breaks the Jupyter environment on a server.
Installing the previous version of jupyter_client via following command fixes this issue:
conda install -c anaconda jupyter_client=5.3.1
Related
I was playing around with different flake8 plugins today and after uninstalling one of them and installing a new one, flake8 --version no longer works for me.
the flake8 packages I had at the time were
(python3) $ flake8 --version 3.8.4 (flake8-bugbear: 20.11.1, mccabe: 0.6.1, naming: 0.11.1, pycodestyle: 2.6.0, pyflakes: 2.2.0) CPython 3.8.2 on Darwin
after which I had ran
pip uninstalled flake8-bugbear
pip install flake8-docstrings
pip uninstall flake8-docstrings
pip install flake8-comprehensions
It now breaks with this error on flake8 --version
(python3) $ flake8 --version
Traceback (most recent call last):
File "/Users/dtan/code/python3/bin/flake8", line 8, in <module>
sys.exit(main())
File "/Users/dtan/code/python3/lib/python3.8/site-packages/flake8/main/cli.py", line 22, in main
app.run(argv)
File "/Users/dtan/code/python3/lib/python3.8/site-packages/flake8/main/application.py", line 363, in run
self._run(argv)
File "/Users/dtan/code/python3/lib/python3.8/site-packages/flake8/main/application.py", line 350, in _run
self.initialize(argv)
File "/Users/dtan/code/python3/lib/python3.8/site-packages/flake8/main/application.py", line 332, in initialize
self.parse_configuration_and_cli(
File "/Users/dtan/code/python3/lib/python3.8/site-packages/flake8/main/application.py", line 182, in parse_configuration_and_cli
self.options, self.args = aggregator.aggregate_options(
File "/Users/dtan/code/python3/lib/python3.8/site-packages/flake8/options/aggregator.py", line 45, in aggregate_options
parsed_config = config_parser.parse()
File "/Users/dtan/code/python3/lib/python3.8/site-packages/flake8/options/config.py", line 312, in parse
return self.merge_user_and_local_config()
File "/Users/dtan/code/python3/lib/python3.8/site-packages/flake8/options/config.py", line 277, in merge_user_and_local_config
config = self.parse_local_config()
File "/Users/dtan/code/python3/lib/python3.8/site-packages/flake8/options/config.py", line 240, in parse_local_config
return self._parse_config(config)
File "/Users/dtan/code/python3/lib/python3.8/site-packages/flake8/options/config.py", line 217, in _parse_config
value = method(self.program_name, option_name)
File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/configparser.py", line 828, in getboolean
return self._get_conv(section, option, self._convert_to_boolean,
File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/configparser.py", line 808, in _get_conv
return self._get(section, conv, option, raw=raw, vars=vars,
File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/configparser.py", line 803, in _get
return conv(self.get(section, option, **kwargs))
File "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/configparser.py", line 1163, in _convert_to_boolean
raise ValueError('Not a boolean: %s' % value)
ValueError: Not a boolean: true # Print the source code generating the error/warning in question
I've already tried uninstalling & reinstalling flake8 with no luck. I assume that something is broken on the documentation stuff since doing flake8 --help will also throw this error
It seems one of the plugins had added a config parser and changed one of the configuration files. When uninstalled the parser was removed but it left the changes in config file(s).
You need to run through all flake8 config files and remove config sections for uninstalled plugins.
Question
In Jupyter notebook, how to solve the issue of Python interpreter not found.
Environment
Ubuntu 18.04
Anaconda environment with Python 3.7
Problem
Start a jupyter notebook and create a notebook with Python 3 kernel and get the error. nlp_in_tensorflow was a conda environment already removed.
Traceback (most recent call last):
File "/home/user/conda/envs/cs231n/lib/python3.7/site-packages/tornado/web.py", line 1704, in _execute
result = await result
File "/home/user/conda/envs/cs231n/lib/python3.7/site-packages/tornado/gen.py", line 769, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/home/user/conda/envs/cs231n/lib/python3.7/site-packages/notebook/services/sessions/handlers.py", line 72, in post
type=mtype))
File "/home/user/conda/envs/cs231n/lib/python3.7/site-packages/tornado/gen.py", line 762, in run
value = future.result()
File "/home/user/conda/envs/cs231n/lib/python3.7/site-packages/tornado/gen.py", line 769, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/home/user/conda/envs/cs231n/lib/python3.7/site-packages/notebook/services/sessions/sessionmanager.py", line 88, in create_session
kernel_id = yield self.start_kernel_for_session(session_id, path, name, type, kernel_name)
File "/home/user/conda/envs/cs231n/lib/python3.7/site-packages/tornado/gen.py", line 762, in run
value = future.result()
File "/home/user/conda/envs/cs231n/lib/python3.7/site-packages/tornado/gen.py", line 769, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/home/user/conda/envs/cs231n/lib/python3.7/site-packages/notebook/services/sessions/sessionmanager.py", line 101, in start_kernel_for_session
self.kernel_manager.start_kernel(path=kernel_path, kernel_name=kernel_name)
File "/home/user/conda/envs/cs231n/lib/python3.7/site-packages/tornado/gen.py", line 762, in run
value = future.result()
File "/home/user/conda/envs/cs231n/lib/python3.7/site-packages/notebook/services/kernels/kernelmanager.py", line 176, in start_kernel
kernel_id = await maybe_future(self.pinned_superclass.start_kernel(self, **kwargs))
File "/home/user/conda/envs/cs231n/lib/python3.7/site-packages/jupyter_client/multikernelmanager.py", line 185, in start_kernel
km.start_kernel(**kwargs)
File "/home/user/conda/envs/cs231n/lib/python3.7/site-packages/jupyter_client/manager.py", line 313, in start_kernel
self.kernel = self._launch_kernel(kernel_cmd, **kw)
File "/home/user/conda/envs/cs231n/lib/python3.7/site-packages/jupyter_client/manager.py", line 220, in _launch_kernel
return launch_kernel(kernel_cmd, **kw)
File "/home/user/conda/envs/cs231n/lib/python3.7/site-packages/jupyter_client/launcher.py", line 131, in launch_kernel
proc = Popen(cmd, **kwargs)
File "/home/user/conda/envs/cs231n/lib/python3.7/subprocess.py", line 800, in __init__
restore_signals, start_new_session)
File "/home/user/conda/envs/cs231n/lib/python3.7/subprocess.py", line 1551, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: '/home/user/conda/envs/nlp_in_tensorflow/bin/python3': '/home/user/conda/envs/nlp_in_tensorflow/bin/python3'
Cause
The kernel.json file of the Python 3 kernel was pointing to the deleted environment.
$ jupyter kernelspec list
Available kernels:
python3 /home/oonisim/.local/share/jupyter/kernels/python3
$ cat ~/.local/share/jupyter/kernels/python3/kernel.json
{
"argv": [
"/home/user/conda/envs/nlp_in_tensorflow/bin/python3", <----- Referring to the deleted environment
"-m",
"ipykernel_launcher",
"-f",
"{connection_file}"
],
"display_name": "Python 3",
"language": "python"
}
Resource
What to do when things go wrong - Python Environments
Multiple python environments, whether based on Anaconda or Python
Virtual environments, are often the source of reported issues. In many
cases, these issues stem from the Notebook server running in one
environment, while the kernel and/or its resources, derive from
another environment.
Another thing to check is the kernel.json file that will be located in
the aforementioned kernel specs directory identified by running
jupyter kernelspec list. This file will contain an argv stanza that
includes the actual command to run when launching the kernel.
Oftentimes, when reinstalling python environments, a previous
kernel.json will reference an python executable from an old or
non-existent location. As a result, it’s always a good idea when
encountering kernel startup issues to validate the argv stanza to
ensure all file references exist and are appropriate.
Fix
Removed ~/.local/share/jupyter/kernels/python3/kernel.json.
Related issues
Jupyter Notebook is loading incorrect Python kernel #2563
Running Jupyter with multiple Python and IPython paths - 3. How Jupyter knows what Python to use
Jupyter is set-up to be able to use a wide range of "kernels", or
execution engines for the code. These can be Python 2, Python 3, R,
Julia, Ruby... there are dozens of possible kernels to use. But in
order for this to happen, Jupyter needs to know where to look for the
associated executable: that is, it needs to know which path the python
sits in.
These paths are specified in jupyter's kernelspec, and it's possible
for the user to adjust them to their desires. For example, here's the
list of kernels that I have on my system:
I tried to use the Anaconda Navigator, but I'm getting this kernel error.
I had previously installed python 3.8 without Anaconda and had installed jupyter in it using pip, then I uninstalled it and installed Anaconda again.
Since then this error arises whenever I try to compile a file and even in the jupyter notebook.
I tried :
1.) Reinstalling Anaconda
2.) Updating the setup tools
None of these worked.
Traceback (most recent call last):
File "C:\Users\DELLL\Anaconda3\lib\site-packages\tornado\web.py", line 1699, in _execute
result = await result
File "C:\Users\DELLL\Anaconda3\lib\site-packages\tornado\gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "C:\Users\DELLL\Anaconda3\lib\site-packages\notebook\services\sessions\handlers.py", line 72, in post
type=mtype))
File "C:\Users\DELLL\Anaconda3\lib\site-packages\tornado\gen.py", line 735, in run
value = future.result()
File "C:\Users\DELLL\Anaconda3\lib\site-packages\tornado\gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "C:\Users\DELLL\Anaconda3\lib\site-packages\notebook\services\sessions\sessionmanager.py", line 88, in create_session
kernel_id = yield self.start_kernel_for_session(session_id, path, name, type, kernel_name)
File "C:\Users\DELLL\Anaconda3\lib\site-packages\tornado\gen.py", line 735, in run
value = future.result()
File "C:\Users\DELLL\Anaconda3\lib\site-packages\tornado\gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "C:\Users\DELLL\Anaconda3\lib\site-packages\notebook\services\sessions\sessionmanager.py", line 101, in start_kernel_for_session
self.kernel_manager.start_kernel(path=kernel_path, kernel_name=kernel_name)
File "C:\Users\DELLL\Anaconda3\lib\site-packages\tornado\gen.py", line 735, in run
value = future.result()
File "C:\Users\DELLL\Anaconda3\lib\site-packages\tornado\gen.py", line 209, in wrapper
yielded = next(result)
File "C:\Users\DELLL\Anaconda3\lib\site-packages\notebook\services\kernels\kernelmanager.py", line 168, in start_kernel
super(MappingKernelManager, self).start_kernel(**kwargs)
File "C:\Users\DELLL\Anaconda3\lib\site-packages\jupyter_client\multikernelmanager.py", line 110, in start_kernel
km.start_kernel(**kwargs)
File "C:\Users\DELLL\Anaconda3\lib\site-packages\jupyter_client\manager.py", line 240, in start_kernel
self.write_connection_file()
File "C:\Users\DELLL\Anaconda3\lib\site-packages\jupyter_client\connect.py", line 547, in write_connection_file
kernel_name=self.kernel_name
File "C:\Users\DELLL\Anaconda3\lib\site-packages\jupyter_client\connect.py", line 212, in write_connection_file
with secure_write(fname) as f:
File "C:\Users\DELLL\Anaconda3\lib\contextlib.py", line 112, in __enter__
return next(self.gen)
File "C:\Users\DELLL\Anaconda3\lib\site-packages\jupyter_client\connect.py", line 102, in secure_write
with os.fdopen(os.open(fname, open_flag, 0o600), mode) as f:
PermissionError: [Errno 13] Permission denied: 'C:\\Users\\DELLL\\AppData\\Roaming\\jupyter\\runtime\\kernel-4058ed7c-98d6-40c9-8b3b-2cbb069740d8.json'
Issue resolved.
The problem:
I had previously installed jupyter using pip install, when I was working on python 3.8.
Now, I uninstalled python 3.8 and installed Anaconda instead. This again reinstalled jupyter, thus was the cause of the problem.
To resolve this, I uninstalled jupyter from AnacondaPrompt using conda uninstall jupyter , and then reinstalled it, this time from conda install jupyter.
This resolved the kernel error.
This is permission issue for that particular folder
Set the environment path variables C:\Users\DELL\AppData\Roaming\jupyter\runtime
give the permission and it will work
I am trying to use jupyter notebook with Python 3.7 on Windows10 for work and am running behind my office network proxy. I was able to run the notebook all fine till a few days ago. Now it keeps showing that the kernel is dead whenever I open the notebook. I get this error to be specific:
File "C:\Users\shreeya.mody\AppData\Local\Continuum\anaconda3\lib\site-packages\tornado\web.py", line 1699, in _execute
result = await result
File "C:\Users\shreeya.mody\AppData\Local\Continuum\anaconda3\lib\site-packages\tornado\gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "C:\Users\shreeya.mody\AppData\Local\Continuum\anaconda3\lib\site-packages\notebook\services\sessions\handlers.py", line 72, in post
type=mtype))
File "C:\Users\shreeya.mody\AppData\Local\Continuum\anaconda3\lib\site-packages\tornado\gen.py", line 735, in run
value = future.result()
File "C:\Users\shreeya.mody\AppData\Local\Continuum\anaconda3\lib\site-packages\tornado\gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "C:\Users\shreeya.mody\AppData\Local\Continuum\anaconda3\lib\site-packages\notebook\services\sessions\sessionmanager.py", line 88, in create_session
kernel_id = yield self.start_kernel_for_session(session_id, path, name, type, kernel_name)
File "C:\Users\shreeya.mody\AppData\Local\Continuum\anaconda3\lib\site-packages\tornado\gen.py", line 735, in run
value = future.result()
File "C:\Users\shreeya.mody\AppData\Local\Continuum\anaconda3\lib\site-packages\tornado\gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "C:\Users\shreeya.mody\AppData\Local\Continuum\anaconda3\lib\site-packages\notebook\services\sessions\sessionmanager.py", line 101, in start_kernel_for_session
self.kernel_manager.start_kernel(path=kernel_path, kernel_name=kernel_name)
File "C:\Users\shreeya.mody\AppData\Local\Continuum\anaconda3\lib\site-packages\tornado\gen.py", line 735, in run
value = future.result()
File "C:\Users\shreeya.mody\AppData\Local\Continuum\anaconda3\lib\site-packages\tornado\gen.py", line 209, in wrapper
yielded = next(result)
File "C:\Users\shreeya.mody\AppData\Local\Continuum\anaconda3\lib\site-packages\notebook\services\kernels\kernelmanager.py", line 168, in start_kernel
super(MappingKernelManager, self).start_kernel(**kwargs)
File "C:\Users\shreeya.mody\AppData\Local\Continuum\anaconda3\lib\site-packages\jupyter_client\multikernelmanager.py", line 110, in start_kernel
km.start_kernel(**kwargs)
File "C:\Users\shreeya.mody\AppData\Local\Continuum\anaconda3\lib\site-packages\jupyter_client\manager.py", line 240, in start_kernel
self.write_connection_file()
File "C:\Users\shreeya.mody\AppData\Local\Continuum\anaconda3\lib\site-packages\jupyter_client\connect.py", line 547, in write_connection_file
kernel_name=self.kernel_name
File "C:\Users\shreeya.mody\AppData\Local\Continuum\anaconda3\lib\site-packages\jupyter_client\connect.py", line 212, in write_connection_file
with secure_write(fname) as f:
File "C:\Users\shreeya.mody\AppData\Local\Continuum\anaconda3\lib\contextlib.py", line 112, in __enter__
return next(self.gen)
File "C:\Users\shreeya.mody\AppData\Local\Continuum\anaconda3\lib\site-packages\jupyter_client\connect.py", line 102, in secure_write
with os.fdopen(os.open(fname, open_flag, 0o600), mode) as f:
PermissionError: [Errno 13] Permission denied: 'C:\\Users\\shreeya.mody\\AppData\\Roaming\\jupyter\\runtime\\kernel-0068da95-ca03-4be1-b2c0-4814f6f887f3.json'
What I have tried
I have exhausted all the solutions online but nothing so far has worked for me
Checked permission for files. Looks correct to me
Uninstalled and reinstalled Anaconda multiple times
Installed anaconda on a work VM to duplicate the error but it works fine there which makes me think that the error is connected to the kernel files somehow that I cannot point at.
Started notebook from Anaconda Prompt
I want to work on Jupyter notebook on my local machine but no solution I have come across works for me.
The command line commands from the comments help:
conda clean -tipsy
conda uninstall jupyter
conda install jupyter
But after the lines the conda environment is almost completely empty. In my case I needed to install numpy and pandas libraries.
Last version of anaconda, windows 10, python 3.6.
Installing tensorflow seems to break pip.
>conda create -n py6 python=3.6
>activate py6
>conda install tensorflow
>pip install tweepy
Collecting tweepy
Exception:
Traceback (most recent call last):
File "C:\Programs\Anaconda3\envs\py6\lib\site-packages\pip\basecommand.py", line 215, in main
status = self.run(options, args)
File "C:\Programs\Anaconda3\envs\py6\lib\site-packages\pip\commands\install.py", line 335, in run
wb.build(autobuilding=True)
File "C:\Programs\Anaconda3\envs\py6\lib\site-packages\pip\wheel.py", line 749, in build
self.requirement_set.prepare_files(self.finder)
File "C:\Programs\Anaconda3\envs\py6\lib\site-packages\pip\req\req_set.py", line 380, in prepare_files
ignore_dependencies=self.ignore_dependencies))
File "C:\Programs\Anaconda3\envs\py6\lib\site-packages\pip\req\req_set.py", line 554, in _prepare_file
require_hashes
File "C:\Programs\Anaconda3\envs\py6\lib\site-packages\pip\req\req_install.py", line 278, in populate_link
self.link = finder.find_requirement(self, upgrade)
File "C:\Programs\Anaconda3\envs\py6\lib\site-packages\pip\index.py", line 465, in find_requirement
all_candidates = self.find_all_candidates(req.name)
File "C:\Programs\Anaconda3\envs\py6\lib\site-packages\pip\index.py", line 423, in find_all_candidates
for page in self._get_pages(url_locations, project_name):
File "C:\Programs\Anaconda3\envs\py6\lib\site-packages\pip\index.py", line 568, in _get_pages
page = self._get_page(location)
File "C:\Programs\Anaconda3\envs\py6\lib\site-packages\pip\index.py", line 683, in _get_page
return HTMLPage.get_page(link, session=self.session)
File "C:\Programs\Anaconda3\envs\py6\lib\site-packages\pip\index.py", line 811, in get_page
inst = cls(resp.content, resp.url, resp.headers)
File "C:\Programs\Anaconda3\envs\py6\lib\site-packages\pip\index.py", line 731, in __init__
namespaceHTMLElements=False,
TypeError: parse() got an unexpected keyword argument 'transport_encoding'
Use of tweepy is just an example, pip cannot install any package.
The same happens when installing tensorflow using pip, and when using a python 3.5 virtual environment.
Probably this is due to some package update gone wrong, and it will be fixed in the next update.
Meanwhile, any fix or any careful selection of working version numbers is welcome.
This issues is reported in the following ticket : https://github.com/tensorflow/tensorboard/issues/588
To solve this, you need to repair html5lib.
Or alternatively,
you can make use of anaconda to re-install
conda install -c anaconda html5lib