I can’t install or update a package because I get (something like) this:
error: could not prepare transaction
error: failed to commit transaction (conflicting files)
libname: /insert/file/name/here exists in filesystem
Errors occurred, no packages were upgraded.
Why is this happening?
The package manager, pacman, has detected an unexpected file already exists on disk. By design it will not overwrite files that already exist. This is a design feature, not a flaw - package managers are designed to keep track of installed files.
This issue normally happens because you’ve manually added, copied, or created a file. It can also happen when you install software using a downloaded executable, run a make install, or use a third-party package system such as conda. It also occurs when you install an AUR package which installs files that conflict with a repo package.
When using a third-party installer you should always specify an alternative installation location, such as under your home directory, or under /opt or /usr/local/. Never install directly under / or /usr.
How can I fix this?
The better way
The first step is to identify which, if any, package owns the file. This can be easily done with:
pacman -Qo /path/to/file
If this identifies a conflicting package you can decide to remove it with pacman -R. If no package is identified you can delete the file, e.g. rm /path/to/file (or move it to a backup location, e.g. mv /path/to/file /path/to/file.backup).
The faster way
pacman has an --overwrite option which will allow it to overwrite files. If you are sure you want to, you can tell it to
sudo pacman -S $PACKAGE --overwrite 'path/to/*'
This will (re)install the $PACKAGE and overwrite any files under the directory path/to/
This can be very useful if your local database has “lost” a package you’ve already installed (and so every file in the package “conflicts”).
The “I don’t care” way
sudo pacman -S $PACKAGE --overwrite '*'
Example
sudo pacman -S languagetool --overwrite usr/bin/languagetool,usr/share/java/languagetool/*
Where can I read more?
This post was inspired by (and adapted from):
https://bbs.archlinux.org/viewtopic.php?id=56373
The above post also has links to further reading.
Credit: Originally posted by Jonathon