Pacman -Syu (error: failed to commit transaction (conflicting files))

Support
,
1

So, It’s been a while since I don’t update my system.

so I ran the good old “sudo pacman -Syu”, and that was my output:

:: Proceed with installation? [Y/n] 
(597/597) checking keys in keyring                                                         [####################################################] 100%
(597/597) checking package integrity                                                       [####################################################] 100%
(597/597) loading package files                                                            [####################################################] 100%
(597/597) checking for file conflicts                                                      [####################################################] 100%
error: failed to commit transaction (conflicting files)
python-markupsafe: /usr/lib/python3.10/site-packages/markupsafe/__init__.py exists in filesystem
python-markupsafe: /usr/lib/python3.10/site-packages/markupsafe/__pycache__/__init__.cpython-310.pyc exists in filesystem
python-markupsafe: /usr/lib/python3.10/site-packages/markupsafe/__pycache__/_native.cpython-310.pyc exists in filesystem
python-markupsafe: /usr/lib/python3.10/site-packages/markupsafe/_native.py exists in filesystem
python-markupsafe: /usr/lib/python3.10/site-packages/markupsafe/_speedups.c exists in filesystem
python-markupsafe: /usr/lib/python3.10/site-packages/markupsafe/_speedups.cpython-310-x86_64-linux-gnu.so exists in filesystem
python-markupsafe: /usr/lib/python3.10/site-packages/markupsafe/_speedups.pyi exists in filesystem
python-markupsafe: /usr/lib/python3.10/site-packages/markupsafe/py.typed exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__init__.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/__init__.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/_identifier.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/async_utils.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/bccache.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/compiler.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/constants.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/debug.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/defaults.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/environment.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/exceptions.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/ext.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/filters.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/idtracking.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/lexer.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/loaders.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/meta.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/nativetypes.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/nodes.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/optimizer.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/parser.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/runtime.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/sandbox.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/tests.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/utils.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/__pycache__/visitor.cpython-310.pyc exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/_identifier.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/async_utils.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/bccache.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/compiler.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/constants.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/debug.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/defaults.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/environment.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/exceptions.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/ext.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/filters.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/idtracking.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/lexer.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/loaders.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/meta.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/nativetypes.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/nodes.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/optimizer.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/parser.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/py.typed exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/runtime.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/sandbox.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/tests.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/utils.py exists in filesystem
python-jinja: /usr/lib/python3.10/site-packages/jinja2/visitor.py exists in filesystem
Errors occurred, no packages were upgraded.

Any thoughts?

Thanks in advance.

2 
sudo pamman -Syu --overwrite "/usr/lib/python3.10/*"
3

My wild guess:
You have the markupsafe and jinja2 packages installed globally through pip instead of either:

  • installing them for your user only
  • using the system package manager
python -m pip show markupsafe jinja2

And now those packages are to be installed from the system package manager, and conflict with those installed through pip. Use pip to uninstall those, then retry your system update.

python -m pip uninstall markupsafe jinja2
sudo pacman -Syu

When installing packages using pip, it is recommended to use a virtual environment to prevent conflicts with system packages in /usr. Alternatively, pip install --user can be used to install packages into the user scheme instead of /usr. pipx and Conda integrate environment management into their workflows.
Python - ArchWiki

1 Like