PermissionError when starting IPython console kernels on macOS and Linux

[paosferrazza]

Description

What steps will reproduce the problem?

The error is:

Traceback (most recent call last):
File "/home/ermes/anaconda3/lib/python3.11/site‑packages/spyder/plugins/ipythonconsole/widgets/main_widget.py", line 2142, in create_kernel_manager_and_kernel_client
kernel_manager.start_kernel(stderr=stderr_handle,
File "/home/ermes/anaconda3/lib/python3.11/site‑packages/jupyter_core/utils/init.py", line 173, in wrapped
return loop.run_until_complete(inner)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ermes/anaconda3/lib/python3.11/asyncio/base_events.py", line 653, in run_until_complete
return future.result()
^^^^^^^^^^^^^^^
File "/home/ermes/anaconda3/lib/python3.11/site‑packages/jupyter_client/manager.py", line 96, in wrapper
raise e
File "/home/ermes/anaconda3/lib/python3.11/site‑packages/jupyter_client/manager.py", line 87, in wrapper
out = await method(self, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ermes/anaconda3/lib/python3.11/site‑packages/jupyter_client/manager.py", line 439, in _async_start_kernel
await self._async_launch_kernel(kernel_cmd, **kw)
File "/home/ermes/anaconda3/lib/python3.11/site‑packages/jupyter_client/manager.py", line 354, in _async_launch_kernel
connection_info = await self.provisioner.launch_kernel(kernel_cmd, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ermes/anaconda3/lib/python3.11/site‑packages/jupyter_client/provisioning/local_provisioner.py", line 210, in launch_kernel
self.process = launch_kernel(cmd, **scrubbed_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ermes/anaconda3/lib/python3.11/site‑packages/jupyter_client/launcher.py", line 170, in launch_kernel
raise ex
File "/home/ermes/anaconda3/lib/python3.11/site‑packages/jupyter_client/launcher.py", line 155, in launch_kernel
proc = Popen(cmd, **kwargs) # noqa
^^^^^^^^^^^^^^^^^^^^
File "/home/ermes/anaconda3/lib/python3.11/subprocess.py", line 1026, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "/home/ermes/anaconda3/lib/python3.11/subprocess.py", line 1950, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied: '/home/ermes/anaconda3/lib/python3.11/site‑packages/spyder/plugins/ipythonconsole/scripts/conda‑activate.sh'

Traceback

Traceback (most recent call last):
  File "/home/ermes/anaconda3/lib/python3.11/site-packages/spyder/plugins/ipythonconsole/plugin.py", line 648, in run_script
    self.get_widget().run_script(
  File "/home/ermes/anaconda3/lib/python3.11/site-packages/spyder/plugins/ipythonconsole/widgets/main_widget.py", line 2343, in run_script
    client = self.create_client_for_file(
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ermes/anaconda3/lib/python3.11/site-packages/spyder/plugins/ipythonconsole/widgets/main_widget.py", line 1833, in create_client_for_file
    client.allow_rename = False
    ^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'allow_rename'

Versions

• Spyder version: 5.5.2 (conda)
• Python version: 3.11.5 64-bit
• Qt version: 5.15.2
• PyQt5 version: 5.15.10
• Operating System: Linux-6.5.0-25-generic-x86_64-with-glibc2.35

Dependencies

# Mandatory:
atomicwrites >=1.2.0             :  1.4.0 (OK)
chardet >=2.0.0                  :  4.0.0 (OK)
cloudpickle >=0.5.0              :  2.2.1 (OK)
cookiecutter >=1.6.0             :  2.5.0 (OK)
diff_match_patch >=20181111      :  20200713 (OK)
intervaltree >=3.0.2             :  3.1.0 (OK)
IPython >=8.13.0,<9.0.0,!=8.17.1 :  8.20.0 (OK)
jedi >=0.17.2,<0.20.0            :  0.18.1 (OK)
jellyfish >=0.7                  :  1.0.1 (OK)
jsonschema >=3.2.0               :  4.19.2 (OK)
keyring >=17.0.0                 :  23.13.1 (OK)
nbconvert >=4.0                  :  7.10.0 (OK)
numpydoc >=0.6.0                 :  1.5.0 (OK)
parso >=0.7.0,<0.9.0             :  0.8.3 (OK)
pexpect >=4.4.0                  :  4.8.0 (OK)
pickleshare >=0.4                :  0.7.5 (OK)
psutil >=5.3                     :  5.9.0 (OK)
pygments >=2.0                   :  2.15.1 (OK)
pylint >=2.5.0,<3.1              :  2.16.2 (OK)
pylint_venv >=3.0.2              :  3.0.3 (OK)
pyls_spyder >=0.4.0              :  0.4.0 (OK)
pylsp >=1.10.0,<1.11.0           :  1.10.0 (OK)
pylsp_black >=2.0.0,<3.0.0       :  2.0.0 (OK)
qdarkstyle >=3.2.0,<3.3.0        :  3.2.3 (OK)
qstylizer >=0.2.2                :  0.2.2 (OK)
qtawesome >=1.2.1,<1.3.0         :  1.2.2 (OK)
qtconsole >=5.5.1,<5.6.0         :  5.5.1 (OK)
qtpy >=2.1.0                     :  2.4.1 (OK)
rtree >=0.9.7                    :  1.0.1 (OK)
setuptools >=49.6.0              :  68.0.0 (OK)
sphinx >=0.6.6                   :  5.0.2 (OK)
spyder_kernels >=2.5.1,<2.6.0    :  2.5.1 (OK)
textdistance >=4.2.0             :  4.2.1 (OK)
three_merge >=0.1.1              :  0.1.1 (OK)
watchdog >=0.10.3                :  2.1.6 (OK)
xdg >=0.26                       :  0.27 (OK)
zmq >=24.0.0                     :  25.1.2 (OK)

# Optional:
cython >=0.21                    :  None (NOK)
matplotlib >=3.0.0               :  3.8.0 (OK)
numpy >=1.7                      :  1.23.5 (OK)
pandas >=1.1.1                   :  1.5.3 (OK)
scipy >=0.17.0                   :  1.10.0 (OK)
sympy >=0.7.3                    :  1.12 (OK)

[ccordoba12]

Hey @paosferrazza, thanks for reporting. Please open a terminal, run there this command

ls -la /home/ermes/anaconda3/lib/python3.11/site‑packages/spyder/plugins/ipythonconsole/scripts/conda‑activate.sh

and report back the result. That will let us know what's happening in your case.

[paosferrazza]

~$ ls -la /home/ermes/anaconda3/lib/python3.11/site-packages/spyder/plugins/ipythonconsole/scripts/conda-activate.sh
-rw-rw-r-- 2 ermes ermes 518 mar 13 22:15 /home/ermes/anaconda3/lib/python3.11/site-packages/spyder/plugins/ipythonconsole/scripts/conda-activate.sh

[remisalmon]

Same issue here on macOS, spyder is looking for conda‑activate.sh in site‑packages but the file is conda-activate.sh in site-packages, the dash symbol is a different...

PermissionError: [Errno 13] Permission denied: '<$pathto>/lib/python3.11/site‑packages/spyder/plugins/ipythonconsole/scripts/conda‑activate.sh'

> ls -la <$pathto>/lib/python3.11/site‑packages/spyder/plugins/ipythonconsole/scripts/conda‑activate.sh
ls: cannot access '<$pathto>/lib/python3.11/site‑packages/spyder/plugins/ipythonconsole/scripts/conda‑activate.sh': No such file or directory
> ls -la $pathto/lib/python3.11/site-packages/spyder/
plugins/ipythonconsole/scripts/conda-activate.sh
-rw-r--r-- 3 remisalmon staff 518 Mar 13 15:24 <$pathto>/lib/python3.11/site-packages/spyder/plugins/ipythonconsole/scripts/conda-activate.sh

[waeiski]

Same issue exists on Linux (Manjaro) as well.

[JC-NH]

Similar error starting kernal

• Spyder version: 5.5.2 (conda)
• Python version: 3.12.2 64-bit
• Qt version: 5.15.2
• PyQt5 version: 5.15.10
• Operating System: Linux-5.15.146.1-microsoft-standard-WSL2-x86_64-with-glibc2.35

The error is:

Traceback (most recent call last):
File "/home/jim/anaconda3/envs/DSX/lib/python3.12/site‑packages/spyder/plugins/ipythonconsole/widgets/main_widget.py", line 2142, in create_kernel_manager_and_kernel_client
kernel_manager.start_kernel(stderr=stderr_handle,
File "/home/jim/anaconda3/envs/DSX/lib/python3.12/site‑packages/jupyter_core/utils/init.py", line 165, in wrapped
return loop.run_until_complete(inner)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jim/anaconda3/envs/DSX/lib/python3.12/asyncio/base_events.py", line 685, in run_until_complete
return future.result()
^^^^^^^^^^^^^^^
File "/home/jim/anaconda3/envs/DSX/lib/python3.12/site‑packages/jupyter_client/manager.py", line 96, in wrapper
raise e
File "/home/jim/anaconda3/envs/DSX/lib/python3.12/site‑packages/jupyter_client/manager.py", line 87, in wrapper
out = await method(self, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jim/anaconda3/envs/DSX/lib/python3.12/site‑packages/jupyter_client/manager.py", line 439, in _async_start_kernel
await self._async_launch_kernel(kernel_cmd, **kw)
File "/home/jim/anaconda3/envs/DSX/lib/python3.12/site‑packages/jupyter_client/manager.py", line 354, in _async_launch_kernel
connection_info = await self.provisioner.launch_kernel(kernel_cmd, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jim/anaconda3/envs/DSX/lib/python3.12/site‑packages/jupyter_client/provisioning/local_provisioner.py", line 210, in launch_kernel
self.process = launch_kernel(cmd, **scrubbed_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jim/anaconda3/envs/DSX/lib/python3.12/site‑packages/jupyter_client/launcher.py", line 170, in launch_kernel
raise ex
File "/home/jim/anaconda3/envs/DSX/lib/python3.12/site‑packages/jupyter_client/launcher.py", line 155, in launch_kernel
proc = Popen(cmd, **kwargs) # noqa
^^^^^^^^^^^^^^^^^^^^
File "/home/jim/anaconda3/envs/DSX/lib/python3.12/subprocess.py", line 1026, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "/home/jim/anaconda3/envs/DSX/lib/python3.12/subprocess.py", line 1953, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied: '/home/jim/anaconda3/envs/DSX/lib/python3.12/site‑packages/spyder/plugins/ipythonconsole/scripts/conda‑activate.sh'

Under "/home/jim/anaconda3/envs" I have two DSX directories. One created 12/30/2022 for which I have no permission to access the lib directory. and one created 3/13/2024 where I do have access to conda-activate.sh

[JC-NH]

As an addendum to the last post: Reverting to spyder 5.5.1, the kernel does now start. While only one DSX environment is listed by "conda env list" the two folders still exist in "/home/jim/anaconda3/envs"

[dalthviz]

Hi there, checking seems like the conda-activate.sh script is installed without executable permissions :/ Also, as mentioned at #21892 (comment) another thing that is missleading is that in the console error message the dash character is replaced, that causes an error when trying to check the related path in a terminal (with a message that the file/path doesn't exists). As a workaround seems like manually locating and adding executable permission to the conda-activate.sh works so something like:

cd <your env path up to site-packages>/site-packages/spyder/plugins/ipythonconsole/scripts
chmod +x conda-activate.sh

Not totally sure why the script is not preserving the executable bit on, maybe an error happened while I was building the wheel that I didn't noticed? 🤔

[JC-NH]

Daniel, Thanks for the help. You were correct about the dash in the error message was replaced. I followed your instructions and changed the permissions on conda-activate.sh and everything seems to work.

…

________________________________ From: Daniel Althviz Moré ***@***.***> Sent: Friday, March 15, 2024 4:42 PM To: spyder-ide/spyder ***@***.***> Cc: JC-NH ***@***.***>; Comment ***@***.***> Subject: Re: [spyder-ide/spyder] Kernel doesn't start - permission denied (Issue #21892) Hi there, checking seems like the conda-activate.sh script is installed without executable permissions :/ Also, as mentioned at #21892 (comment)<#21892 (comment)> another thing that is missleading is that in the console error message the dash character is replaced, that causes an error when trying to check the related path in a terminal (with a message that the file/path doesn't exists). As a workaround seems like manually locating and adding executable permission to the conda-activate.sh works so something like: cd <your env path up to site-packages>/site-packages/spyder/plugins/ipythonconsole/scripts chmod +x conda-activate.sh Not totally sure why the script is not preserving the executable bit on, maybe an error happened while I was building the wheel that I didn't noticed? 🤔 — Reply to this email directly, view it on GitHub<#21892 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A5AXSLNPLPA4TL6ZLFNNOQLYYNMKDAVCNFSM6AAAAABEV34ZH6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMBQGQYTGNJQGU>. You are receiving this because you commented.Message ID: ***@***.***>

[ccordoba12]

Hey everyone, as @dalthviz mentioned, this is caused by conda-activate.sh not having the executable bit on Mac and Linux.

We'll fix that by releasing 5.5.3 as soon as possible with that small change. In the meantime, you can follow @dalthviz's instructions to work around it.

[ccordoba12]

Closing to get started with the release.