filesystem Update Error /bin exists in filesystem

cfr · 2013-06-13 18:47:57

@zero-giulio,
In addition to using code tags and English, where did you get those commands from? They are not the commands on the front page i.e. in the news i.e. the official instructions for updating.

toni · 2013-06-13 18:48:13

HI all,
I am just upgrading my system, and I am going to do step 5 commented in the arch home page which says:

# pacman -Syu --ignore filesystem,bash
# pacman -S bash
# pacman -Su

So I guess if I have to do these steps or only is necessary to perform the typical one:

# pacman -Syu

cfr · 2013-06-13 18:50:46

@toni,
You need to follow *all* the steps in order. When you get to step 5, you need to use those 3 commands in that order. pacman -Syu will fail with errors. Those commands will update your system successfully (if you've completed steps 1-4).

toni · 2013-06-13 19:04:50

cfr wrote:

@toni,
You need to follow *all* the steps in order. When you get to step 5, you need to use those 3 commands in that order. pacman -Syu will fail with errors. Those commands will update your system successfully (if you've completed steps 1-4).

I only have a problem with step 3, all other steps are checked and correct, only pending last step but before I have a problem in step 3:

find /bin /sbin /usr/sbin -exec pacman -Qo -- {} + >/dev/null
error: Ningún paquete posee /sbin/fsck.btrfs

I have seen this link:

https://btrfs.wiki.kernel.org/index.php … fsck.btrfs

which says:
"Traditional filesystems need to run their respective fsck utility in case the filesystem was not unmounted cleanly and the log needs to be replayed before mount. "

I think I am using it, see my /etc/fstab:

# 
# /etc/fstab: static file system information
#
# <file system>	<dir>	<type>	<options>	<dump>	<pass>
tmpfs		/tmp	tmpfs	nodev,nosuid	0	0
/dev/sdb10 /home ext4 defaults 0 1
/dev/sdb11 swap swap defaults 0 0
/dev/sdb5 /boot ext4 defaults 0 1
#/dev/sdb6 /tmp ext4 defaults 0 1
/dev/sdb7 /var ext4 defaults 0 1
/dev/sdb8 / btrfs defaults 0 0
/dev/sdb9 /usr ext4 defaults 0 0

so I do not know what to do with /sbin/fsck.btrfs since it is said in step 3 it is necessary to move to /usr/bin. What do I have to do with it?

Thanks!

Scimmia · 2013-06-13 19:05:16

zero-giulio, so with a big long list of errors, you decided to continue with the update anyway? It didn't occur to you that you need to fix the errors?

Check post #265 for the fix procedure.

Scimmia · 2013-06-13 19:07:54

toni wrote:

I have seen this link:
https://btrfs.wiki.kernel.org/index.php … fsck.btrfs
...
so I do not know what to do with /sbin/fsck.btrfs since it is said in step 3 it is necessary to move to /usr/bin. What do I have to do with it?
Thanks!

If you followed the advice in that link and just copied /bin/true, just delete the file, it's unnecessary.

toni · 2013-06-13 19:26:22

Scimmia wrote:

toni wrote:
I have seen this link:
https://btrfs.wiki.kernel.org/index.php … fsck.btrfs
...
so I do not know what to do with /sbin/fsck.btrfs since it is said in step 3 it is necessary to move to /usr/bin. What do I have to do with it?
Thanks!
If you followed the advice in that link and just copied /bin/true, just delete the file, it's unnecessary.

Hi, I did what you say and I did step 5 but I have seen some things in the terminal that I think something was wrong when performing below command:

pacman -Syu --ignore filesystem,bash

>>> Updating module dependencies. Please wait ...
>>> Generating initial ramdisk, using mkinitcpio.  Please wait...
==> Building image from preset: /etc/mkinitcpio.d/linux.preset: 'default'
  -> -k /boot/vmlinuz-linux -c /etc/mkinitcpio.conf -g /boot/initramfs-linux.img
==> Starting build: 3.9.5-1-ARCH
  -> Running build hook: [base]
  -> Running build hook: [udev]
  -> Running build hook: [usr]
  -> Running build hook: [block]
==> WARNING: Possibly missing firmware for module: aic94xx
==> WARNING: Possibly missing firmware for module: bfa
  -> Running build hook: [fsck]
  -> Running build hook: [resume]
  -> Running build hook: [lvm2]
==> ERROR: file not found: `/usr/sbin/dmsetup'
  -> Running build hook: [filesystems]
  -> Running build hook: [shutdown]
  -> Running build hook: [keyboard]
==> Generating module dependencies
==> Creating gzip initcpio image: /boot/initramfs-linux.img
==> WARNING: errors were encountered during the build. The image may not be complete.
==> Building image from preset: /etc/mkinitcpio.d/linux.preset: 'fallback'
  -> -k /boot/vmlinuz-linux -c /etc/mkinitcpio.conf -g /boot/initramfs-linux-fallback.img -S autodetect
==> Starting build: 3.9.5-1-ARCH
  -> Running build hook: [base]
  -> Running build hook: [udev]
  -> Running build hook: [usr]
  -> Running build hook: [block]
==> WARNING: Possibly missing firmware for module: aic94xx
==> WARNING: Possibly missing firmware for module: bfa
  -> Running build hook: [fsck]
  -> Running build hook: [resume]
  -> Running build hook: [lvm2]
==> ERROR: file not found: `/usr/sbin/dmsetup'
  -> Running build hook: [filesystems]
  -> Running build hook: [shutdown]
  -> Running build hook: [keyboard]
==> Generating module dependencies
==> Creating gzip initcpio image: /boot/initramfs-linux-fallback.img
==> WARNING: errors were encountered during the build. The image may not be complete.
error: el comando falló al ejecutarse

the other two commands:

# pacman -S bash
# pacman -Su

were carried out correctly:

so before restarting... to avoid problems... I would like to know what I have to do to solve the issues, could you help me?

thanks!

EDIT:
I have found this:
https://bugs.archlinux.org/task/33828

and I have done this after executing the three commands on step 5:

sudo mkinitcpio -p linux

so the output is:

$ sudo mkinitcpio -p linux
==> Building image from preset: /etc/mkinitcpio.d/linux.preset: 'default'
  -> -k /boot/vmlinuz-linux -c /etc/mkinitcpio.conf -g /boot/initramfs-linux.img
==> Starting build: 3.9.5-1-ARCH
  -> Running build hook: [base]
  -> Running build hook: [udev]
  -> Running build hook: [usr]
  -> Running build hook: [block]
==> WARNING: Possibly missing firmware for module: aic94xx
==> WARNING: Possibly missing firmware for module: bfa
  -> Running build hook: [fsck]
  -> Running build hook: [resume]
  -> Running build hook: [lvm2]
  -> Running build hook: [filesystems]
  -> Running build hook: [shutdown]
  -> Running build hook: [keyboard]
==> Generating module dependencies
==> Creating gzip initcpio image: /boot/initramfs-linux.img
==> Image generation successful
==> Building image from preset: /etc/mkinitcpio.d/linux.preset: 'fallback'
  -> -k /boot/vmlinuz-linux -c /etc/mkinitcpio.conf -g /boot/initramfs-linux-fallback.img -S autodetect
==> Starting build: 3.9.5-1-ARCH
  -> Running build hook: [base]
  -> Running build hook: [udev]
  -> Running build hook: [usr]
  -> Running build hook: [block]
==> WARNING: Possibly missing firmware for module: aic94xx
==> WARNING: Possibly missing firmware for module: bfa
  -> Running build hook: [fsck]
  -> Running build hook: [resume]
  -> Running build hook: [lvm2]
  -> Running build hook: [filesystems]
  -> Running build hook: [shutdown]
  -> Running build hook: [keyboard]
==> Generating module dependencies
==> Creating gzip initcpio image: /boot/initramfs-linux-fallback.img
==> Image generation successful

is it correct what I have done?

Last edited by toni (2013-06-13 19:32:26)

Scimmia · 2013-06-13 19:30:33

The firmware errors are only a problem if you're using those firmwares. It's normal to have the errors with the current version of mkinitcpio if you're not using them.

The dmsetup error is more troubling. That's part of device-mapper, which is in base and needed by a number of packages. Try reinstalling device-mapper and regenerating your initramfs.

toni · 2013-06-13 19:39:51

Scimmia wrote:

The firmware errors are only a problem if you're using those firmwares. It's normal to have the errors with the current version of mkinitcpio if you're not using them.
The dmsetup error is more troubling. That's part of device-mapper, which is in base and needed by a number of packages. Try reinstalling device-mapper and regenerating your initramfs.

I have regenerated initramfs and all go ok, but I forgot to say that I get another warning in first command in step 5:

warning: directory permissions differ on /var/log/gdm/
filesystem: 711  package: 1770

Is this good? or bad? Do I have to do something? What does it mean?

Last edited by toni (2013-06-13 19:40:27)

Scimmia · 2013-06-13 19:50:01

Thing to worry too much about. Personally, I wouldn't want anything in /var/log to be world executable, so I'd probably change it, but no big deal. If you want to be able to access GDM logs as a normal user, just leave it.

Last edited by Scimmia (2013-06-13 19:59:36)

johnpuppa · 2013-06-13 19:50:54

Hello guys, I'm in trouble. I have upgraded the system this evening and now I can't access to it. when I try to start it I get a message which says to try to pass init to the kernel. and the system goes in kernel panic right after.. I can't post the message...
I tried to follow the passages written here while upgrading.. https://www.archlinux.org/news/binaries … ervention/

I have another partition from which I can mount that one with arch. But to this point I'm stuck..
It seems that there are no file in /sbin..
Please if you have any Idea, let me know..

toni · 2013-06-13 20:01:31

Scimmia wrote:

Thing to worry too much about. Personally, I wouldn't want anything in /var/log to be world executable, so I'd probably change it, but no big deal.

Finally I have updated correctly the system. Also, I have restarted arch without problems.

But I am curious to know one thing: Why after updating it continues existing the folders /sbin /usr/sbin /bin? I thought that once system updated those folders will be deleted automatically or something as they are not needed anymore as new folder will be /usr/bin from now on, why they are still maintained?

Scimmia · 2013-06-13 20:01:44

is /sbin a dir or a symlink?

Scimmia · 2013-06-13 20:03:14

There are no directories (yes, directories, not folders) for /bin /sbin and /usr/sbin, they are now just symlinks.

johnpuppa · 2013-06-13 20:12:38

It's a directory I don't understand what happened..

cfr · 2013-06-13 20:15:34

@toni,
Note that your fstab is incorrect. At the end of the lines, where you have "0 1", you should have "0 2" i.e. for /home /boot and /var. Normally, you'd use "0 1" for / but since you are using btrfs, "0 0" is correct.

Why do you have "0 0" for /usr rather than "0 2". This means that that partition will never be checked for errors even though it is ext4 and a suitable tool exists.

Perhaps more importantly, I wonder if you are aware that having /usr on a separate partition is not recommended or supported. Not that you necessarily should change this if it is working for you but something to be aware of.

Scimmia · 2013-06-13 20:15:47

If it's still a dir, the filesystem package wasn't updated. There's a huge thread in the Pacman Updates forum about this. Post #265 will tell you how to fix it. You can do it from your other partition by chrooting in (follow the steps in the wiki regarding mounting of extra filesystems) and running the pacman command without --root /mnt and removing /mnt from any other paths.

johnpuppa · 2013-06-13 20:32:56

well thanks, But also chroot doesn't work.. I tried it and I keep receiving /bin/bash: No such file or directory. No I'm trying to make a bootable pendrive to see if it works from there..

Scimmia · 2013-06-13 21:11:05

Which is why the wiki specifies the shell as /usr/bin/bash in the chroot command.

Gnux · 2013-06-13 21:19:03

dwal42 wrote:

UPDATE:
I personally fixed this by running '# rm -rf /bin; rm -rf /usr/sbin' then '# pacman -Su'. Seems to be working now but YMMV.

That intuitive fix works for me. Many many thx for it!!! So simple...That tip should be appended to the announcement..,

jasonwryan · 2013-06-13 21:19:09

Merging with the sticky with ALL the answers...

WorMzy · 2013-06-13 21:44:21

Gnux wrote:

dwal42 wrote:
UPDATE:
I personally fixed this by running '# rm -rf /bin; rm -rf /usr/sbin' then '# pacman -Su'. Seems to be working now but YMMV.
That intuitive fix works for me. Many many thx for it!!! So simple...That tip should be appended to the announcement..,

No, it really shouldn't. Congratulations, you've probably now broken several of your unsupported packages.

Scimmia · 2013-06-13 23:00:15

Gnux wrote:

dwal42 wrote:
UPDATE:
I personally fixed this by running '# rm -rf /bin; rm -rf /usr/sbin' then '# pacman -Su'. Seems to be working now but YMMV.
That intuitive fix works for me. Many many thx for it!!! So simple...That tip should be appended to the announcement..,

Yes, please don't do this, it's a horrible idea.

papajonpizza · 2013-06-14 01:55:33

[Arch Linux is awesome. My daily driver was Linux Mint for 2 years.]

For me, combuster's post #13 was the eye-opener that prepared me for the upgrade. Thank you. It basically told me not to reboot until pacman -Su has ran "clean". I even ran pacman -Syu a couple of times after that to make sure.

I did have issues after reboot that said / was not mounted couldn't find UUID..., but I figured it would be an easy fix with my Arch bootable USB. Simple check of the fstab, maybe a run of #grub-install --recheck /dev/sda or #grub-mkconfig -o /boot/grub/grub.cfg (neither fixed it)

# mkinitcpio -p linux

Above fixed the problem of ".... couldn't find UUID..." and a google search pointed to the Arch Linux forums for the solution.

Just a general comment.. I'm very thankful for this wonderful Linux distro and I don't understand why anyone "complains/whines/etc" or even think they have the right to.

I'm very attached to my ultrabook. I bring it everywhere as part of my work is being on-call (Network Engineer). Yet, I still went with the upgrade late last night. It's simple, really. If I had to re-install from scratch, it's not a problem as I have my data backed up. Oh, no time right now? boot a USB live CD of Linux Mint (or any distro) until you have the time to re-install. No need to stress

combuster wrote:

Do NOT, I repeat DO NOT exit the terminal with root priviliges untill you do a
pacman -Su
after
pacman -Syu --ignore filesystem
I had to chroot from flash and pacstrap the filesystem package from testing to boot at all. Even in the same session I couldn't get a terminal with root privileges. My mistake...

zero-giulio · 2013-06-14 07:32:55

I apologize for the language.
It was the first time I copy/paste commands on board and I did care of language (next time I'll pay attention, I promise).

cfr wrote:

@zero-giulio,
In addition to using code tags and English, where did you get those commands from? They are not the commands on the front page i.e. in the news i.e. the official instructions for updating.

Why are you saying that?
Commands are the ones in the homepage:

pacman -Qqo /usr/sbin | pacman -Qm -
find /bin /sbin /usr/sbin -exec pacman -Qo -- {} + >/dev/null
sudo pacman -Su --ignore filesystem,bash
sudo pacman -S bash
sudo pacman -Su

[I miss the command with paclist <repo> because I do not have non-official repo in pacman.conf]

Scimmia wrote:

zero-giulio, so with a big long list of errors, you decided to continue with the update anyway? It didn't occur to you that you need to fix the errors?
Check post #265 for the fix procedure.

Which errors?
The first command reportes nothing.
The second command tell me no packages contains /bin, /sbin etc...
The third and the fourth command reported no errors.

What's wrong?

Arch Linux

#551 2013-06-13 18:47:57

Re: filesystem Update Error /bin exists in filesystem

#552 2013-06-13 18:48:13

Re: filesystem Update Error /bin exists in filesystem

#553 2013-06-13 18:50:46

Re: filesystem Update Error /bin exists in filesystem

#554 2013-06-13 19:04:50

Re: filesystem Update Error /bin exists in filesystem

#555 2013-06-13 19:05:16

Re: filesystem Update Error /bin exists in filesystem

#556 2013-06-13 19:07:54

Re: filesystem Update Error /bin exists in filesystem

#557 2013-06-13 19:26:22

Re: filesystem Update Error /bin exists in filesystem

#558 2013-06-13 19:30:33

Re: filesystem Update Error /bin exists in filesystem

#559 2013-06-13 19:39:51

Re: filesystem Update Error /bin exists in filesystem

#560 2013-06-13 19:50:01

Re: filesystem Update Error /bin exists in filesystem

#561 2013-06-13 19:50:54

Re: filesystem Update Error /bin exists in filesystem

#562 2013-06-13 20:01:31

Re: filesystem Update Error /bin exists in filesystem

#563 2013-06-13 20:01:44

Re: filesystem Update Error /bin exists in filesystem

#564 2013-06-13 20:03:14

Re: filesystem Update Error /bin exists in filesystem

#565 2013-06-13 20:12:38

Re: filesystem Update Error /bin exists in filesystem

#566 2013-06-13 20:15:34

Re: filesystem Update Error /bin exists in filesystem

#567 2013-06-13 20:15:47

Re: filesystem Update Error /bin exists in filesystem

#568 2013-06-13 20:32:56

Re: filesystem Update Error /bin exists in filesystem

#569 2013-06-13 21:11:05

Re: filesystem Update Error /bin exists in filesystem

#570 2013-06-13 21:19:03

Re: filesystem Update Error /bin exists in filesystem

#571 2013-06-13 21:19:09

Re: filesystem Update Error /bin exists in filesystem

#572 2013-06-13 21:44:21

Re: filesystem Update Error /bin exists in filesystem

#573 2013-06-13 23:00:15

Re: filesystem Update Error /bin exists in filesystem

#574 2013-06-14 01:55:33

Re: filesystem Update Error /bin exists in filesystem

#575 2013-06-14 07:32:55

Re: filesystem Update Error /bin exists in filesystem

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