Need help with system update

[ramon395]

so after having a problem at boot (bailing out error) i managed to fix it by running fsck -f on my partition and hitting y for about 50 files to overwrite etc, this happened after firefox crashing while watching a youtube video.
now for some reason i’ve been unable to update my system, here’s my terminal output:

[ramon@ramon-m61pmes2p ~]$ LANG=C yay -Syu
:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
 endeavouros is up to date
:: Starting full system upgrade...
resolving dependencies...
error: could not open file /var/lib/pacman/local/qt5-base-5.15.1-3/desc: No such file or directory
error: could not open file /var/lib/pacman/local/rhash-1.4.0-1/desc: No such file or directory
looking for conflicting packages...

Packages (8) bison-3.7.2-1  gpm-1.20.7.r38.ge82d1a6-3  imagemagick-7.0.10.33-1  iw-5.9-1
             libtool-2.4.6+42+gb88cebd5-14  mesa-20.2.0-2  openssh-8.4p1-1  whois-5.5.7-1

Total Installed Size:  107,09 MiB
Net Upgrade Size:        4,39 MiB

:: Proceed with installation? [Y/n] y
(8/8) checking keys in keyring                               [--------------------------------] 100%
(8/8) checking package integrity                             [--------------------------------] 100%
(8/8) loading package files                                  [--------------------------------] 100%
(8/8) checking for file conflicts                            [--------------------------------] 100%
error: failed to commit transaction (conflicting files)
libtool: /usr/bin/libtool exists in filesystem
libtool: /usr/bin/libtoolize exists in filesystem
libtool: /usr/include/libltdl/lt_dlloader.h exists in filesystem
libtool: /usr/include/libltdl/lt_error.h exists in filesystem
libtool: /usr/include/libltdl/lt_system.h exists in filesystem
libtool: /usr/include/ltdl.h exists in filesystem
libtool: /usr/lib/libltdl.so exists in filesystem
libtool: /usr/lib/libltdl.so.7 exists in filesystem
libtool: /usr/lib/libltdl.so.7.3.1 exists in filesystem
libtool: /usr/share/aclocal/libtool.m4 exists in filesystem
libtool: /usr/share/aclocal/ltargz.m4 exists in filesystem
libtool: /usr/share/aclocal/ltdl.m4 exists in filesystem
libtool: /usr/share/aclocal/ltoptions.m4 exists in filesystem
libtool: /usr/share/aclocal/ltsugar.m4 exists in filesystem
libtool: /usr/share/aclocal/ltversion.m4 exists in filesystem
libtool: /usr/share/aclocal/lt~obsolete.m4 exists in filesystem
libtool: /usr/share/info/libtool.info-1.gz exists in filesystem
libtool: /usr/share/info/libtool.info-2.gz exists in filesystem
libtool: /usr/share/info/libtool.info.gz exists in filesystem
libtool: /usr/share/libtool/COPYING.LIB exists in filesystem
libtool: /usr/share/libtool/Makefile.am exists in filesystem
libtool: /usr/share/libtool/Makefile.in exists in filesystem
libtool: /usr/share/libtool/README exists in filesystem
libtool: /usr/share/libtool/aclocal.m4 exists in filesystem
libtool: /usr/share/libtool/build-aux/compile exists in filesystem
libtool: /usr/share/libtool/build-aux/config.guess exists in filesystem
libtool: /usr/share/libtool/build-aux/config.sub exists in filesystem
libtool: /usr/share/libtool/build-aux/depcomp exists in filesystem
libtool: /usr/share/libtool/build-aux/install-sh exists in filesystem
libtool: /usr/share/libtool/build-aux/ltmain.sh exists in filesystem
libtool: /usr/share/libtool/build-aux/missing exists in filesystem
libtool: /usr/share/libtool/config-h.in exists in filesystem
libtool: /usr/share/libtool/configure exists in filesystem
libtool: /usr/share/libtool/configure.ac exists in filesystem
libtool: /usr/share/libtool/libltdl/lt__alloc.h exists in filesystem
libtool: /usr/share/libtool/libltdl/lt__argz_.h exists in filesystem
libtool: /usr/share/libtool/libltdl/lt__dirent.h exists in filesystem
libtool: /usr/share/libtool/libltdl/lt__glibc.h exists in filesystem
libtool: /usr/share/libtool/libltdl/lt__private.h exists in filesystem
libtool: /usr/share/libtool/libltdl/lt__strl.h exists in filesystem
libtool: /usr/share/libtool/libltdl/lt_dlloader.h exists in filesystem
libtool: /usr/share/libtool/libltdl/lt_error.h exists in filesystem
libtool: /usr/share/libtool/libltdl/lt_system.h exists in filesystem
libtool: /usr/share/libtool/libltdl/slist.h exists in filesystem
libtool: /usr/share/libtool/loaders/dld_link.c exists in filesystem
libtool: /usr/share/libtool/loaders/dlopen.c exists in filesystem
libtool: /usr/share/libtool/loaders/dyld.c exists in filesystem
libtool: /usr/share/libtool/loaders/load_add_on.c exists in filesystem
libtool: /usr/share/libtool/loaders/loadlibrary.c exists in filesystem
libtool: /usr/share/libtool/loaders/preopen.c exists in filesystem
libtool: /usr/share/libtool/loaders/shl_load.c exists in filesystem
libtool: /usr/share/libtool/lt__alloc.c exists in filesystem
libtool: /usr/share/libtool/lt__argz.c exists in filesystem
libtool: /usr/share/libtool/lt__dirent.c exists in filesystem
libtool: /usr/share/libtool/lt__strl.c exists in filesystem
libtool: /usr/share/libtool/lt_dlloader.c exists in filesystem
libtool: /usr/share/libtool/lt_error.c exists in filesystem
libtool: /usr/share/libtool/ltdl.c exists in filesystem
libtool: /usr/share/libtool/ltdl.h exists in filesystem
libtool: /usr/share/libtool/ltdl.mk exists in filesystem
libtool: /usr/share/libtool/slist.c exists in filesystem
libtool: /usr/share/man/man1/libtool.1.gz exists in filesystem
libtool: /usr/share/man/man1/libtoolize.1.gz exists in filesystem
Errors occurred, no packages were upgraded.
error installing repo packages

[jonathon]

@ramon395

error: could not open file /var/lib/pacman/local/qt5-base-5.15.1-3/desc: No such file or directory
error: could not open file /var/lib/pacman/local/rhash-1.4.0-1/desc: No such file or directory

[FAQ] error: could not open file /var/lib/pacman/local/…/{desc,files,mtree}: No such file or directory

Your local package database and/or metadata may become corrupted if an update process is interrupted, for example if you hard power off during an update. Metadata corruption will generally manifest in a message similar to: error: could not open file /var/lib/pacman/local/$pkgname-$pkgver-$pkgrel/desc: No such file or directory error: could not open file /var/lib/pacman/local/$pkgname-$pkgver-$pkgrel/files: No such file or directory error: could not open file /var/lib/pacman/local/$pkgname-$pkg…

@ramon395

error: failed to commit transaction (conflicting files)
libtool: /usr/bin/libtool exists in filesystem

[FAQ] Package installation says FILENAME exists in filesystem; “Failed to commit transaction (conflicting files)”

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 de…

[ramon395]

which command should i use to overwrite libtool ? still a bit confused here sorry

[jonathon]

Which bit of the above thread related to conflicting files (and how to fix/overwrite them) is confusing? Let me know so I can rewrite it to make it as clear as possible.

[ramon395]

i would like to have a suggestion for the most recommended terminal commands to run here and fix the problem, i just don’t feel too confident, i am not very experienced with that sorta of problem, right now i am getting this when running pacman -Qo /path/to/file:

[ramon@ramon-m61pmes2p ~]$ LANG=C pacman -Qo /path/to/file
error: could not open file /var/lib/pacman/local/qt5-base-5.15.1-3/files: No such file or directory
error: could not open file /var/lib/pacman/local/rhash-1.4.0-1/files: No such file or directory
error: No package owns /path/to/file
[ramon@ramon-m61pmes2p ~]$ 

[jonathon]

You are conflating the two issues, for which I have posted two links.

Take the two issues separately and fix them in turn.

[ramon395]

is there any risk to break the system if i just try to reinstall qt5-base and rhash ?

[jonathon]

None, that is one of the steps from the first thread above (though you will have to put placeholder files in place to allow that to happen).

[ramon395]

i already ran these commands this morning:

sudo touch /var/lib/pacman/local/qt5-base-5.15.1-3/desc
sudo touch /var/lib/pacman/local/rhash-1.4.0-1/desc

and i noticed commands like this won’t work:

sudo pacman -S qt5-base

[jonathon]

@ramon395

i noticed commands like this won’t work:

If you post the full output someone might be able to provide specific help rather than guess.

[ramon395]

LANG=C sudo touch /var/lib/pacman/local/rhash-1.4.0-1/desc
[ramon@ramon-m61pmes2p ~]$ LANG=C sudo pacman -S rhash
warning: rhash-1.4.0-1 is up to date -- reinstalling
resolving dependencies...
looking for conflicting packages...
error: could not open file /var/lib/pacman/local/rhash-1.4.0-1/files: No such file or directory
warning: could not fully load metadata for package rhash-1.4.0-1
error: failed to prepare transaction (invalid or corrupted package)
[ramon@ramon-m61pmes2p ~]$ 

[jonathon]

You have addressed the first missing file (desc), but there is another one to put in place (files) before reinstalling the package will work.

[ramon395]

So basically now i need to run:

sudo touch /var/lib/pacman/local/rhash-1.4.0-1/files

?

[ramon395]

Apparently the first issue is gone, just one more to fix

[jonathon]

This is probably one of the worst issues you can face with corrupt local metadata, so after you fix this you’ll be able to fix anything.

[ramon395]

tried to run a bunch of terminal commands here, but none of these worked, i need to backup these files before trying this ?

sudo pacman -S libtool --overwrite usr/bin/libtool,usr/bin/libtoolize,usr/include/libltdl/*
sudo pacman -S libtool --overwrite usr/include/ltdl.h
sudo pacman -S libtool --overwrite usr/lib/*
sudo pacman -S libtool --overwrite usr/share/aclocal/*
sudo pacman -S libtool --overwrite usr/share/info/*
sudo pacman -S libtool --overwrite usr/share/libtool/*
sudo pacman -S libtool --overwrite usr/share/libtool/build-aux/*
sudo pacman -S libtool --overwrite usr/share/libtool/libltdl/*
sudo pacman -S libtool --overwrite usr/share/libtool/loaders/*
sudo pacman -S libtool --overwrite usr/share/man/man1/libtool.1.gz
sudo pacman -S libtool --overwrite usr/share/man/man1/libtoolize.1.gz

[manuel]

The question is: why do you have these conflicts?
It could be that you have installed another similar package from the AUR.

So could you show the output of command:

  pacman -Qs libtool

[ramon395]

[ramon@ramon-m61pmes2p ~]$ pacman -Qs libtool
[ramon@ramon-m61pmes2p ~]$ 

[manuel]

You could try this from the links of @jonathon :

sudo pacman -S libtool --overwrite '*'

but make sure your personal data is backed up.

[ramon395]

can i run the command exactly like it is or is it just a template ?