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I ran sudo pacman -Syu and I got some interesting errors reading:

error: failed to commit transaction (conflicting files)

and a long list of files followed by exists in filesystem. Full output is here: http://ix.io/lLw

It appears that many of these files are not associated with a package when I checked them with pacman -Qo <path-to-file>, but I did not check them all. I had a weak connection when I ran pacman -Syu, but I get the same errors when I updated later: http://ix.io/lLx

What should I do? Should I check all files and delete the ones that do not have an associated package? Should I force update (with sudo pacman -S --force <package-name>?)

Update

I tried running sudo pacman -S --force <package-name> and got this:

[my-pc]/home/average-joe$ pacman -Qo /usr/lib/python3.5/site-packages/PyYAML-3.11-py3.5.egg-info
error: No package owns /usr/lib/python3.5/site-packages/PyYAML-3.11-py3.5.egg-info

It looks like pacman -S --force <package does not overwrite directories that contain files. From the man:

Using --force will not allow overwriting a directory with a file or installing packages with conflicting files and directories.

Should I just delete the conflicting directories? (they do not have associated packages)

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5
  • 7
    why do you have conflicting files in the first place? when using a package manager, try not to tap on its toes (e.g. by installing software in places the package manager rightfully thinks is theirs; if you must install things manually, install to /usr/local/ rather than /usr/)
    – umläute
    Nov 2, 2015 at 12:37
  • 1
    @umläute I am not exactly sure where the conflicting files came from, but I suspect they are related to my installation of docker-compose which I installed using sudo pip install -U docker-compose==1.5.0rc3 on this page. Perhaps sudo pip install conflicts with pacman?
    – modulitos
    Nov 3, 2015 at 7:47
  • 2
    @umläute Getting wrong -S updates (partial installs, etc) will let you that scenario. Case of me --force worked all times.
    – m3nda
    May 23, 2017 at 17:15
  • See comment below to "fast" usage of the --overwrite command, because --force is not working anymore.
    – m3nda
    Jan 30, 2020 at 1:53
  • This will often happen for CUPS wrappers: Brother printer config files and libraries are packaged in several AUR sources. And trizen -S <package> --overwrite "*" or \* won’t work: the * argument isn’t passed on to pacman. Not sure how to properly escape this, but after downloading all packages, trizen will tell you the exact pacman command it is going to execute. Then simply Ctrl + C, copy that command, fix the "*" argument and hit Enter.
    – Sebastian Simon
    Dec 30, 2020 at 1:55

8 Answers 8

Reset to default
94

After pacman finally deprecated the --force option and made the surrogate --overwrite option work as expected, the following usage pattern should be noted.

A command to reproduce the --force option that blindly overwrites anything that conflicts is this:

sudo pacman -S --overwrite \* <package_name>

Or

sudo pacman -S --overwrite "*" <package_name>

The tricky part is escaping the wildcard to stop the shell from expanding it first.

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3
  • This time nothing worked for me, caused by dependancy loop, I had no more choice than uninstall the module with pip then issue again the pacman install one. So sad :-/ that creators or those packages don't look at those problems.
    – m3nda
    Jan 30, 2020 at 1:57
  • Doesn't work. It still prints an error about existing file in the filesystem. However, suggested idea below about simply removing the conflicting files and then installing as usual worked for me.
    – Hi-Angel
    Apr 7, 2022 at 19:47
  • It worked for me. In my case I had faced a package issue like edk2-armvirt already exists in filesystem.
    – joseluisq
    May 10, 2022 at 6:24
34

Ok, it looks like running sudo pacman -S --force <package-name> works, but it doesn't resolve conflicting directories. In such cases, running sudo rm -rf on the conflicting directories, followed by sudo pacman -S --force <package-name> works.

Now my pacman -Syu resolves well.

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  • 15
    --force is deprecated; use --overwrite instead.
    – Ankit Balyan
    Jun 14, 2018 at 8:37
  • 7
    --force is working for me but --overwrite is not
    – eirenikos
    Jun 18, 2018 at 13:19
  • 3
    sudo pacman -Syu --force worked for me, but overwrite wasn't recognized.
    – spydon
    Jul 2, 2018 at 8:03
  • no syntax works with --force, this answer should be edited to refer to the other one
    – Labo
    Nov 9, 2020 at 15:00
  • This is out of date. You need to use --overwrite instead of --force.
    – Volker Weißmann
    Dec 13, 2020 at 14:12
24

tl;dr: Uninstall the conflicting application before running pacman.

pacman (and other package managers) keep an index of packages and files that they manage (pacman --query --list). Some files, such as configuration, will be marked as modifiable and will not be overwritten during upgrade (except in special circumstances, where the package manager will typically move away the old file before creating the new one). Other files will be marked as unmodifiable. If another application changes those files in any way without updating the index accordingly there's no way for the package manager to know what to do with those files during an upgrade.

Many applications installed using the standard ./configure && make && sudo make install pattern can be uninstalled using sudo make uninstall. If you have installed the application in some other way you might have to something else to uninstall it. In general it can be a good idea to keep a copy of installation files somewhere (for example ~/install) to be able to reliably uninstall them in such cases. Just removing the conflicting files will probably leave other files lying around, which could conceivably cause other problems.

When installing software with other package managers there are ways to isolate those from the system files. This is an established best practice for example during software development, where you really want to keep versions consistent and avoid conflicts with other software. Examples include:

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  • 2
    See my comment to @umlaute above. I think the conflict was from a sudo pip install command. Perhaps I should avoid using pip with sudo?
    – modulitos
    Nov 3, 2015 at 7:48
13

The correct way to upgrade and overwrite conflicting packages is:

sudo pacman --overwrite "*" -Syu
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5

TLDR;

  1. Get a list of the offending files (copy and paste pacman's output into a file).
  2. Use awk to strip out everything but the file paths into a new list.
  3. Use while to move the offending files out of the way, based on the list.
  4. Run sudo pacman -Syu again.

    edited to add TLDR and fix typos

Although I'm pretty sure I haven't been doing anything stupid, I've had this problem maybe every other time I've tried to update since I've been using Manjaro; three or four times within two months. Point being, this fixes it.

Get a list of your files.

When the update fails in your terminal window, you get this:

error: failed to commit transaction (conflicting files)
evilfile: /usr/bin/evilfile exists in filesystem
libx000: /usr/lib/libx000.so.f.u.loser exists in filesystem
accountsservice: /usr/share/locale/ru/LC_MESSAGES/accounts-service.mo.yu.dnt.evn.spk.russian exists in filesystem

... and a lot more.

  • Copy the output from the terminal, and put it in a file. I used nano, and named mine "files," as in ~/work/files.

  • Strip extraneous info:

    cat files | awk '{print $2}' >> ~/work/files2

    This takes the second "word" from each line and prints it to files2.

Deal with the files

  • You could delete them, move them, or rename them.

  • If something breaks, it's easiest to fix if we break it by moving it instead of deleting or renaming it:
    mkdir ~/work/oldfiles while read -r file; do sudo mv -- "$file" ~/work/oldfiles/$file; done < files2

  • If you really want to delete them, which there is no reason to do (DANGER DANGER): while read -r file; do sudo rm -- "$file"; done < files2

Updating

  • To get --overwrite to work, which we need to do to get pacman to realize the package isn't broken, you need the following syntax:

    sudo pacman -S package_name --overwrite /location/of/thing

    • In my case: sudo pacman -S libidn2 --overwrite /usr/lib/libidn2.so.0
    • Following the example: sudo pacman -S libx000 --overwrite /usr/lib/libx000.so.f.u.loser

  • I had a cute problem where if I deleted the libidn2.so.0 symlink, nothing worked, and when I put it back, I got the "exists on filesystem" error. The above, with --overwrite, is all that worked for me.

  • Finally:

    sudo pacman -Syu

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1
  • This solved the problem for me, thank you very much! Though I used the following routine as the other gave me a double forward slash in file name. for file in $(cat ./files.txt); do sudo mv "$file" ./oldfiles; done
    – Nikole
    Dec 12, 2022 at 16:20
3

I was installing packages that I usually install with pip via pacman because of this. But some packages arent found in pacman repos. I think we should avoid installing pip with sudo privilegies and istead:

pip install pillow --user

--user flag makes pip install packages in your home directory instead, which doesn't require any special privileges.https://stackoverflow.com/questions/42988977/what-is-the-purpose-pip-install-user

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0

If you have many files as me,

sudo pacman --force -Syyu

resolves all issues.

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2
  • option --force is deprecated; use --overwrite instead
    – Mahmoud
    Jul 4, 2019 at 22:01
  • --overwrite seems must specify what to overwrite. currently use --force every thing is fine
    – xsilen T
    Sep 29, 2019 at 13:03
0

when you conflicting files/ file already exists. do the following.

pacman -Qo "path_to_file"

if the out is "No package owns this file" then you can delete the file without any worry.

for me usually i get file already exists error on /usr/lib/python3.8/"folder_X"/.... so i run pacman -Qo /usr/lib/python3.8/folder_X which usually return "No Package owns this file" and i just remove it.

sudo rm -rf /usr/lib/python3.8/folder_X

till date i have not had a situation where a file or folder was actually owned by a package. so i can't really advice on what to do in that situation.

Hope this Helps

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