• Upgrade failing due to files already existing?


    Hi-

    For the last several days, upgrades have been failing for me with messages that files already exist on my filesystem (previously it was wine which I’ve since removed). Here’s the most recent update attempt:

    $ sudo pacman -Syu
    :: Synchronizing package databases...
     antergos is up to date
     core is up to date
     extra is up to date
     community is up to date
     multilib is up to date
    :: Starting full system upgrade...
    warning: python2-mutagen: local (1.42.0-2) is newer than antergos (1.38-2)
    resolving dependencies...
    looking for conflicting packages...
    
    Packages (6) iproute2-5.1.0-1  lib32-systemd-242.29-1  man-pages-5.01-1  systemd-242.29-1  systemd-libs-242.29-1  systemd-sysvcompat-242.29-1
    
    Total Installed Size:  32.47 MiB
    Net Upgrade Size:       0.06 MiB
    
    :: Proceed with installation? [Y/n] 
    (6/6) checking keys in keyring                                                                                                                                            [#########################################################################################################] 100%
    (6/6) checking package integrity                                                                                                                                          [#########################################################################################################] 100%
    (6/6) loading package files                                                                                                                                               [#########################################################################################################] 100%
    (6/6) checking for file conflicts                                                                                                                                         [#########################################################################################################] 100%
    error: failed to commit transaction (conflicting files)
    systemd-sysvcompat: /usr/bin/halt exists in filesystem
    systemd-sysvcompat: /usr/bin/init exists in filesystem
    systemd-sysvcompat: /usr/bin/poweroff exists in filesystem
    systemd-sysvcompat: /usr/bin/reboot exists in filesystem
    systemd-sysvcompat: /usr/bin/runlevel exists in filesystem
    systemd-sysvcompat: /usr/bin/shutdown exists in filesystem
    systemd-sysvcompat: /usr/bin/telinit exists in filesystem
    systemd-sysvcompat: /usr/share/man/man8/halt.8.gz exists in filesystem
    systemd-sysvcompat: /usr/share/man/man8/poweroff.8.gz exists in filesystem
    systemd-sysvcompat: /usr/share/man/man8/reboot.8.gz exists in filesystem
    systemd-sysvcompat: /usr/share/man/man8/runlevel.8.gz exists in filesystem
    systemd-sysvcompat: /usr/share/man/man8/shutdown.8.gz exists in filesystem
    systemd-sysvcompat: /usr/share/man/man8/telinit.8.gz exists in filesystem
    Errors occurred, no packages were upgraded
    

    Any ideas to fix are greatly appreciated.

    Thanks!

  • @trey
    I guess you can simply remove those conflicting files and upgrade again.

    But to be on the safe side, backup your data first, and create an Antergos installer USB drive if you don’t have one now.

  • Hi-

    I started that process (removing the files in question) with a previous upgrade attempt of a different package. It seems both laborious (especially the sheer number in the case of ‘wine’ and the fonts associated with it) and wrong in the case here of removing the ‘reboot,’ ‘halt,’ ‘shutdown’ and other such executable files.

    I’m curious why the upgrade is failing here for files that are expected to be on the filesystem. Shouldn’t an upgrade replace or upgrade the existing files in question if needed.

    It appears there’s something more going on here. Is everyone not affected by this (I assume not) and in my case why is it happening?

  • @trey
    Hard to say, may be many reasons. E.g. some AUR packages may cause trouble if they override or hide official packages. Also upgrading system too seldom may cause issues.

    Could you show the output of command

    ls -l /usr/bin/halt
    

    EDIT: one tip: edit /etc/pacman.conf and move the [antergos] definition as last. That allows certain upstream packages to upgrade better.

  • $ ls -l /usr/bin/halt
    lrwxrwxrwx 1 root root 9 Apr 29 09:24 /usr/bin/halt -> systemctl
    
  • @trey
    How often do you upgrade your system?

    I have

    $ ls -l /usr/bin/halt 
    lrwxrwxrwx 1 root root 9 2019-05-10 23:28 /usr/bin/halt -> systemctl
    

    so the date is different.

  • @manuel

    I normally upgrade several times a week.

  • Any ideas on how to fix are greatly appreciated.

  • OK, well I removed the packages in question and did the upgrade. Still seems wrong to have to do that, but…

  • @trey
    BTW, how do you have local python2-mutagen newer than the Antergos version?

  • Good question. I’m not really sure what happened there…

  • @trey
    That may point to the culprit…

    Anyway, in Arch based systems similar upgrade issue is not unheard of. Rolling release model provides lots of updates, and sometimes there are small issues caused by an error by the people providing the latest packages.

    That’s why actively looking at the Arch and Antergos pages is useful.

  • @manuel said in

    BTW, how do you have local python2-mutagen newer than the Antergos version?

    Just a piece of information. I, too, have the same warning for a couple of months or so. I never bothered to look into it as my system is functional & upgradable…

  • @anarch

    Did you reorder the repos at /etc/pacman.conf? i mean, placing arch before antergos repos may cause this…

    If so, that could be fixed with pacman using -uu option

  • No, mine is quite an old system. I never touched the order of the repos since we applied the Antergos priority repo & that s what I meant by " never bothered to look into it ". TBO, the current situation of our distro confuses me & if I had to look deeper into the system, that would be drastic. I mean…be done with the Antergos repo altogether.
    Anyway, it s something I will have to take care of, somehow, some time.
    Cheers 👍

  • That python2-mutagen is an old relic in Antergos repos, and should be removed from the Antergos repo.

    But it is still there, so to get rid of that warning, either uninstall the package, or reorder repos in /etc/pacman.conf.

  • This is probably the 4th time this has happened in the past week. When attempting to upgrade my installed packages, one or more will fail with a message that a number of packages already exist on the file system.

    Until recently, I’ve ‘addressed’ this by manually removing the offending packages with ‘rm -rf’. However, the error today is way too many packages for me to bother with. What could be going on? Why would I get this error?

    The upgrade is:

    Packages (4) btrfs-progs-5.1-1  libmagick6-6.9.10.46-1  libuv-1.29.1-1  perl-alien-build-1.73-1
    

    Here’s a truncated example of the output:

    (4/4) checking for file conflicts                                                                                                                                                                             [##################################################################################################################################] 100%
    error: failed to commit transaction (conflicting files)
    perl-alien-build: /usr/share/man/man3/Alien::Base.3pm.gz exists in filesystem
    perl-alien-build: /usr/share/man/man3/Alien::Base::Authoring.3pm.gz exists in filesystem
    perl-alien-build: /usr/share/man/man3/Alien::Base::FAQ.3pm.gz exists in filesystem
    perl-alien-build: /usr/share/man/man3/Alien::Base::PkgConfig.3pm.gz exists in filesystem
    perl-alien-build: /usr/share/man/man3/Alien::Base::Wrapper.3pm.gz exists in filesystem
    perl-alien-build: /usr/share/man/man3/Alien::Build.3pm.gz exists in filesystem
    perl-alien-build: /usr/share/man/man3/Alien::Build::CommandSequence.3pm.gz exists in filesystem
    perl-alien-build: /usr/share/man/man3/Alien::Build::Interpolate.3pm.gz exists in filesystem
    perl-alien-build: /usr/share/man/man3/Alien::Build::Interpolate::Default.3pm.gz exists in filesystem
    perl-alien-build: /usr/share/man/man3/Alien::Build::MM.3pm.gz exists in filesystem
    perl-alien-build: /usr/share/man/man3/Alien::Build::Manual::Alien.3pm.gz exists in filesystem
    perl-alien-build: /usr/share/man/man3/Alien::Build::Manual::AlienAuthor.3pm.gz exists in filesystem
    perl-alien-build: /usr/share/man/man3/Alien::Build::Manual::AlienUser.3pm.gz exists in filesystem
    perl-alien-build: /usr/share/man/man3/Alien::Build::Manual::Contributing.3pm.gz exists in filesystem
    perl-alien-build: /usr/share/man/man3/Alien::Build::Manual::FAQ.3pm.gz exists in filesystem
    perl-alien-build: /usr/share/man/man3/Alien::Build::Manual::PluginAuthor.3pm.gz exists in filesystem
    perl-alien-build: /usr/share/man/man3/Alien::Build::Plugin.3pm.gz exists in filesystem
    perl-alien-build: /usr/share/man/man3/Alien::Build::Plugin::Build.3pm.gz exists in filesystem
    perl-alien-build: /usr/share/man/man3/Alien::Build::Plugin::Build::Autoconf.3pm.gz exists in filesystem
    
upgrade81 due14 failing10 existing5 Posts 19Views 182
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