Arch Linux

zeek

Member

Registered: 2010-01-07

Posts: 12

[Solved] pacman failed to synchronize all databases (unexpected error)

Pacman was running fine until the upgrade to v.7.0
Now, when I run pacman I get the following error mssg
  Error: Synchronizing package databases...
         failed to synchronize all databases (unexpected error)

I don't know how the mismatches below occurred during the upgrade

  $   pacman -Qkk pacman
backup file: pacman: /etc/makepkg.conf (Modification time mismatch)
backup file: pacman: /etc/makepkg.conf (Size mismatch)
backup file: pacman: /etc/makepkg.conf (SHA256 checksum mismatch)
backup file: pacman: /etc/pacman.conf (Modification time mismatch)
backup file: pacman: /etc/pacman.conf (Size mismatch)
backup file: pacman: /etc/pacman.conf (SHA256 checksum mismatch)
backup file: pacman: /etc/makepkg.conf.d/rust.conf (Modification time mismatch)
backup file: pacman: /etc/makepkg.conf.d/rust.conf (Size mismatch)
backup file: pacman: /etc/makepkg.conf.d/rust.conf (SHA256 checksum mismatch)
pacman: 422 total files, 0 altered files
 

Why would the errors below occur as pacman was working fine before the update?
Any suggestion on how to resolve these errors?

 $ sudo pacman -Syuv --debug

debug: pacman v7.0.0 - libalpm v15.0.0
debug: config: new section 'options'
debug: config: HoldPkg: pacman
debug: config: HoldPkg: glibc
debug: config: Architecture: auto
debug: config: arch: x86_64
debug: config: verbosepkglists
debug: config: chomp
debug: config: sandboxuser: 
debug: config: SigLevel: Required
debug: config: SigLevel: DatabaseOptional
debug: config: LocalFileSigLevel: Optional
debug: config: new section 'core'
debug: config file /etc/pacman.conf, line 80: including /etc/pacman.d/mirrorlist
debug: config: new section 'extra'
debug: config file /etc/pacman.conf, line 86: including /etc/pacman.d/mirrorlist
debug: config: finished parsing /etc/pacman.conf
debug: setup_libalpm called
debug: option 'logfile' = /var/log/pacman.log
debug: option 'gpgdir' = /etc/pacman.d/gnupg/
debug: option 'hookdir' = /etc/pacman.d/hooks/
debug: option 'cachedir' = /var/cache/pacman/pkg/
debug: registering sync database 'core'
debug: database path for tree core set to /var/lib/pacman/sync/core.db
debug: "/var/lib/pacman/sync/core.db.sig" is not readable: No such file or directory
debug: sig path /var/lib/pacman/sync/core.db.sig could not be opened
debug: got error 43 at _alpm_gpgme_checksig (../lib/libalpm/signing.c: 599) : missing PGP signature
debug: missing optional signature
debug: setting usage of 15 for core repository
debug: adding new server URL to database 'core': https://mirrors.ocf.berkeley.edu/archlinux/core/os/x86_64
debug: adding new server URL to database 'core': https://mirror.arizona.edu/archlinux/core/os/x86_64
debug: adding new server URL to database 'core': https://mirrors.xtom.com/archlinux/core/os/x86_64
debug: adding new server URL to database 'core': https://opencolo.mm.fcix.net/archlinux/core/os/x86_64
debug: adding new server URL to database 'core': https://codingflyboy.mm.fcix.net/archlinux/core/os/x86_64
debug: adding new server URL to database 'core': https://mirror.fcix.net/archlinux/core/os/x86_64
debug: adding new server URL to database 'core': https://arch.hu.fo/archlinux/core/os/x86_64
debug: adding new server URL to database 'core': https://mirror.sfo12.us.leaseweb.net/archlinux/core/os/x86_64
debug: adding new server URL to database 'core': https://us.mirrors.cicku.me/archlinux/core/os/x86_64
debug: adding new server URL to database 'core': https://ridgewireless.mm.fcix.net/archlinux/core/os/x86_64
debug: adding new server URL to database 'core': https://ziply.mm.fcix.net/archlinux/core/os/x86_64
debug: adding new server URL to database 'core': https://archlinux.doridian.net/core/os/x86_64
debug: adding new server URL to database 'core': https://irltoolkit.mm.fcix.net/archlinux/core/os/x86_64
debug: adding new server URL to database 'core': https://southfront.mm.fcix.net/archlinux/core/os/x86_64
debug: adding new server URL to database 'core': https://mnvoip.mm.fcix.net/archlinux/core/os/x86_64
debug: adding new server URL to database 'core': https://nocix.mm.fcix.net/archlinux/core/os/x86_64
debug: adding new server URL to database 'core': https://america.mirror.pkgbuild.com/core/os/x86_64
debug: adding new server URL to database 'core': https://mirror.adectra.com/archlinux/core/os/x86_64
debug: adding new server URL to database 'core': https://mirror.ette.biz/archlinux/core/os/x86_64
debug: adding new server URL to database 'core': https://iad.mirrors.misaka.one/archlinux/core/os/x86_64
debug: registering sync database 'extra'
debug: database path for tree extra set to /var/lib/pacman/sync/extra.db
debug: "/var/lib/pacman/sync/extra.db.sig" is not readable: No such file or directory
debug: sig path /var/lib/pacman/sync/extra.db.sig could not be opened
debug: got error 43 at _alpm_gpgme_checksig (../lib/libalpm/signing.c: 599) : missing PGP signature
debug: missing optional signature
debug: setting usage of 15 for extra repository
debug: adding new server URL to database 'extra': https://mirror.arizona.edu/archlinux/extra/os/x86_64
debug: adding new server URL to database 'extra': https://mirrors.xtom.com/archlinux/extra/os/x86_64
debug: adding new server URL to database 'extra': https://opencolo.mm.fcix.net/archlinux/extra/os/x86_64
debug: adding new server URL to database 'extra': https://codingflyboy.mm.fcix.net/archlinux/extra/os/x86_64
debug: adding new server URL to database 'extra': https://mirror.fcix.net/archlinux/extra/os/x86_64
debug: adding new server URL to database 'extra': https://arch.hu.fo/archlinux/extra/os/x86_64
debug: adding new server URL to database 'extra': https://mirror.sfo12.us.leaseweb.net/archlinux/extra/os/x86_64
debug: adding new server URL to database 'extra': https://iad.mirrors.misaka.one/archlinux/extra/os/x86_64
debug: option 'sandboxuser' = 
error: failed to synchronize all databases (unexpected error)
debug: unregistering database 'local'
debug: unregistering database 'core'
debug: unregistering database 'extra'

I am trying to understand but would appreciate any assistance on a resolution.
Thank you for your time.
Cheers

Last edited by zeek (2024-09-16 23:35:12)

Scimmia

Fellow

Registered: 2012-09-01

Posts: 11,958

Re: [Solved] pacman failed to synchronize all databases (unexpected error)

Post your pacman.conf. Something is really strange with the mirrors between the repos being different and sandboxuser being blank.

zeek

Member

Registered: 2010-01-07

Posts: 12

Re: [Solved] pacman failed to synchronize all databases (unexpected error)

/etc/pacman.conf

# GENERAL OPTIONS
#
[options]
# The following paths are commented out with their default values listed.
# If you wish to use different paths, uncomment and update the paths.
#RootDir     = /
#DBPath      = /var/lib/pacman/
#CacheDir    = /var/cache/pacman/pkg/
#LogFile     = /var/log/pacman.log
#GPGDir      = /etc/pacman.d/gnupg/
#HookDir     = /etc/pacman.d/hooks/
HoldPkg      = pacman glibc
#XferCommand = /usr/bin/curl -L -C - -f -o %o %u
#XferCommand = /usr/bin/wget --passive-ftp -c -O %o %u
#CleanMethod = KeepInstalled
Architecture = auto

# Pacman won't upgrade packages listed in IgnorePkg and members of IgnoreGroup
#IgnorePkg   =
#IgnoreGroup =

#NoUpgrade   =
#NoExtract   =

# Misc options
#UseSyslog
Color
#NoProgressBar
#TotalDownload  #cf: pacman.conf(5) 4TotalDLs. Eg: Progress shows 10MB/200MB
CheckSpace
VerbosePkgLists
ParallelDownloads = 5
ILoveCandy
DownloadUser =
#DisableSandbox

# By default, pacman accepts packages signed by keys that its local keyring
# trusts (see pacman-key and its man page), as well as unsigned packages.
SigLevel    = Required DatabaseOptional
LocalFileSigLevel = Optional
#RemoteFileSigLevel = Required

# NOTE: You must run `pacman-key --init` before first using pacman; the local
# keyring can then be populated with the keys of all official Arch Linux
# packagers with `pacman-key --populate archlinux`.

#
# REPOSITORIES
#   - can be defined here or included from another file
#   - pacman will search repositories in the order defined here
#   - local/custom mirrors can be added here or in separate files
#   - repositories listed first will take precedence when packages
#     have identical names, regardless of version number
#   - URLs will have $repo replaced by the name of the current repo
#   - URLs will have $arch replaced by the name of the architecture
#
# Repository entries are of the format:
#       [repo-name]
#       Server = ServerName
#       Include = IncludePath
#
# The header [repo-name] is crucial - it must be present and
# uncommented to enable the repo.
#

# The testing repositories are disabled by default. To enable, uncomment the
# repo name header and Include lines. You can add preferred servers immediately
# after the header, and they will be used before the default mirrors.

#[core-testing]
#Include = /etc/pacman.d/mirrorlist

[core]
Include = /etc/pacman.d/mirrorlist

#[extra-testing]
#Include = /etc/pacman.d/mirrorlist

[extra]
Include = /etc/pacman.d/mirrorlist

# If you want to run 32 bit applications on your x86_64 system,
# enable the multilib repositories as required here.

#[multilib-testing]
#Include = /etc/pacman.d/mirrorlist

#[multilib]
#Include = /etc/pacman.d/mirrorlist

# An example of a custom package repository.  See the pacman manpage for
# tips on creating your own repositories.
#[custom]
#SigLevel = Optional TrustAll
#Server = file:///home/custompkgs
#Server = file:///run/media/zp/dl1/aurpkgs

seth

Member

Registered: 2012-09-03

Posts: 57,175

Re: [Solved] pacman failed to synchronize all databases (unexpected error)

DownloadUser =

What was the plan behind that?
Try

DownloadUser = alpm

---

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Scimmia

Fellow

Registered: 2012-09-01

Posts: 11,958

Re: [Solved] pacman failed to synchronize all databases (unexpected error)

That is likely the problem at hand. https://gitlab.archlinux.org/archlinux/ … =heads#L38

I'm still concerned by the different mirror list between core and extra. If you're pulling them from different servers, at some point they will be out of sync and you will end up with things not working. I don't see how that's possible from the pacman.conf you posted, though. I see a problem with TotalDownload, comments can't start in the middle of the line, but the entire line is commented out so that shouldn't matter right now. What's /etc/pacman.d/mirrorlist look like?

zeek

Member

Registered: 2010-01-07

Posts: 12

Re: [Solved] pacman failed to synchronize all databases (unexpected error)

Scimmia & Seth
    DownloadUser = alpm

As to why 'alpm' was missing, I really don't know. My /etc/pacman.conf.pacnew does have it.
Most likely merging the pacnew with vimdiff and a momentary lapse of
    random non-genious keyboard tapping

pacman is now able to upgrade as evidenced by the line:  starting full system upgrade...

:: Synchronizing package databases...
 core            117.2 KiB   461 KiB/s 00:00 [-------------------------------------] 100%
 extra             7.4 MiB  20.0 MiB/s 00:00 [-------------------------------------] 100%
error: restricting filesystem access failed because the landlock rule for the temporary download directory could not be added!
:: Starting full system upgrade...

Scimmia: etc/pacman.d/mirrorlist
I ran reflector the day after pacman got upgraded to v.7.0

################################################################################
################# Arch Linux mirrorlist generated by Reflector #################
################################################################################

# With:       reflector --verbose --country US --age 12 -n 20 -p https --sort rate --save /etc/pacman.d/mirrorlist
# When:       2024-09-15 02:57:26 UTC
# From:       https://archlinux.org/mirrors/status/json/
# Retrieved:  2024-09-15 02:56:06 UTC
# Last Check: 2024-09-15 02:45:22 UTC

Server = https://mirrors.ocf.berkeley.edu/archlinux/$repo/os/$arch
Server = https://mirror.arizona.edu/archlinux/$repo/os/$arch
Server = https://mirrors.xtom.com/archlinux/$repo/os/$arch
Server = https://opencolo.mm.fcix.net/archlinux/$repo/os/$arch
Server = https://codingflyboy.mm.fcix.net/archlinux/$repo/os/$arch
Server = https://mirror.fcix.net/archlinux/$repo/os/$arch
Server = https://arch.hu.fo/archlinux/$repo/os/$arch
Server = https://mirror.sfo12.us.leaseweb.net/archlinux/$repo/os/$arch
Server = https://us.mirrors.cicku.me/archlinux/$repo/os/$arch
Server = https://ridgewireless.mm.fcix.net/archlinux/$repo/os/$arch
Server = https://ziply.mm.fcix.net/archlinux/$repo/os/$arch
Server = https://archlinux.doridian.net/$repo/os/$arch
Server = https://irltoolkit.mm.fcix.net/archlinux/$repo/os/$arch
Server = https://southfront.mm.fcix.net/archlinux/$repo/os/$arch
Server = https://mnvoip.mm.fcix.net/archlinux/$repo/os/$arch
Server = https://nocix.mm.fcix.net/archlinux/$repo/os/$arch
Server = https://america.mirror.pkgbuild.com/$repo/os/$arch
Server = https://mirror.adectra.com/archlinux/$repo/os/$arch
Server = https://mirror.ette.biz/archlinux/$repo/os/$arch
Server = https://iad.mirrors.misaka.one/archlinux/$repo/os/$arch

Scimmia: 'TotalDownload'
Corrected: Thanks.

I see the new error mssg: 'restricting filesystem access failed because the landlock rule...'
I remember seeing a comment just recently about this very topic. I will look up the post on returning home.

I feel like I have taken enough of your time.

I wish you both and your families all the best.
Thank you very much.
Cheers

PS: I will mark this post as solved as I needed pacman to at least update my system.

seth

Member

Registered: 2012-09-03

Posts: 57,175

Re: [Solved] pacman failed to synchronize all databases (unexpected error)

error: restricting filesystem access failed because the landlock rule for the temporary download directory could not be added!
:: Starting full system upgrade...

uname -a
findmnt -T /var/cache/pacman/pkg

---

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Scimmia

Fellow

Registered: 2012-09-01

Posts: 11,958

Re: [Solved] pacman failed to synchronize all databases (unexpected error)

Well I don't see anything strange with that mirrorlist, and it matches what pacman sees for core, extra is just skipping a bunch of them. Unless it was just a copy/paste error?