I'm on Pop-os 22.04 and I updated my default Python from 3.10 to 3.11. After updating python I'm getting this error every time I try to do "sudo apt update"
$ sudo apt update
**Note: Skiped first few lines, those were not errors.**
Traceback (most recent call last):
File "/usr/lib/cnf-update-db", line 3, in <module>
import apt_pkg
ModuleNotFoundError: No module named 'apt_pkg'
Reading package lists... Done
E: Problem executing scripts APT::Update::Post-Invoke-Success 'if /usr/bin/test -w /var/lib/command-not-found/ -a -e /usr/lib/cnf-update-db; then /usr/lib/cnf-update-db > /dev/null; fi'
E: Sub-process returned an error code
If I change my default python version back to 3.10 this error doesn't occure anymore.
I did this to change my python version:
$ sudo update-alternatives --config python3
There are 2 choices for the alternative python3 (providing /usr/bin/python3).
Selection Path Priority Status
------------------------------------------------------------
0 /usr/bin/python3.11 2 auto mode
* 1 /usr/bin/python3.10 1 manual mode
2 /usr/bin/python3.11 2 manual mode
Press <enter> to keep the current choice[*], or type selection number: 2
Extremely Sorry for my bad English
Related
I have a bash script where i will be creating conda virtual environment and install packages into it.
currently we are using conda version 4.5.12 with python 3.6 in my virtual environment.
Am trying to upgrade conda version to 4.9.2 with python 3.6.
conda --version
4.9.2
This is the command i use inside my script
conda create -y --name virtual_env python=3.6
This Runs and fails during Download and Extracting Packages Step. Below is the Error Report
Traceback (most recent call last):
File "/root/project/miniconda/lib/python3.9/site-packages/conda/exceptions.py", line 1079, in __call__
return func(*args, **kwargs)
File "/root/project/miniconda/lib/python3.9/site-packages/conda/cli/main.py", line 84, in _main
exit_code = do_call(args, p)
File "/root/project/miniconda/lib/python3.9/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
return getattr(module, func_name)(args, parser)
File "/root/project/miniconda/lib/python3.9/site-packages/conda/cli/main_create.py", line 41, in execute
install(args, parser, 'create')
File "/root/project/miniconda/lib/python3.9/site-packages/conda/cli/install.py", line 317, in install
handle_txn(unlink_link_transaction, prefix, args, newenv)
File "/root/project/miniconda/lib/python3.9/site-packages/conda/cli/install.py", line 346, in handle_txn
unlink_link_transaction.execute()
File "/root/project/miniconda/lib/python3.9/site-packages/conda/core/link.py", line 249, in execute
self._execute(tuple(concat(interleave(itervalues(self.prefix_action_groups)))))
File "/root/project/miniconda/lib/python3.9/site-packages/conda/core/link.py", line 712, in _execute
raise CondaMultiError(tuple(concatv(
conda.CondaMultiError: No compatible shell found!
()
Experts Please help.
Adding briefs of the script
#!/bin/bash
set -e
install_conda_for_linux(){
#
# Determine Installation Location for non Windows systems
#
#Get path where miniconda needs to get installed and remove if anything exixsts already#
downloaded_file=$base_dir/$conda_file
output_formatted Removing file: $downloaded_file
rm -f $downloaded_file
#
# Download Miniconda
#
output_formatted Downloading Miniconda from: $conda_url '\n' Saving file in: $base_dir
curl -L $conda_url > $base_dir/$conda_file
#
# Install Miniconda
#
rm -rf $install_dir
bash $base_dir/$conda_file -b -p $install_dir
#
# Modify PATH
#
conda_path=$install_dir/bin
export PATH=$conda_path:\$PATH
conda_version=`conda --version`
}
#
# Variables
#
pyversion=3
python_version="3.6.10"
conda_version="4.9.2"
skip_install=$1
base_url='https://repo.anaconda.com/miniconda'
virtual_env=venv
#conda_file is only specified for use in messages below on Windows, as it is manual install, which must be done before running this script.
declare -A conda_file_map
conda_file_map[Linux]="Miniconda${pyversion}-py39_${conda_version}-Linux-x86_64.sh"
conda_file=${conda_file_map[${os_type}]}
#
# Installation of conda and its dependencies
#
if [ ${skip_install} != 'true' ];then
conda_url=${base_url}/${conda_file}
install_conda_for_linux
#
# Create Environment
#
output_formatted Creating new virtual environment: $virtual_env for python_version $python_version
conda create -y -vv --name $virtual_env python=$python_version
Here's your bug:
conda_path=$install_dir/bin
export PATH=$conda_path:\$PATH
Let's say install_dir=/path/to/install, and the starting value of PATH is PATH=/bin:/usr/bin:/usr/local/bin (which is how which sh finds /bin/sh or /usr/bin/sh).
After you ran this command, because of the backslash, you don't have PATH=/path/to/install/bin:/bin:/usr/bin:/usr/local/bin (which is what you want), but instead you have PATH=/path/to/install/bin:$PATH; the backslash caused the literal string $PATH to be added to your variable, instead of the string that's contained therein.
Thus, /bin and /usr/bin are no longer listed in your PATH variable, so which can't find them.
To fix this, just make it:
conda_path=$install_dir/bin
PATH=$conda_path:$PATH
The big fix is changing \$PATH to just $PATH -- but beyond that, you don't need the export (changes to variables that are already in the environment are automatically re-exported), and having it adds complexity for no good reason.
Take the example of pip
We can do
1) Assume command is there and run pip install somepackage. Fail if it gives an exit 1
pip install somepackage || exit 1
2) Attempt to install pip
wget <path online to pip>; pip install somepackage
3) Check pip exists
pip --version || wget <path online to pip> && pip install somepackage
Is there a better way than either of these to check for the existance with the least resource usage
Your Python script doesn't have code like
try:
import requests
except ImportError:
import subprocess
subprocess.call(["pip", "install", "requests"])
Instead, you have an installer that ensures that requests has been installed
before you run your script.
The same logic applies to your shell script. It isn't your script's job to install pip if it's missing; whoever runs the script should ensure that pip is installed before you run the script. If you do anything, it should simply be to note that pip wasn't found.
if ! command -v pip > /dev/null; then
printf 'pip not found; check your PATH or install pip before continuing\n' >&2
exit 1
fi
pip install some package
if ! type pip;
then
wget ...
pip install whatever
fi
type is a shell builtin that returns true if the command can be found and false otherwise.
Im trying to install OpenStack using Devstack in CentOS 7 ,Im using the following documentation as the guide, but im encountering an error which is shown.This is the output while running ./stack.sh.Im running./clean.sh and ./unstack.sh before running ./stack.sh.
Obtaining file:///opt/stack/keystone
Complete output from command python setup.py egg_info:
ERROR:root:Error parsing
Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/pbr/core.py", line 96, in pbr
attrs = util.cfg_to_args(path, dist.script_args)
File "/usr/lib/python2.7/site-packages/pbr/util.py", line 259, in cfg_to_args
pbr.hooks.setup_hook(config)
File "/usr/lib/python2.7/site-packages/pbr/hooks/__init__.py", line 25, in setup_hook
metadata_config.run()
File "/usr/lib/python2.7/site-packages/pbr/hooks/base.py", line 27, in run
self.hook()
File "/usr/lib/python2.7/site-packages/pbr/hooks/metadata.py", line 26, in hook
self.config['name'], self.config.get('version', None))
File "/usr/lib/python2.7/site-packages/pbr/packaging.py", line 839, in get_version
name=package_name))
Exception: Versioning for this project requires either an sdist tarball, or access to an upstream git repository. It's also possible that there is a mismatch between the package name in setup.cfg and the argument given to pbr.version.VersionInfo. Project name keystone was given, but was not able to be found.
error in setup command: Error parsing /opt/stack/keystone/setup.cfg: Exception: Versioning for this project requires either an sdist tarball, or access to an upstream git repository. It's also possible that there is a mismatch between the package name in setup.cfg and the argument given to pbr.version.VersionInfo. Project name keystone was given, but was not able to be found.
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /opt/stack/keystone/
You are using pip version 9.0.3, however version 18.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
+inc/python:pip_install:1 exit_trap
+./stack.sh:exit_trap:515 local r=1
++./stack.sh:exit_trap:516 jobs -p
+./stack.sh:exit_trap:516 jobs=
+./stack.sh:exit_trap:519 [[ -n '' ]]
+./stack.sh:exit_trap:525 '[' -f '' ']'
+./stack.sh:exit_trap:530 kill_spinner
+./stack.sh:kill_spinner:425 '[' '!' -z '' ']'
+./stack.sh:exit_trap:532 [[ 1 -ne 0 ]]
+./stack.sh:exit_trap:533 echo 'Error on exit'
Error on exit
+./stack.sh:exit_trap:535 type -p generate-subunit
+./stack.sh:exit_trap:536 generate-subunit 1545131409 150 fail
+./stack.sh:exit_trap:538 [[ -z /opt/stack/logs ]]
+./stack.sh:exit_trap:541 /opt/stack/devstack/tools/worlddump.py -d /opt/stack/logs
World dumping... see /opt/stack/logs/worlddump-2018-12-18-111239.txt for details
+./stack.sh:exit_trap:550 exit 1
I need to run a while loop to install Python dependencies. In the Python world recently there are 2 ways to install dependencies which have become established:
using conda (for some people this is the "robust/stable/desired way", provided by a "Python distribution" called Anaconda/Miniconda),
using pip (in the last few years included as the official way of Python itself).
The "pseudocode" should be:
try to install the dependency with the conda command
if it fails then install it with the pip command
In the Python world dependencies are specified in a requirements.txt file, usually exact versions (==) as one dependency per line with the pattern <MY_DEPENDENCY>==<MY_VERSION>.
The equivalent bash desired command is: while read requirement; do conda install --yes $requirement || pip install $requirement; done < requirements.txt, however this does not work in the GNU make/Makefile world for reasons that I don't completely get.
I've tried a few different flavors of that while loop - all unsuccessful. Basically once the conda command fails I am not able to go on with the pip attempt. I am not sure why this happens (as it works in "normal bash") and I can not find a way to manage some sort of low-level try/catch pattern (for those familiar with high level programming languages).
This is my last attempt which is not working because it stops when conda fails:
foo-target:
# equivalent to bash: conda install --yes $requirement || pip install $requirement;
while read requirement; do \
conda install --yes $requirement ; \
[ $$? != 0 ] || pip install $requirement; \
done < requirements.txt
How do I make sure I try to install each requirement inside requirements.txt first with conda, when conda fails then with pip?
Why is my code not working? I see people pointing to the differences between sh and bash, but I am not able to isolate the issue.
Edit:
I ended up working around using the bash command inside the Makefile, but I find this solution not ideal, because I need to maintain yet another chunk of code in a one-line bash script (see below), is there a way to keep all the stuff inside a Makefile avoiding bash at all?
The Makefile target:
foo-target:
bash install-python-dependencies.sh
The bash one line script:
#!/usr/bin/env bash
while read requirement; do conda install --yes $requirement || pip install $requirement; done < requirements.txt
I can run the script directly from the command line (bash), I can also run it from within the Makefile, but I would like to get rid of the bash script and always execute make foo-target without using bash (avoiding bash even inside the Makefile).
As shown above, your makefile will work as you expect, other than that you have to escape the $ in shell variables like $$requirement.
I couldn't reproduce your problem with a simplified example to emulate the behavior:
foo-target:
for i in 1 2 3; do \
echo conda; \
test $$i -ne 2; \
[ $$? -eq 0 ] || echo pip; \
done
gives the expected output:
$ make
conda
conda
pip
conda
Have you added the .POSIX: target to your makefile, that you don't show here? If I do that then I get the behavior you claim to see:
conda
make: *** [Makefile:2: foo-target] Error 1
The reason for this is described in the manual for .POSIX:
In particular, if this target is mentioned then recipes will be invoked as if the shell had been passed the '-e' flag: the first failing command in a recipe will cause the recipe to fail immediately.
If you want to keep .POSIX mode but not get this error the simplest way is to use the method you show in your first example; I don't know why you stopped using it:
foo-target:
while read requirement; do \
conda install --yes $$requirement || pip install $$requirement; \
done < requirements.txt
When I run:
sudo apt-get update
sudo apt-get upgrade
from the command line, it works.
If I put the same line a script file maintain.script:
echo UPDATING SYSTEM SOFTWARE – UPDATE
sudo apt-get update
echo UPDATING SYSTEM SOFTWARE – UPGRADE
sudo apt-get upgrade
and run:
sudo ./maintain.sh
I get errors:
E: Invalid operation update
E: Invalid operation upgrade
I have marked the script as an executable.
Updated After Comment from FSQ
Here is the script file:
#!/bin/bash
echo "UPDATING SYSTEM SOFTWARE – UPDATE"
apt-get update
echo "UPDATING SYSTEM SOFTWARE – UPGRADE"
apt-get upgrade
echo "UPDATING SYSTEM SOFTWARE – DISTRIBUTION"
apt-get dist-upgrade
echo "REMOVING APPLICATION ORPHANS"
apt-get autoremove –purge
echo "UPDATING FIRMWARE"
rpi-update
Here is the command:
pi#raspberrypi2 ~/projects $ sudo ./maintain.sh
Here is the result:
: not foundsh: 1: ./maintain.sh: #!/bin/bash
UPDATING SYSTEM SOFTWARE – UPDATE
E: Invalid operation update
UPDATING SYSTEM SOFTWARE – UPGRADE
E: Invalid operation upgrade
UPDATING SYSTEM SOFTWARE – DISTRIBUTION
E: Invalid operation dist-upgrade
REMOVING APPLICATION ORPHANS
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package –purge
UPDATING FIRMWARE
: not foundsh: 11: ./maintain.sh: rpi-update
It was a file format problem. I was editing the files over a folder share using Windows notepad, which uses a different \r\n to Linux.
Here is the command that corrected my script file:
sed -i 's/\r//' maintain.sh
Here is a script file I use to do all the script files in a folder, and make sure they are executable:
#!/bin/bash
echo "Correcting script file formats"
for file in *.sh
do
echo $file
sed -i 's/\r//' $file
chmod +x $file
done
Add this to the start of your script? #!/bin/bash
This is how it would work on ubuntu not sure about raspbian