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#1 2017-09-09 19:40:54

AndreasGB
Member
Registered: 2016-01-05
Posts: 18

[Solved] Errors installing filesystem, /bin exists in filesystem

Hi,

I just ran pacman -Syu after about a week or two without updating and now updating filesystem fails with the following errors

error: failed to commit transaction (conflicting files)
filesystem: /bin exists in filesystem
filesystem: /etc/arch-release exists in filesystem
filesystem: /etc/mtab exists in filesystem
filesystem: /etc/profile.d/locale.sh exists in filesystem
filesystem: /lib exists in filesystem
filesystem: /lib64 exists in filesystem
filesystem: /sbin exists in filesystem
filesystem: /usr/lib/os-release exists in filesystem
filesystem: /usr/lib64 exists in filesystem
filesystem: /usr/local/share/man exists in filesystem
filesystem: /usr/sbin exists in filesystem
filesystem: /usr/share/factory/etc/crypttab exists in filesystem
filesystem: /usr/share/factory/etc/fstab exists in filesystem
filesystem: /usr/share/factory/etc/group exists in filesystem
filesystem: /usr/share/factory/etc/gshadow exists in filesystem
filesystem: /usr/share/factory/etc/host.conf exists in filesystem
filesystem: /usr/share/factory/etc/hosts exists in filesystem
filesystem: /usr/share/factory/etc/issue exists in filesystem
filesystem: /usr/share/factory/etc/ld.so.conf exists in filesystem
filesystem: /usr/share/factory/etc/motd exists in filesystem
filesystem: /usr/share/factory/etc/passwd exists in filesystem
filesystem: /usr/share/factory/etc/profile exists in filesystem
filesystem: /usr/share/factory/etc/resolv.conf exists in filesystem
filesystem: /usr/share/factory/etc/securetty exists in filesystem
filesystem: /usr/share/factory/etc/shadow exists in filesystem
filesystem: /usr/share/factory/etc/shells exists in filesystem
filesystem: /usr/share/man/man7/archlinux.7.gz exists in filesystem
filesystem: /var/lock exists in filesystem
filesystem: /var/mail exists in filesystem
filesystem: /var/run exists in filesystem

As well as updating gptfdisk:

gptfdisk: /usr/bin/cgdisk exists in filesystem
gptfdisk: /usr/bin/fixparts exists in filesystem
gptfdisk: /usr/bin/gdisk exists in filesystem
gptfdisk: /usr/bin/sgdisk exists in filesystem
gptfdisk: /usr/share/man/man8/cgdisk.8.gz exists in filesystem
gptfdisk: /usr/share/man/man8/fixparts.8.gz exists in filesystem
gptfdisk: /usr/share/man/man8/gdisk.8.gz exists in filesystem
gptfdisk: /usr/share/man/man8/sgdisk.8.gz exists in filesystem

How can I fix this? Forcing does not seem like an option since that would delete critical system files.

EDIT: I also forced fsck now, there were no problems found.

Last edited by AndreasGB (2017-09-13 15:16:55)

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#2 2017-09-09 19:42:45

jasonwryan
Anarchist
From: .nz
Registered: 2009-05-09
Posts: 30,424
Website

Re: [Solved] Errors installing filesystem, /bin exists in filesystem

Don't truncate log output; paste the full output of `pacman -Syu`: https://bbs.archlinux.org/viewtopic.php?id=57855

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#3 2017-09-09 19:59:18

AndreasGB
Member
Registered: 2016-01-05
Posts: 18

Re: [Solved] Errors installing filesystem, /bin exists in filesystem

Thanks, will do that from now on. Here is the full output:

 sudo LANG=en_US.utf8 pacman -Syu
[sudo] Passwort für andreas: 
:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
:: Starting full system upgrade...
resolving dependencies...
looking for conflicting packages...

Packages (121) acpi_call-1.1.0-72  android-tools-8.0.0_r4-2  android-udev-20170902-1  anki-2.1.0beta15-1  babl-0.1.30-1  binutils-2.29.0-1  btrfs-progs-4.12.1-1  chromium-61.0.3163.79-1  cmake-3.9.2-2
               coreutils-8.28-1  docker-1:17.07.0-1  e2fsprogs-1.43.6-1  expat-2.2.4-1  fakeroot-1.22-1  feh-2.20-1  file-5.32-1  filesystem-2017.03-2  fontconfig-2.12.5-1  gcc-7.2.0-2  gcc-libs-7.2.0-2
               gd-2.2.5-1  gdb-8.0.1-1  gdb-common-8.0.1-1  glibc-2.26-3  gnome-online-accounts-3.24.3-1  gnupg-2.2.0-1  gpm-1.20.7-8  gptfdisk-1.0.3-1  graphicsmagick-1.3.26-3  gvim-8.0.1066-1
               hexchat-2.12.4-6  hunspell-1.6.2-1  iana-etc-20170824-1  imagemagick-6.9.9.11-1  iproute2-4.13.0-1  irssi-1.0.4-3  k3b-1:17.08.1-1  kaccounts-integration-17.08.1-1  kdebase-runtime-17.08.1-1
               kdelibs-4.14.36-1  lib32-gcc-libs-7.2.0-1  lib32-glibc-2.26-2  lib32-libelf-0.169-2  lib32-libsm-1.2.2-2  lib32-libxau-1.0.8-2  lib32-libxinerama-1.1.3-2  lib32-mesa-17.1.8-2
               lib32-ncurses-6.0+20170527-2  lib32-sdl-1.2.15-7  libblockdev-2.11-1  libgcrypt-1.8.1-1  libinput-1.8.2-1  libkcddb-17.08.1-1  libkexiv2-17.08.1-1  libkipi-17.08.1-1  libldap-2.4.45-4
               liblouis-3.3.0-1  libmms-0.6.4-2  libpng-1.6.32-1  libproxy-0.4.15-6  libpulse-11.0-1  libraw-0.18.3-1  libreoffice-fresh-5.4.1-1  libtommath-1.0.1-1  libtool-2.4.6+40+g6ca5e224-1
               libvirt-3.7.0-1  libxml2-2.9.5+6+g07e227ed-1  libxslt-1.1.29+42+gac341cbd-2  linux-4.12.10-1  linux-api-headers-4.12.7-1  linux-headers-4.12.10-1  mesa-17.2.0-2  mkinitcpio-23-2  nano-2.8.7-1
               ncurses-6.0+20170902-1  okular-17.08.1-1  p11-kit-0.23.8-1  pacman-mirrorlist-20170907-1  pango-1.40.12-1  perl-5.26.0-4  perl-algorithm-diff-1.1903-3  perl-anyevent-4:7.14-3
               perl-anyevent-i3-0.17-2  perl-canary-stability-2012-3  perl-common-sense-3.74-3  perl-error-0.17025-2  perl-file-basedir-0.07-3  perl-file-which-1.21-3  perl-inc-latest-0.500-3
               perl-ipc-system-simple-1.25-3  perl-json-xs-3.03-4  perl-libintl-perl-1.28-1  perl-module-build-0.4224-5  perl-regexp-common-2016010801-4  perl-types-serialiser-1.0-3  perl-xml-parser-2.44-6
               perl-xml-simple-2.24-3  perl-xml-xpath-1.40-3  php-7.1.9-1  pulseaudio-11.0-1  python-markdown-2.6.9-1  python-setuptools-1:36.3.0-1  python2-construct-2.8.14-1  python2-psutil-5.3.0-1
               python2-pyasn1-0.3.4-1  python2-setuptools-1:36.3.0-1  python2-tornado-4.5.2-1  qemu-2.10.0-1  qemu-arch-extra-2.10.0-1  rhash-1.3.5-2  signon-kwallet-extension-17.08.1-1  spectacle-17.08.1-1
               subversion-1.9.7-3  sudo-1.8.21.p2-1  thin-provisioning-tools-0.7.1-1  typescript-2.5.2-1  vim-runtime-8.0.1066-1  vulkan-icd-loader-1.0.57.0-1  x86_energy_perf_policy-4.13-1
               xf86-video-intel-1:2.99.917+781+gc8990575-1  xmms2-0.8DrO_o.949.gca15e830-5

Total Installed Size:  2115.30 MiB
Net Upgrade Size:       -23.59 MiB

:: Proceed with installation? [Y/n] Y
(121/121) checking keys in keyring                                                                                             [#############################################################################] 100%
(121/121) checking package integrity                                                                                           [#############################################################################] 100%
(121/121) loading package files                                                                                                [#############################################################################] 100%
(121/121) checking for file conflicts                                                                                          [#############################################################################] 100%
error: failed to commit transaction (conflicting files)
filesystem: /bin exists in filesystem
filesystem: /etc/arch-release exists in filesystem
filesystem: /etc/mtab exists in filesystem
filesystem: /etc/profile.d/locale.sh exists in filesystem
filesystem: /lib exists in filesystem
filesystem: /lib64 exists in filesystem
filesystem: /sbin exists in filesystem
filesystem: /usr/lib/os-release exists in filesystem
filesystem: /usr/lib64 exists in filesystem
filesystem: /usr/local/share/man exists in filesystem
filesystem: /usr/sbin exists in filesystem
filesystem: /usr/share/factory/etc/crypttab exists in filesystem
filesystem: /usr/share/factory/etc/fstab exists in filesystem
filesystem: /usr/share/factory/etc/group exists in filesystem
filesystem: /usr/share/factory/etc/gshadow exists in filesystem
filesystem: /usr/share/factory/etc/host.conf exists in filesystem
filesystem: /usr/share/factory/etc/hosts exists in filesystem
filesystem: /usr/share/factory/etc/issue exists in filesystem
filesystem: /usr/share/factory/etc/ld.so.conf exists in filesystem
filesystem: /usr/share/factory/etc/motd exists in filesystem
filesystem: /usr/share/factory/etc/passwd exists in filesystem
filesystem: /usr/share/factory/etc/profile exists in filesystem
filesystem: /usr/share/factory/etc/resolv.conf exists in filesystem
filesystem: /usr/share/factory/etc/securetty exists in filesystem
filesystem: /usr/share/factory/etc/shadow exists in filesystem
filesystem: /usr/share/factory/etc/shells exists in filesystem
filesystem: /usr/share/man/man7/archlinux.7.gz exists in filesystem
filesystem: /var/lock exists in filesystem
filesystem: /var/mail exists in filesystem
filesystem: /var/run exists in filesystem
gptfdisk: /usr/bin/cgdisk exists in filesystem
gptfdisk: /usr/bin/fixparts exists in filesystem
gptfdisk: /usr/bin/gdisk exists in filesystem
gptfdisk: /usr/bin/sgdisk exists in filesystem
gptfdisk: /usr/share/man/man8/cgdisk.8.gz exists in filesystem
gptfdisk: /usr/share/man/man8/fixparts.8.gz exists in filesystem
gptfdisk: /usr/share/man/man8/gdisk.8.gz exists in filesystem
gptfdisk: /usr/share/man/man8/sgdisk.8.gz exists in filesystem
Errors occurred, no packages were upgraded.

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#4 2017-09-09 20:11:17

loqs
Member
Registered: 2014-03-06
Posts: 17,325

Re: [Solved] Errors installing filesystem, /bin exists in filesystem

What is the output of

# pacman -Qkk filesystem gptfdisk

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#5 2017-09-09 21:04:16

Trilby
Inspector Parrot
Registered: 2011-11-29
Posts: 29,523
Website

Re: [Solved] Errors installing filesystem, /bin exists in filesystem

AndreasGB wrote:

I just ran pacman -Syu after about a week or two without updating

title wrote:

Errors installing filesystem-2017.03-2

Err ... what?

A week or two, or a month or six?

"UNIX is simple and coherent..." - Dennis Ritchie, "GNU's Not UNIX" -  Richard Stallman

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#6 2017-09-09 21:15:45

AndreasGB
Member
Registered: 2016-01-05
Posts: 18

Re: [Solved] Errors installing filesystem, /bin exists in filesystem

loqs wrote:

What is the output of

# pacman -Qkk filesystem gptfdisk
sudo LANG=en_US.utf8 pacman -Qkk filesystem gptfdisk
error: package 'filesystem' was not found
error: package 'gptfdisk' was not found
Trilby wrote:
AndreasGB wrote:

I just ran pacman -Syu after about a week or two without updating

title wrote:

Errors installing filesystem-2017.03-2

Err ... what?

A week or two, or a month or six?

Really not more than three weeks, the date confused me too. Maybe it was an optional dependency?

Thanks for the help so far, really appreciate it.

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#7 2017-09-09 21:30:08

loqs
Member
Registered: 2014-03-06
Posts: 17,325

Re: [Solved] Errors installing filesystem, /bin exists in filesystem

So there may be an issue with the mirror you are syncing with as well as the local pacman database appearing to have issues.
What is the out of the following

$ pacman -Si filesystem
$ pacman -Dk

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#8 2017-09-09 21:40:31

WorMzy
Forum Moderator
From: Scotland
Registered: 2010-06-16
Posts: 11,846
Website

Re: [Solved] Errors installing filesystem, /bin exists in filesystem

Please post your /var/log/pacman.log*, as well as the output of

find /var/lib/pacman/local -name "*filesystem*" -or -name "*gptfdisk*" | xargs ls -la

*Use a pastebin if necessary: https://wiki.archlinux.org/index.php/Li … in_clients

Sakura:-
Mobo: MSI MAG X570S TORPEDO MAX // Processor: AMD Ryzen 9 5950X @4.9GHz // GFX: AMD Radeon RX 5700 XT // RAM: 32GB (4x 8GB) Corsair DDR4 (@ 3000MHz) // Storage: 1x 3TB HDD, 6x 1TB SSD, 2x 120GB SSD, 1x 275GB M2 SSD

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#9 2017-09-09 23:37:15

AndreasGB
Member
Registered: 2016-01-05
Posts: 18

Re: [Solved] Errors installing filesystem, /bin exists in filesystem

loqs wrote:

So there may be an issue with the mirror you are syncing with as well as the local pacman database appearing to have issues.
What is the out of the following

$ pacman -Si filesystem
$ pacman -Dk
LANG=en_US.utf8 pacman -Si filesystem
Repository      : core
Name            : filesystem
Version         : 2017.03-2
Description     : Base Arch Linux files
Architecture    : x86_64
URL             : https://www.archlinux.org
Licenses        : GPL
Groups          : base
Provides        : None
Depends On      : iana-etc
Optional Deps   : None
Conflicts With  : None
Replaces        : None
Download Size   : 10.20 KiB
Installed Size  : 13.00 KiB
Packager        : Sébastien Luttringer <seblu@seblu.net>
Build Date      : Sun 26 Mar 2017 11:57:57 PM CEST
Validated By    : MD5 Sum  SHA-256 Sum  Signature
LANG=en_US.utf8 pacman -Dk
error: missing 'filesystem' dependency for 'fakeroot'
error: missing 'filesystem' dependency for 'glibc'
error: missing 'gptfdisk' dependency for 'libblockdev'
error: missing 'filesystem>=2011.10-1' dependency for 'mkinitcpio'
WorMzy wrote:

Please post your /var/log/pacman.log*, as well as the output of

find /var/lib/pacman/local -name "*filesystem*" -or -name "*gptfdisk*" | xargs ls -la

*Use a pastebin if necessary: https://wiki.archlinux.org/index.php/Li … in_clients

The find command yields an empty result, as a consequence, it prints my current working directory.

Here are the 3000 log entries from pacman.log https://gist.github.com/AndreasGB/6075c … 993015cedf

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#10 2017-09-10 02:46:22

cfr
Member
From: Cymru
Registered: 2011-11-27
Posts: 7,132

Re: [Solved] Errors installing filesystem, /bin exists in filesystem

Do you remember why you needed

[2017-07-23 18:32] [PACMAN] Running 'pacman -S --force filesystem'

in July? I have only 2 occurrences of --force for filesystem in my pacman.log: one in 2011 and the other in 2012. Admittedly, I don't remember why I needed them.

You seem to have updated the database and then tried to reinstall filesystem (and (re)install gptfdisk), then forced filesystem and finally updated the system. That seems a rather dangerous way to proceed yikes.

Last edited by cfr (2017-09-10 02:55:42)

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#11 2017-09-10 10:14:08

AndreasGB
Member
Registered: 2016-01-05
Posts: 18

Re: [Solved] Errors installing filesystem, /bin exists in filesystem

cfr wrote:

Do you remember why you needed

[2017-07-23 18:32] [PACMAN] Running 'pacman -S --force filesystem'

in July? I have only 2 occurrences of --force for filesystem in my pacman.log: one in 2011 and the other in 2012. Admittedly, I don't remember why I needed them.

You seem to have updated the database and then tried to reinstall filesystem (and (re)install gptfdisk), then forced filesystem and finally updated the system. That seems a rather dangerous way to proceed yikes.


I am not entirely sure anymore why I forced filesystem, but I think it conflicted with two config files that I had never modified so I figured forcing it would be ok.

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#12 2017-09-10 10:53:20

WorMzy
Forum Moderator
From: Scotland
Registered: 2010-06-16
Posts: 11,846
Website

Re: [Solved] Errors installing filesystem, /bin exists in filesystem

Okay, well hopefully you've read the pacman man page since then and determined that --force is not an option you should be using in that situation (or in most other situations).

At this point I think the best way forward is to recreate the database entries for these packages, then check for inconsistent files. Going by your pacman.log, you should have version 1.0.1-2 of gptdisk installed, so if you don't have that version in your pacman cache, grab it from the Arch Linux Archive. The filesystem package is still at the same version you have installed, so you don't need to do anything extra to get that package, just:

pacman -S --dbonly filesystem

Install the gptfdisk package with

pacman -U --dbonly /path/to/gptfdisk-1.0.1-2-x86_64.pkg.tar.xz

Finally, check the consistency of these packages with

pacman -Qkk filesystem gptfdisk

You're probably fine ignoring the warnings for the filesystem package, but post them here just in case.

Once you're happy that the packages are in an acceptable state, do a full system upgrade again. Post any problems you get.


EDIT: Of course, this is just dealing with the symptoms, we still have no idea what actaully happened to your pacman database in the first place. Perhaps you could shed some light on that? It's very unusual for a database entry to completely vanish, let alone two database entries at the same time.

Last edited by WorMzy (2017-09-10 10:56:01)

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Mobo: MSI MAG X570S TORPEDO MAX // Processor: AMD Ryzen 9 5950X @4.9GHz // GFX: AMD Radeon RX 5700 XT // RAM: 32GB (4x 8GB) Corsair DDR4 (@ 3000MHz) // Storage: 1x 3TB HDD, 6x 1TB SSD, 2x 120GB SSD, 1x 275GB M2 SSD

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#13 2017-09-10 11:15:04

AndreasGB
Member
Registered: 2016-01-05
Posts: 18

Re: [Solved] Errors installing filesystem, /bin exists in filesystem

Thank you for helping me, the output of pacman -Qkk was:

LANG=en_US.utf8 pacman -Qkk filesystem gptfdisk                                                                                                                                                           1 ↵
backup file: filesystem: /etc/fstab (Modification time mismatch)
backup file: filesystem: /etc/fstab (Size mismatch)
backup file: filesystem: /etc/group (Modification time mismatch)
backup file: filesystem: /etc/group (Size mismatch)
backup file: filesystem: /etc/gshadow (Modification time mismatch)
backup file: filesystem: /etc/gshadow (Size mismatch)
backup file: filesystem: /etc/passwd (Modification time mismatch)
backup file: filesystem: /etc/passwd (Size mismatch)
backup file: filesystem: /etc/resolv.conf (Modification time mismatch)
backup file: filesystem: /etc/resolv.conf (Size mismatch)
backup file: filesystem: /etc/shadow (Modification time mismatch)
backup file: filesystem: /etc/shadow (Size mismatch)
backup file: filesystem: /etc/shells (Modification time mismatch)
backup file: filesystem: /etc/shells (Size mismatch)
filesystem: 105 total files, 0 altered files
warning: gptfdisk: /usr/share/doc/gdisk/NEWS (No such file or directory)
warning: gptfdisk: /usr/share/doc/gdisk/README (No such file or directory)
gptfdisk: 17 total files, 2 altered files

The upgrade seems to have worked now.

A possible reason for the damaged database might be that I have had multiple filesystem corruptions that I guess came from not having hooks disabling bcache when suspending.

I now have those which seems to have somewhat fixed that problem, but my laptop still sometimes has weird touble coming back from suspend, but the log files don't show anything, and this only happens after it ran for 5+ days so I have no idea how to debug this properly. This recently resulted in corruption again.

Last edited by AndreasGB (2017-09-10 11:15:48)

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#14 2017-09-10 13:23:14

WorMzy
Forum Moderator
From: Scotland
Registered: 2010-06-16
Posts: 11,846
Website

Re: [Solved] Errors installing filesystem, /bin exists in filesystem

Okay, that's beyond the scope of this thread. Please mark this one as solved, and if you need help with the identifying the cause of the corruption, please open a new thread with as much information as you can (full journals from affected sessions, hardware information about your disk, mount options, etc)

Sakura:-
Mobo: MSI MAG X570S TORPEDO MAX // Processor: AMD Ryzen 9 5950X @4.9GHz // GFX: AMD Radeon RX 5700 XT // RAM: 32GB (4x 8GB) Corsair DDR4 (@ 3000MHz) // Storage: 1x 3TB HDD, 6x 1TB SSD, 2x 120GB SSD, 1x 275GB M2 SSD

Making lemonade from lemons since 2015.

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#15 2017-09-10 19:03:22

cfr
Member
From: Cymru
Registered: 2011-11-27
Posts: 7,132

Re: [Solved] Errors installing filesystem, /bin exists in filesystem

AndreasGB wrote:

Thank you for helping me, the output of pacman -Qkk was:

warning: gptfdisk: /usr/share/doc/gdisk/NEWS (No such file or directory)
warning: gptfdisk: /usr/share/doc/gdisk/README (No such file or directory)

If you still don't have these files after a full system upgrade, I'd reinstall gptfdisk to keep pacman happy.

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