filesystem Update Error /bin exists in filesystem

fsckd · 2013-06-06 14:04:24

I split your thread from the big sticky because I think it involves a little more than just the merge. If I'm wrong, we can move it back.

Boot into a live environment and give us the output of,

lsblk -o NAME,TYPE,UUID,FSTYPE

Edit: undo split, see here.

Sulman · 2013-06-06 14:54:56

Scimmia wrote:

FIX GUIDE: For those that screwed up the filesystem update can't boot anymore
(since I don't like coellobranco's, I figured I should post my own)
1) Boot an Arch Install Disk. Set up your network if you need to (see Beginner's Guide).
2) Mount all of the partitions you use to /mnt. This includes not only the root partition, but /usr, /var, etc (to /mnt/usr, /mnt/var/, etc).
3) Run "pacman --root /mnt -Qo /mnt/bin /mnt/sbin /mnt/usr/sbin". Ideally, it should tell you that /mnt/bin and /mnt/sbin don't exist and that /mnt/usr/sbin is owned by "filesytem". If you get any other packages listed, they need to be fixed or uninstalled! If they're packages from the official repos, upgrade them with "pacman --root /mnt -S <pkgname>. If they're packages you don't need, you can uninstall them with "pacman --root /mnt -Rs <pkgname>". Remember, if they're not critical for your system, you can always reinstall them later once you get back up and going.
4) Run "find /mnt/bin /mnt/sbin /mnt/usr/sbin -exec pacman --root /mnt -Qo -- {} + >/dev/null" This will tell you of any untracked files in the relevant directories. Any files it finds need to be deleted or moved. I suggest putting any scripts you made in /usr/local/bin so they don't get in the way. If you removed any files from /mnt/bin or /mnt/sbin, check these dirs afterwards to see if they're empty. If they are, delete them.
5) Run "ls -l /mnt /mnt/usr/sbin". At this point /mnt/bin and /mnt/sbin shouldn't exist and /mnt/usr/sbin should be empty. If that's not the case, stop. Come back here and ask for help.
6) Run "pacman --root /mnt -Su". This should install the filesystem package without any errors. Once that is done, your system should be functional again.

Thank you. I'd followed the front page instructions this morning, but I still got caught out; plus I had EFI drama to sort out too. This really helped.

southerncross · 2013-06-06 15:39:07

southerncross wrote:

Scimmia wrote:
grub - if you want to keep it, install grub-legacy from the AUR, it's already fixed. Alternative - install a supported bootloader like syslinux or grub2
gen-init-cpio - hasn't been used in years, remove it
cpufreqd - the AUR package has been updated, update yours.
dcron - you'll have to fix it yourself. There's instructions in the AUR comments
initscripts - are you using it? If you're booting with systemd, just remove it. If you're not, upgrade to systemd. If you don't want to do that, you're on your own.
tcp_wrappers - removed from the repos long ago, you're probably not using it. Unless pacman complains, just remove it. If pacman does complain (ie you still use it), it's been fixed in the AUR, update.

Thanks a lot Scimmia. I see I have some work to do and I'll come back here in case of issues.
TC!

So... the upgrade went fine. However I am now left with a very weird wifi card problem and for some reason I can only boot on KDE, not on Gnome (it stays hanging). Time for another thread. Thanks!

otters · 2013-06-06 17:04:39

I got a similar problem, when I rebooting it says can't mount /dev/sda3.
I mounted the root dir of archlinux on /dev/sda3.
the output of lsblk is followed:
NAME TYPE UUID FSTYPE
sda disk
sda1 part 0009B46A0005EE25 ntfs
sda2 part
sda3 part 00d26322-f7ac-4ecb-bdc5-29a5187aecc7 ext4
sda4 part c1e2e862-69d5-4614-8eb8-8b74d43118c3 ext4
sda5 part 000CB5D300064E7D ntfs
sda6 part 0001D777000A46C3 ntfs
sdb disk 2013-05-31-23-04-19-00 iso9660
sdb1 part 2013-05-31-23-04-19-00 iso9660
sr0 rom
loop0 loop squashfs
loop1 loop f5fa8d02-203c-4081-945b-0998427d363c ext4
arch_root-image dm f5fa8d02-203c-4081-945b-0998427d363c ext4
loop2 loop f5fa8d02-203c-4081-945b-0998427d363c ext4
arch_root-image dm f5fa8d02-203c-4081-945b-0998427d363c ext4

Scimmia · 2013-06-06 17:19:36

Francuss wrote:

but when i reboot I'm getting:
ERROR: device 'UUID=7cf13....' not found, Skippink fsck
ERROR: Unable to find root device 'UUID=7cf13....'.
you are being dropped to a recovery shell
type 'exit' to try and continue booting
sh: can't access tty:job control turned off

otters wrote:

I got a similar problem, when I rebooting it says can't mount /dev/sda3.
I mounted the root dir of archlinux on /dev/sda3
....

Sounds like you guys need to regenerate your initramfs. If you didn't follow the instructions to ignore bash, mkinitcpio wouldn't be able to generate a valid initramfs if a kernel upgrade was done. You now have an initramfs with old kernel modules, so you can't access your root fs.

Francuss, the procedure to follow for this upgrade is on the front page. My link in post 3 was a draft version that was modified later to take care of this problem

fsckd, pretty sure we are dealing with an issue specific to this upgrade, might as well merge back.

Last edited by Scimmia (2013-06-06 17:30:56)

Francuss · 2013-06-06 17:26:36

Thanks for the prompt reply
I did lsblk, but it shows a lot of full lines.

Is there a way to copy this output to the other computer I am using now to post on this forum or should I copy it manually letter by letter?

Scimmia I followed just the instructions by Allan, referred to on the post 3 on the first page of the original thread.

Last edited by Francuss (2013-06-06 17:29:38)

Scimmia · 2013-06-06 17:32:44

Francuss wrote:

Scimmia I followed just the instructions by Allan, referred to on the post 3 on the first page of the original thread.

Francuss, yeah, I modified my post to provide more info while you were modifying yours. The instructions you used were a draft that was found to have issues and was modified before the final release.

I would suggest subscribing to the arch-announce mailing list so you always get official notice of important updates.

Last edited by Scimmia (2013-06-06 18:05:28)

otters · 2013-06-06 18:31:24

Scimmia, thank you very much, my arch works again.
I boot in a live environment, and chroot to my arch, then
# mkinitcpio -p linux
the initramfs regenerated.
After reboot, I login to my arch again.

otters · 2013-06-06 18:35:56

Francuss, I think if you can run lsblk on this computer, then the network might work too.
Just redirect the output of lsblk to a file, and you can get the file out by network.
It may be a bit faster than letter by letter copy....

parcival · 2013-06-06 18:46:03

Hi everyone,

I'd appreciate if someone holds my hand for a little while performing this upgrade.

Sticking to the instructions in the latest news I get this output:

[root@CADUCEUS pkg]# pacman -Qqo /bin /sbin /usr/sbin | pacman -Qm -
[root@CADUCEUS pkg]# paclist <repo> | awk ' { print $1 } ' | pacman -Ql - | grep ' /s\?bin/\| /usr/sbin/'
bash: syntax error near unexpected token `|'
[root@CADUCEUS pkg]# find /bin /sbin /usr/sbin -exec pacman -Qo -- {} + >/dev/null
[root@CADUCEUS pkg]#

In other words, step 1 and 3 seem to be totally fine, but I have no clue what to do with the unexpected token as googling that didn't seem to provide a meaningful result. Can anybody tell me what to do before I advance to

pacman -Syu --ignore filesystem,bash

(I didn't mess with IgnorePkg or IgnoreGroup)

Slurp · 2013-06-06 18:48:42

i think you have to replace <repo> with the name of the unofficial repo you are using.

Scimmia · 2013-06-06 18:48:55

parcival, <repo> needs to be replaced with the name of the unofficial repo you're trying to check.

parcival · 2013-06-06 18:54:56

Ah, ok, thanks. In that case I don't need this command as I just have core, extra, and community activated in my /etc/pacman.conf

Guess I'll take the plunge then.

Update: My upgrade went smoothly, but I'd really like just to thank everyone who helps here; the people who write in the wiki (that's where google originally lead me to), the people who take care of the news, and people who help here in the forum.

Last edited by parcival (2013-06-06 19:09:30)

Francuss · 2013-06-06 19:06:14

Scimmia wrote:

Sounds like you guys need to regenerate your initramfs. If you didn't follow the instructions to ignore bash, mkinitcpio wouldn't be able to generate a valid initramfs if a kernel upgrade was done. You now have an initramfs with old kernel modules, so you can't access your root fs.
Francuss, the procedure to follow for this upgrade is on the front page. My link in post 3 was a draft version that was modified later to take care of this problem

Sorry Scimmia but do you have a link for the front page, I looked again at the first page of the thread but it seems you are referring to some other page.
thanks

Scimmia · 2013-06-06 19:08:02

www.archlinux.org

fsckd · 2013-06-06 20:13:31

Thanks Scimmia, merging back to keep everything together (and because the other thread keeps getting referenced).

Francuss · 2013-06-06 23:58:13

Scimmia wrote:

Sounds like you guys need to regenerate your initramfs. If you didn't follow the instructions to ignore bash, mkinitcpio wouldn't be able to generate a valid initramfs if a kernel upgrade was done. You now have an initramfs with old kernel modules, so you can't access your root fs.
Francuss, the procedure to follow for this upgrade is on the front page. My link in post 3 was a draft version that was modified later to take care of this problem

I tried to chroot and do the step that I missed following the old method:
pacman -S bash

it did it without errors, but the same, after rebooting got the same error

So chroot again following:

otters wrote:

I boot in a live environment, and chroot to my arch, then
# mkinitcpio -p linux
the initramfs regenerated.

and was able to login again to my system, so many thanks
there is no more network connection now. Perhaps this mkinitramfs thing resetted something

Scimmia · 2013-06-06 23:59:57

the initramfs has nothing to do with networking AFAIK.

rzrscm · 2013-06-07 00:22:17

Cool.

Last edited by rzrscm (2013-06-07 00:28:29)

Trilby · 2013-06-07 00:25:07

Yes. Read the front page news or read nearly any recent forum thread.

Please put some degree of effort in finding an answer before you start a new thread.

EDIT: Or read the thread this was rightfully merged into.

Last edited by Trilby (2013-06-07 00:27:05)

jasonwryan · 2013-06-07 00:26:04

Merging with the mega stickied thread...

dvh · 2013-06-07 02:09:13

thanks, Scimmia. I am already using systemd, so i don't know why i still had initscripts and/or sysvinit. and I hate to mess with grub, so i did not update that. I guess I will need to do so.

as for my earlier rant, maybe I was a little harsh. so I apologize for my tone. still don't think that "fix it" is a complete solution, but I will back off. i am a user, not a developer, so i do not have any idea how to fix packages so that they install in a different location. either way, i got past this in a brute force way. i do appreciate the effort that developers put in.

-dvh

kgas · 2013-06-07 11:07:19

-- the merger went well for two laptops (coincidentally both are x86_64) and for two i686 I had the issues. In one i686 I need to rename the /usr/sbin to do filesystem update and in another I need to purge some packages (hpio/tcp-wrapper/grub) tho' point 1/3 mentioned in the home page did not complain any issues.(I used the method what Scimmia put here) -- for records.

I

nesk · 2013-06-07 13:51:07

Hi,
ARM Archlinux here, on a system with 1Gb RAM.
Can't get a command from front page to run successfully:

pacman -Qqo /bin /sbin /usr/sbin | pacman -Qm -
error: memory exhausted in argument parsing

Any advice?

Trilby · 2013-06-07 13:54:59

Yes ask on the forum for your distro: http://archlinuxarm.org/forum/

Arch Linux

#326 2013-06-06 14:04:24

Re: filesystem Update Error /bin exists in filesystem

#327 2013-06-06 14:54:56

Re: filesystem Update Error /bin exists in filesystem

#328 2013-06-06 15:39:07

Re: filesystem Update Error /bin exists in filesystem

#329 2013-06-06 17:04:39

Re: filesystem Update Error /bin exists in filesystem

#330 2013-06-06 17:19:36

Re: filesystem Update Error /bin exists in filesystem

#331 2013-06-06 17:26:36

Re: filesystem Update Error /bin exists in filesystem

#332 2013-06-06 17:32:44

Re: filesystem Update Error /bin exists in filesystem

#333 2013-06-06 18:31:24

Re: filesystem Update Error /bin exists in filesystem

#334 2013-06-06 18:35:56

Re: filesystem Update Error /bin exists in filesystem

#335 2013-06-06 18:46:03

Re: filesystem Update Error /bin exists in filesystem

#336 2013-06-06 18:48:42

Re: filesystem Update Error /bin exists in filesystem

#337 2013-06-06 18:48:55

Re: filesystem Update Error /bin exists in filesystem

#338 2013-06-06 18:54:56

Re: filesystem Update Error /bin exists in filesystem

#339 2013-06-06 19:06:14

Re: filesystem Update Error /bin exists in filesystem

#340 2013-06-06 19:08:02

Re: filesystem Update Error /bin exists in filesystem

#341 2013-06-06 20:13:31

Re: filesystem Update Error /bin exists in filesystem

#342 2013-06-06 23:58:13

Re: filesystem Update Error /bin exists in filesystem

#343 2013-06-06 23:59:57

Re: filesystem Update Error /bin exists in filesystem

#344 2013-06-07 00:22:17

Re: filesystem Update Error /bin exists in filesystem

#345 2013-06-07 00:25:07

Re: filesystem Update Error /bin exists in filesystem

#346 2013-06-07 00:26:04

Re: filesystem Update Error /bin exists in filesystem

#347 2013-06-07 02:09:13

Re: filesystem Update Error /bin exists in filesystem

#348 2013-06-07 11:07:19

Re: filesystem Update Error /bin exists in filesystem

#349 2013-06-07 13:51:07

Re: filesystem Update Error /bin exists in filesystem

#350 2013-06-07 13:54:59

Re: filesystem Update Error /bin exists in filesystem

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