[solved]conflicting files for xorg-server-common

dice · 2014-12-29 22:02:44

On update I got this:

Packages (7) cmake-3.1.0-2  numix-themes-2.5-1  python-setuptools-1:9.0.1-1
             python2-setuptools-1:9.0.1-1  xorg-server-1.16.3-2
             xorg-server-common-1.16.3-2  xorg-server-xephyr-1.16.3-2

Total Download Size:    7.35 MiB
Total Installed Size:  36.79 MiB
Net Upgrade Size:       0.10 MiB

:: Proceed with installation? [Y/n] 
:: Retrieving packages ...
 cmake-3.1.0-2-x86_64       4.5 MiB   469K/s 00:10 [----------------------] 100%
 python-setuptools-1...   336.9 KiB   473K/s 00:01 [----------------------] 100%
 python2-setuptools-...   312.4 KiB   485K/s 00:01 [----------------------] 100%
 xorg-server-common-...    26.2 KiB   749K/s 00:00 [----------------------] 100%
 xorg-server-1.16.3-...  1298.2 KiB   555K/s 00:02 [----------------------] 100%
 xorg-server-xephyr-...   884.5 KiB   515K/s 00:02 [----------------------] 100%
 numix-themes-2.5-1-any    58.0 KiB   542K/s 00:00 [----------------------] 100%
(7/7) checking keys in keyring                     [----------------------] 100%
(7/7) checking package integrity                   [----------------------] 100%
(7/7) loading package files                        [----------------------] 100%
(7/7) checking for file conflicts                  [----------------------] 100%
error: failed to commit transaction (conflicting files)
xorg-server-common: /var/lib exists in filesystem
xorg-server-common: /var/lib/xkb/README.compiled exists in filesystem
Errors occurred, no packages were upgraded.

Well yes, they exist and as far as I understand they should exist.

pacman -Qo /var/lib/xkb/README.compiled 
/usr/lib/xkb/README.compiled is owned by xorg-server-common 1.16.3-1

Where is the problem?

Last edited by dice (2014-12-30 18:49:45)

karol · 2014-12-29 22:30:56

$ sudo pacman -Syu 

<cut>

Package (4)               Old Version  New Version  Net Change  Download Size

extra/cmake               3.1.0-1      3.1.0-2        0.00 MiB       4.54 MiB
extra/python-setuptools   1:8.2.1-1    1:9.0.1-1     -0.06 MiB       0.33 MiB
extra/xorg-server         1.16.3-1     1.16.3-2       0.08 MiB       1.32 MiB
extra/xorg-server-common  1.16.3-1     1.16.3-2       0.05 MiB       0.03 MiB

Total Download Size:    6.22 MiB
Total Installed Size:  31.29 MiB
Net Upgrade Size:       0.07 MiB

:: Proceed with installation? [Y/n]
:: Retrieving packages ...
 cmake-3.1.0-2-i686                      4.5 MiB  2.86M/s 00:02 [###################################]  73%
 python-setuptools-1:9.0.1-1-any         4.9 MiB  2.66M/s 00:02 [###################################]  78%
 xorg-server-common-1.16.3-2-i686        4.9 MiB  2.57M/s 00:02 [###################################]  78%
 xorg-server-1.16.3-2-i686               6.2 MiB  2.32M/s 00:03 [###################################] 100%
(4/4) checking keys in keyring                                  [###################################] 100%
(4/4) checking package integrity                                [###################################] 100%
(4/4) loading package files                                     [###################################] 100%
(4/4) checking for file conflicts                               [###################################] 100%
(4/4) checking available disk space                             [###################################] 100%
(1/4) upgrading cmake                                           [###################################] 100%
(2/4) upgrading python-setuptools                               [###################################] 100%
(3/4) upgrading xorg-server-common                              [###################################] 100%
(4/4) upgrading xorg-server                                     [###################################] 100%
$ pacman -Qo /var/lib/xkb/README.compiled
/var/lib/xkb/README.compiled is owned by xorg-server-common 1.16.3-2

Works for me on my 32-bit Arch with [testing] repos enabled.

Leonid.I · 2014-12-29 22:37:59

dice wrote:

Where is the problem?

Most likely, in your local pacman database. What is in your /var/lib/pacman/local/xorg-server-common-1.16.3-1 ?

karol · 2014-12-29 22:42:32

Since pacman can find it

dice wrote:

pacman -Qo /var/lib/xkb/README.compiled 
/usr/lib/xkb/README.compiled is owned by xorg-server-common 1.16.3-1

I'm scratching my head with this one.

lucke · 2014-12-29 22:49:19

What does "pacman -Qo /var/lib" return?

dice · 2014-12-30 08:47:53

ls /var/lib/pacman/local/xorg-server-common-1.16.3-1
total 12K
-rw-r--r-- 1 root root 366 20. Dez 17:07 desc
-rw-r--r-- 1 root root 292 29. Dez 10:57 files
-rw-r--r-- 1 root root 633 20. Dez 14:36 mtree

pacman -Qo /var/lib
error: No package owns /var/lib

lucke · 2014-12-30 10:24:38

Food for thought:

cat /var/lib/pacman/local/xorg-server-common-1.16.3-1/files
%FILES%
usr/
usr/lib/
usr/lib/xorg/
usr/lib/xorg/protocol.txt
usr/share/
usr/share/licenses/
usr/share/licenses/xorg-server-common/
usr/share/licenses/xorg-server-common/COPYING
usr/share/man/
usr/share/man/man1/
usr/share/man/man1/Xserver.1.gz
var/
var/lib/
var/lib/xkb/
var/lib/xkb/README.compiled

pacman -Qo /var/lib
/var/lib/ is owned by alsa-utils 1.0.28-1
/var/lib/ is owned by colord 1.2.7-2
/var/lib/ is owned by dbus 1.8.12-1
/var/lib/ is owned by dhclient 4.3.1-1
/var/lib/ is owned by dhcpcd 6.6.7-1
/var/lib/ is owned by filesystem 2014.10-3
/var/lib/ is owned by iproute2 3.17.0-1
/var/lib/ is owned by iptables 1.4.21-1
/var/lib/ is owned by kdebase-workspace 4.11.14-1
/var/lib/ is owned by krb5 1.13-1
/var/lib/ is owned by mlocate 0.26-5
/var/lib/ is owned by mpd 0.19.7-1
/var/lib/ is owned by networkmanager 0.9.10.0-4
/var/lib/ is owned by nfs-utils 1.3.1-1
/var/lib/ is owned by ntp 4.2.8-1
/var/lib/ is owned by pacman 4.2.0-5
/var/lib/ is owned by preload 0.6.4-6
/var/lib/ is owned by rpcbind 0.2.1-5
/var/lib/ is owned by systemd 218-1
/var/lib/ is owned by udisks2 2.1.3-1
/var/lib/ is owned by upower 0.99.2-1
/var/lib/ is owned by vi 1:050325-4
/var/lib/ is owned by wvstreams 4.6.1-7
/var/lib/ is owned by xkeyboard-config 2.13-1
/var/lib/ is owned by xorg-server-common 1.16.3-1

As karol has pointed out, it is suspicious that in your case pacman thinks README.compiled is in /usr, not /var. And it is suspicious that /var/lib isn't owned by anything, What do "ls -l /var", "cat /var/lib/pacman/local/xorg-server-common-1.16.3-1/files" and "ls -l /var/lib/xkb/README.compiled /usr/lib/xkb/README.compiled" show?

dice · 2014-12-30 14:08:58

Seems there is something wrong with my directory structure. This could be caused by myself being stupid ;) https://bbs.archlinux.org/viewtopic.php?id=185941
Is /var/lib supposed to be symlink to /usr/lib?

ls -l /var
total 72K
drwxr-xr-x   7 root root  4.0K 20. Dez 00:11 abs
lrwxrwxrwx   1 root root     7  4. Jul 14:44 bin -> usr/bin
drwxr-xr-x   6 root root  4.0K 15. Aug 17:33 boot
drwxr-xr-x  10 root root  4.0K 20. Aug 02:08 cache
drwxr-xr-x   3 root root  4.0K 28. Dez 23:18 db
drwxr-xr-x   2 root root  4.0K 31. Mai 2013  empty
drwxr-xr-x 102 root root   12K 19. Aug 18:17 etc
drwxrwxr-x   2 root games 4.0K 10. Feb 2014  games
lrwxrwxrwx   1 root root     8 20. Aug 02:01 lib -> /usr/lib
lrwxrwxrwx   1 root root     7  4. Jul 14:44 lib64 -> usr/lib
drwxr-xr-x   2 root root  4.0K 31. Mai 2013  local
lrwxrwxrwx   1 root root    11 25. Okt 20:41 lock -> ../run/lock
drwxr-xr-x  10 root root  4.0K 30. Dez 14:50 log
lrwxrwxrwx   1 root root    10 25. Okt 20:41 mail -> spool/mail
drwxr-xr-x   2 root root  4.0K 31. Mai 2013  opt
drwx------   2 root root  4.0K 19. Aug 19:14 root
lrwxrwxrwx   1 root root     6 25. Okt 20:41 run -> ../run
lrwxrwxrwx   1 root root     7  4. Jul 14:44 sbin -> usr/bin
drwx------   2 root root  4.0K 19. Aug 19:14 scratch
drwxr-xr-x   9 root root  4.0K 10. Dez 02:16 spool
drwx------   2 root root  4.0K 19. Aug 19:14 srv
drwxrwxrwt  49 root root  4.0K 30. Dez 14:54 tmp
drwx------   2 root root  4.0K 19. Aug 19:14 usr

cat /var/lib/pacman/local/xorg-server-common-1.16.3-1/files
%FILES%
usr/
usr/lib/
usr/lib/xorg/
usr/lib/xorg/protocol.txt
usr/share/
usr/share/licenses/
usr/share/licenses/xorg-server-common/
usr/share/licenses/xorg-server-common/COPYING
usr/share/man/
usr/share/man/man1/
usr/share/man/man1/Xserver.1.gz
var/
usr/lib/xkb/
usr/lib/xkb/README.compiled

ls -l /var/lib/xkb/README.compiled
-rw-r--r-- 1 root root 644 20. Dez 14:36 /var/lib/xkb/README.compiled

ls -l /usr/lib/xkb/README.compiled
-rw-r--r-- 1 root root 644 20. Dez 14:36 /usr/lib/xkb/README.compiled

orschiro · 2014-12-30 14:44:02

Is /var/lib supposed to be symlink to /usr/lib?

~ ❯ ls -l /var
total 84
drwxr-xr-x  7 root root        4096 Jul  1  2014 abs
drwxr-xr-x 15 root root        4096 Dez  6 16:31 cache
drwxr-xr-x  3 root root        4096 Dez 29 08:32 db
drwxr-xr-x  2 root root        4096 Okt 23  2012 empty
drwxrwxr-x  2 root games       4096 Mär 14  2013 games
drwxr-xr-x 44 root root        4096 Dez 30 00:29 lib

At least on my it does not...

dice · 2014-12-30 14:59:13

I just noticed that it looks like have copied / to /var at some point because there are folders like boot, etc, srv, tmp, root
That also explains why /var is taking up that much space (noticed this earlier but hadn't the time and motivation to investigate further...)
Any ideas on how to puzzle the things back to where they belong?

orschiro · 2014-12-30 15:02:02

Did you do that via the command line? Check your shell history files to reveal what commands you used precisely.

dice · 2014-12-30 15:10:45

From the timestamps it apperas to have happpened on 19. August which corresponds to my accident which I have linked before.
I don't know if the history is saved when in chroot but that doesn't really matter because my history does not go back that long.

Edit: typo

Last edited by dice (2014-12-30 15:11:14)

Leonid.I · 2014-12-30 16:59:26

dice wrote:

https://bbs.archlinux.org/viewtopic.php?id=185941

TL;DR: Your system is well and truly b0rked. At this point, the only way to get back to normal is do a complete reinstall. On the bright side, there is nothing like installing Arch on the New Year night

To the issue in the above thread, full-system backups on a Linux-based OS are quite stupid idea to begin with because the core system is free and readily available from mirrors. On a rolling-release distro this is just a recipe for disaster because even FS layout can change. So, a proper backup strategy is preserving _changed_ configs from /etc/ and user's (preferrably non-binary) data.

dice wrote:

Is /var/lib supposed to be symlink to /usr/lib?

No.

dice wrote:

cat /var/lib/pacman/local/xorg-server-common-1.16.3-1/files
%FILES%
usr/
usr/lib/
usr/lib/xorg/
usr/lib/xorg/protocol.txt
usr/share/
usr/share/licenses/
usr/share/licenses/xorg-server-common/
usr/share/licenses/xorg-server-common/COPYING
usr/share/man/
usr/share/man/man1/
usr/share/man/man1/Xserver.1.gz
var/
usr/lib/xkb/
usr/lib/xkb/README.compiled

So, that's the problem: there is supposed to be /var/lib in here...

Trilby · 2014-12-30 17:05:13

Leonid.I wrote:

TL;DR: Your system is well and truly b0rked. At this point, the only way to get back to normal is do a complete reinstall.

That's probably not the only way - but I would second that it is the best way, and quite possibly the only reasonable way. Anything else would take a boatload of investigation, tinkering, testing, fixing, repeating, etc ...

But you can grab your current package list, and if you have a separate home partition you can keep it unmounted through the whole install. Then after a "fresh" reinstall, you can install everything from your current package list, and add your home partition to fstab, and you'll be very nearly back to exactly where you want to be. There are some config files in /etc, but these tend to be simple to recreate (one that comes to mind would be "remembered" wireless networks which would have to be readded).

orschiro · 2014-12-30 17:18:43

There are some config files in /etc, but these tend to be simple to recreate (one that comes to mind would be "remembered" wireless networks which would have to be readded).

One can use etckeeper to backup those easily and keep them versioned.

dice · 2014-12-30 18:40:57

You're right. I'll just reinstall. This will also be an opportunity for me too cleanup(i.e. not installing again) packages which I don't need anymore.
I have a seperate /home partition so that is not much of an issue. I also have a backup of complete /etc to copy config files over if needed.

After all I will start the new year with a fresh and clean system

Edit: Thanks for your help!

Last edited by dice (2014-12-30 18:41:20)

Arch Linux

#1 2014-12-29 22:02:44

[solved]conflicting files for xorg-server-common

#2 2014-12-29 22:30:56

Re: [solved]conflicting files for xorg-server-common

#3 2014-12-29 22:37:59

Re: [solved]conflicting files for xorg-server-common

#4 2014-12-29 22:42:32

Re: [solved]conflicting files for xorg-server-common

#5 2014-12-29 22:49:19

Re: [solved]conflicting files for xorg-server-common

#6 2014-12-30 08:47:53

Re: [solved]conflicting files for xorg-server-common

#7 2014-12-30 10:24:38

Re: [solved]conflicting files for xorg-server-common

#8 2014-12-30 14:08:58

Re: [solved]conflicting files for xorg-server-common

#9 2014-12-30 14:44:02

Re: [solved]conflicting files for xorg-server-common

#10 2014-12-30 14:59:13

Re: [solved]conflicting files for xorg-server-common

#11 2014-12-30 15:02:02

Re: [solved]conflicting files for xorg-server-common

#12 2014-12-30 15:10:45

Re: [solved]conflicting files for xorg-server-common

#13 2014-12-30 16:59:26

Re: [solved]conflicting files for xorg-server-common

#14 2014-12-30 17:05:13

Re: [solved]conflicting files for xorg-server-common

#15 2014-12-30 17:18:43

Re: [solved]conflicting files for xorg-server-common

#16 2014-12-30 18:40:57

Re: [solved]conflicting files for xorg-server-common

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