filesystem Update Error /bin exists in filesystem

mfaridi · 2013-06-08 22:50:37

thanks
but I do not upgrade my system and do not upgrade packages and this problem happen for me, I only install some some packages for use AUR

karol wrote:

What have you done with regard to https://bbs.archlinux.org/viewtopic.php … 8#p1284628 ? Did you update your system?

karol · 2013-06-08 22:54:04

mfaridi, are you sure you can't chroot using a liveCD / liveUSB?

Please don't top post - write your reply under the quote, not above.

WonderWoofy · 2013-06-08 22:55:46

mfaridi, if your system is unable to find all those binaries in their normal paths, obviously you upgraded at least some of the packages. Otherwise, those files would be in place. You really need to go try to fix your system with the advice given here instead of repeating the same barely parseable thing over and over again.

mfaridi · 2013-06-08 23:13:13

thank s all guys I will download livecd of arch linux and chroot it
but you must believe I do not upgrade packages and only install some packages
can I solve this problem without livecd or no

can I find another way to solve solve this problem

Last edited by mfaridi (2013-06-08 23:14:44)

WonderWoofy · 2013-06-08 23:15:48

@mfaridi, read the thread and follow the instructions. You have done nothing but say the same thing over and over again. It doesn't matter what you think you did with your system, the way to fix it is clearly outlined in this thread. READ IT!

tomisacat · 2013-06-09 00:17:59

I upgraded my system followed the notice but I forget to remove /bin /sbin /usr/sbin, so I failed to upgrade filesystem,after that I just reboot my computer and nightmare occurs! I cannot boot my system with systemd it shows kernel panic so I use rc.conf to boot my system,but when I run KDE it cannot run Plasma.Anybody could give me some advice?

Thank you for advance.

WonderWoofy · 2013-06-09 00:19:05

Please search before posting. There is a stickied thread about this already.

bruno321 · 2013-06-09 00:45:49

I followed the instructions to correctly update. After updating filesystem, I get this message:

atención: los permisos de directorio difieren en /mnt/
sistema de archivos: 777  paquete: 755

which translated by me, it would read something as

warning: the directory permissions are different in /mnt
file system: 777 package: 755

What does this mean? Is this alright? Should I do anything about it?

FWIW, my /mnt directory only has three empty directories.

Thanks

Last edited by bruno321 (2013-06-09 00:49:41)

Trilby · 2013-06-09 00:49:48

Bruno, that should not be a problem - it's just a warning.

I gather that you changed the permissions on /mnt/ at some point, which is a reasonable thing* to do if you mount external media there that you want your user to be able to easily access.

* note: I seen arguments that one should only alter permissions of /media/ while leaving /mnt/ to only have root access. I've never really got the point of those arguments though.

brandon88tube · 2013-06-09 00:53:22

OK, I'm one of "those" noobs that screwed something up. Even though I've been using linux for many years now, I still have very little clue as to what I'm doing half of the time. Anyways, the upgrade partially worked and it seemed to remove directories such as /bin etc., but it failed on the last part of installing filesystem. So, I didn't think anything of it at the time and chalked it up to another thing I have to research and exited rooted privileges... Now, I can't do anything because even su seems to be looking for /bin/bash. Unfortunately, I cannot create a symlink to /usr/bin which would solve some of the issues. If I missed something while I was skimming, please let me know before I reboot and end up really screwed.

bruno321 · 2013-06-09 00:55:21

Trilby wrote:

Bruno, that should not be a problem - it's just a warning.
I gather that you changed the permissions on /mnt/ at some point, which is a reasonable thing* to do if you mount external media there that you want your user to be able to easily access.
* note: I seen arguments that one should only alter permissions of /media/ while leaving /mnt/ to only have root access. I've never really got the point of those arguments though.

Thank you very much for a quick and reassuring answer!

jasonwryan · 2013-06-09 01:02:27

Merging with said sticky...

Trilby · 2013-06-09 01:11:39

brandon, if you still have a running terminal (tty or terminal emulator) then you can *hopefully* log in as root by specifying the full path to the shell:

/usr/bin/su -s /usr/bin/bash

Then, if that works you can finish the upgrade with pacman by, again, specifying the full path to pacman:

/usr/bin/pacman -Su

If these fail, there was something several pages back about calling the linker/loader's full path from the command line as a preface to any command - you may need that.

Failing any/all of these, you will probably need a live cd/usb to reboot into.

EDIT: I can't find the reference, but I believe to use the loader it would be:

/usr/lib/ld-linux.so.2 <command>

Last edited by Trilby (2013-06-09 01:22:16)

brandon88tube · 2013-06-09 01:21:00

Thanks Trilby, I was able to log in as root. However, pacman still says there is a conflict with filesystem and it failed to update. I must be misreading something or just don't understand well enough. I'll start by reading over this thread again.

EDIT: I ended up having to remove /sbin because it was still there for some reason even though /bin wasn't. Then I had to remove /usr/sbin because pacman was complaining. Did that and ran pacman -Su and all was good... I think

Last edited by brandon88tube (2013-06-09 01:37:00)

fluffy · 2013-06-09 02:18:09

HI,

I ran the update 48hrs ago as specified on the front page and when the update finished I lost xserver my screen went white then my box powered off (this becoming a regular occurrence as the cpu fan is dying and the cpu temp gets high).

I power cycle on the box and let it boot thinking all is right with the world, but during boot I get the message

ERROR: Root device mounted successfully, but /sbin/init does not exist.
Bailing out, you are on your own. Good luck.

sh: can't access tty; job control turned off
[rootfs /]#

so I panic, and have a beer.

all calmed and relaxed I troll the forums to see if others are having issues, I assumed correctly.

I rebooted the box and edited the grub kernel line to point to

init=/usr/lib/systemd/systemd

then continue to boot, things are looking up it gets past the previous error, but now I am greeted with a wall of failed status messages mixed in with some OK messages then it all comes to a grinding halt with

Failed to mount /boot.
See 'systemctl status boot.mount' for details.
"Dependency failed for local file system" 
10.504602 system-remount-fs[322]: /bin/mount for /dev/pts exited with exit status 1

Great I missed something during the update process and borked my install.

So I use a live cd and get in via chroot and mount all the partitions etc.. I do look at the file system only to see that /bin & /sbin are still there NOT symlinks. I rename the to offending folders and create a symlink to point to /usr/bin for both then check my file system and NO symlinks, run the command again and it says I can't because they already exist.

I srsly don't want to, nor can I afford to rebuild this box, this install has been going strong for 6 years.

Also I became complacent years ago and stopped performing backups b4 I did upgrades. so I really don't want to bite that bullet just yet.

I have 1 hdd with 4 partitions on it
/
/boot
/swap
/home

simple setup no lvm.

what I'm looking for is help around the whole symlink thing, am I going about this trouble shooting the right way or is there another approach?

At this level of booting is there a log dump I can check to see what's going on?

Thanks for your time reading this and any feedback or insight you may offer.

jasonwryan · 2013-06-09 02:19:53

Merging with the stickied thread...

cfr · 2013-06-09 03:08:45

You don't need to create the symlinks. Install/reinstall the filesystem package and it will take care of them for you.

yungtrizzle · 2013-06-09 04:23:57

ewaller wrote:

yungtrizzle wrote:
what sync commands?
SYNC(1)                          User Commands                         SYNC(1)



NAME
       sync - flush file system buffers

SYNOPSIS
       sync [OPTION]

DESCRIPTION
       Force changed blocks to disk, update the super block.

       --help display this help and exit

       --version
              output version information and exit

AUTHOR
       Written by Jim Meyering.

REPORTING BUGS
       Report sync bugs to bug-coreutils@gnu.org
       GNU coreutils home page: <http://www.gnu.org/software/coreutils/>
       General help using GNU software: <http://www.gnu.org/gethelp/>
       Report sync translation bugs to <http://translationproject.org/team/>

COPYRIGHT
       Copyright  (C) 2013 Free Software Foundation, Inc.  License GPLv3+: GNU
       GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
       This is free software: you are free  to  change  and  redistribute  it.
       There is NO WARRANTY, to the extent permitted by law.

SEE ALSO
       sync(2)

       The  full documentation for sync is maintained as a Texinfo manual.  If
       the info and sync programs are properly installed  at  your  site,  the
       command

              info coreutils 'sync invocation'

       should give you access to the complete manual.



GNU coreutils 8.21                 May 2013                            SYNC(1)
issuing
init --system
attempts to replace pid 1 but without success
What we have here is a failure to communicate. I meant: In your bootloader, find the kernel line. Does it have an init= clause now? If so, what does it say. In any event, use init=/usr/bin/bash on the command line in the bootloader. That tells the kernel to use bash as the init system. It works, but bash does not really make a good init system and shutdown is inelegant. issuing two sync commands in a row before exiting bash ensures your disks are left in a clean state. This is an experiment to see if we can even get the system to boot and, if so, provide an environment to maybe fix things.

It boots into a shell but bash complains

 bash : cannot set terminal process (-1) inappropriate device
 bash : no job control in this shell

The sync commands produce no output and exit causes kernel panic (as expected)

fluffy · 2013-06-09 05:28:40

jasonwryan wrote:

Merging with the stickied thread...

Thanks for the assistance and moving to the correct place.

cfr wrote:

You don't need to create the symlinks. Install/reinstall the filesystem package and it will take care of them for you.

Thanks that did the trick ;-)

----------------------

This may be related but, now I can't get past my login GDM all is does is refresh the username is there anyway I can abort this as a 1 off instance so I can get to the shell/ console/ terminal and get via root and see what's going on?

or am I going to have to chroot in again and hunt down the config files and edit them.

If I need to create a new thread I will, I appreciate the help.

Login issue solved, ConsoleKit was causing the issue removed package and its BAU.

Thanks for all your help chaps.

This community is why I love Arch, well that and the distro is awesome ;-)

Last edited by fluffy (2013-06-09 11:28:45)

axelectrik · 2013-06-09 05:29:21

This also happend to me, or something similiar
I tried booting with a Live CD, I copied /bin /sbin from the rootfs and chroot on the system with the problem, then I reinstalled "filesystem"
It couldn't, so I deleted /bin and /sbin, and after reinstalling filesystem, everything was back to normal, obviously I recommend to make a backup from both dirs.

THis fixed a problem where the system couldn't find bash, and couldn't bind /sbin for booting

ewaller · 2013-06-09 05:37:00

Sorry I am jumping in and out of the forums today, a lot of things going on in the real world Okay, the system is not hopeless. When you boot again using bash as your init system, verify that /sbin is a link to /usr/bin and that /usr/bin/init exists and is a link to ../lib/systemd/systemd

ewaller$@$odin ~ 1032 %ls -l /sbin
lrwxrwxrwx 1 root root 7 May 31 11:40 /sbin -> usr/bin
ewaller$@$odin ~ 1033 %ls /usr/bin/init
/usr/bin/init
ewaller$@$odin ~ 1034 %ls -l /usr/bin/init 
lrwxrwxrwx 1 root root 22 May 30 05:55 /usr/bin/init -> ../lib/systemd/systemd
ewaller$@$odin ~ 1035 %

theking2 · 2013-06-09 07:47:44

WorMzy wrote:

Get a list of packages that owns files in /bin, /sbin, and /usr/sbin (tested in bash and zsh):
grep '^s\?bin/\|usr/sbin' /var/lib/pacman/local/*/files | cut -d ":" -f 1 | uniq | cut -d "/" -f 6
Find unpackaged files in /bin, /sbin, and /usr/sbin:
find /bin /sbin /usr/sbin -exec pacman -Qo -- {} + >/dev/null
Again, do NOT use pacman's --force flag to install the filesystem update.

Hi!

I did

pacman -Syu --ignore filesystem

followed by

pacman -Syu

resulting in

error: failed to commit transaction (conflicting files)
filesystem: /bin exists in filesystem
filesystem: /sbin exists in filesystem
filesystem: /usr/sbin exists in filesystem
Errors occurred, no packages were upgraded.

 grep '^s\?bin/\|usr/sbin' /var/lib/pacman/local/*/files | cut -d ":" -f 1 | uniq | cut -d "/" -f 6

gives

filesystem-2013.03-2
gen-init-cpio-2.6.36-1
grub-0.97-21
tcp_wrappers-7.6-12
tgt-1.0.26-2

and

 find /bin /sbin /usr/sbin -exec pacman -Qo -- {} + >/dev/null

gave

error: No package owns /sbin/lsmod

Can someone suggest what to do next?

msthev · 2013-06-09 09:24:36

And why didn't you follow the instructions on the front page? The first command (with `pacman -Qm -`) would have given you the list of packages that need fixing.
Hint: remove those four unsupported packages (all from your list except filesystem), backup and remove /sbin/lsmod, then update. Don't forget to reinstall your bootloader (read about Syslinux if you want something simple).

Last edited by msthev (2013-06-09 09:27:25)

mfaridi · 2013-06-09 09:28:29

Can I use archbang for liveCD for fix this problem ? or use this iso file
http://mirror.aarnet.edu.au/pub/archlin … 1-dual.iso
if I download this ISO file ,can I fix my problem ?

jasonwryan · 2013-06-09 09:36:12

You were warned...

Arch Linux

#401 2013-06-08 22:50:37

Re: filesystem Update Error /bin exists in filesystem

#402 2013-06-08 22:54:04

Re: filesystem Update Error /bin exists in filesystem

#403 2013-06-08 22:55:46

Re: filesystem Update Error /bin exists in filesystem

#404 2013-06-08 23:13:13

Re: filesystem Update Error /bin exists in filesystem

#405 2013-06-08 23:15:48

Re: filesystem Update Error /bin exists in filesystem

#406 2013-06-09 00:17:59

Re: filesystem Update Error /bin exists in filesystem

#407 2013-06-09 00:19:05

Re: filesystem Update Error /bin exists in filesystem

#408 2013-06-09 00:45:49

Re: filesystem Update Error /bin exists in filesystem

#409 2013-06-09 00:49:48

Re: filesystem Update Error /bin exists in filesystem

#410 2013-06-09 00:53:22

Re: filesystem Update Error /bin exists in filesystem

#411 2013-06-09 00:55:21

Re: filesystem Update Error /bin exists in filesystem

#412 2013-06-09 01:02:27

Re: filesystem Update Error /bin exists in filesystem

#413 2013-06-09 01:11:39

Re: filesystem Update Error /bin exists in filesystem

#414 2013-06-09 01:21:00

Re: filesystem Update Error /bin exists in filesystem

#415 2013-06-09 02:18:09

Re: filesystem Update Error /bin exists in filesystem

#416 2013-06-09 02:19:53

Re: filesystem Update Error /bin exists in filesystem

#417 2013-06-09 03:08:45

Re: filesystem Update Error /bin exists in filesystem

#418 2013-06-09 04:23:57

Re: filesystem Update Error /bin exists in filesystem

#419 2013-06-09 05:28:40

Re: filesystem Update Error /bin exists in filesystem

#420 2013-06-09 05:29:21

Re: filesystem Update Error /bin exists in filesystem

#421 2013-06-09 05:37:00

Re: filesystem Update Error /bin exists in filesystem

#422 2013-06-09 07:47:44

Re: filesystem Update Error /bin exists in filesystem

#423 2013-06-09 09:24:36

Re: filesystem Update Error /bin exists in filesystem

#424 2013-06-09 09:28:29

Re: filesystem Update Error /bin exists in filesystem

#425 2013-06-09 09:36:12

Re: filesystem Update Error /bin exists in filesystem

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