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#76 2013-06-03 14:49:47

Mr Green
Forum Fellow
From: U.K.
Registered: 2003-12-21
Posts: 5,804

Re: filesystem Update Error /bin exists in filesystem

It might be worth splitting thread as we are in testing forum...users are going to get confused..


Mr Green

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#77 2013-06-03 14:50:19

indianahorst
Member
Registered: 2008-08-23
Posts: 111

Re: filesystem Update Error /bin exists in filesystem

karol wrote:
indianahorst wrote:

When I came to # pacman -Su, I still got the "exists in filesystem" error. I hadn't the time to fix it at the moment, so I shutdown my system.

Why did you start updating at all then??

Use a liveCD / live USB, chroot, fix the 'exist in the filesystem' errors and open a separate thread if you need further help.

I'm trying it... bootet Parted Magic from USB, chrooted, but

# chroot /mnt/root/ /bin/bash
chroot: can't execute  '/usr/bin/bash': No such file or directory

# chroot /mnt/root/ /usr/bin/bash
chroot: can't execute  '/usr/bin/bash': No such file or directory

Any hints?

/bin, /sbin, and /usr/sbin are all symbolic links to /usr/bin... and in /usr/bin is just a very small subset of core programs!

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#78 2013-06-03 15:09:23

indianahorst
Member
Registered: 2008-08-23
Posts: 111

Re: filesystem Update Error /bin exists in filesystem

Hello,

First of all: I dont use testing or unofficial repos, just the official ones.

A few hours ago, I updated my system following the instructions on
https://www.archlinux.org/news/binaries … ervention/

Step 1-4 were flawlessly, but:

following Step 5, I did

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

When I came to

# pacman -Su

, I still got the "exists in filesystem" error. I hadn't the time to fix it at this moment, so I shutdown my system.

Now I startet it again and just get the error

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

[rootfs /]#

/bin, /sbin, and /usr/sbin are all symbolic links to /usr/bin/
I already booted Parted Magic from Live USB and tried to chroot, but that failed because of the missing bash executable in /usr/bin/.

Is there still a way to fix it?

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#79 2013-06-03 15:11:47

Scimmia
Bug Wrangler
Registered: 2012-09-01
Posts: 7,198

Re: filesystem Update Error /bin exists in filesystem

indianahorst wrote:

When I came to

# pacman -Su

, I still got the "exists in filesystem" error. I hadn't the time to fix it at this moment, so I shutdown my system.

I think we need a facepalm emoticon.

Anyway, do the /bin, /sbin, and /usr/sbin dirs exist? If so, what's in them?

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#80 2013-06-03 15:14:43

s3kt0r
Member
Registered: 2009-01-20
Posts: 208

Re: filesystem Update Error /bin exists in filesystem

Allan is the man, it broke my system big_smile already up and running after a simple changeroot

sudo f'ed it up for me.


box1: Arch (linux-3.17-rc5)
box2: Gentoo (linux-3.17-rc5)
wm: subtle

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#81 2013-06-03 15:20:56

indianahorst
Member
Registered: 2008-08-23
Posts: 111

Re: filesystem Update Error /bin exists in filesystem

Scimmia wrote:
indianahorst wrote:

When I came to

# pacman -Su

, I still got the "exists in filesystem" error. I hadn't the time to fix it at this moment, so I shutdown my system.

I think we need a facepalm emoticon.

It wasn't clear to me, that after the execution of

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

would be in an unbootable stage! There is nowhere a hint in this direction!

Scimmia wrote:

Anyway, do the /bin, /sbin, and /usr/sbin dirs exist? If so, what's in them?

The /bin, /sbin, and /usr/sbin dirs exist, but they are just symlinks to /usr/bin/.

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#82 2013-06-03 15:22:06

karol
Archivist
Registered: 2009-05-06
Posts: 25,440

Re: filesystem Update Error /bin exists in filesystem

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.
FYI this is also happening on NON-testing repos.

The update has passed [testing] and is now available in th non-testing repos.
https://bbs.archlinux.org/viewtopic.php … 4#p1281714

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#83 2013-06-03 15:25:43

Scimmia
Bug Wrangler
Registered: 2012-09-01
Posts: 7,198

Re: filesystem Update Error /bin exists in filesystem

So everything is symlinked correctly, but /usr/bin/bash doesn't exist? Or /usr/bin/init? Sounds like the first pacman update didn't work. You'll need an arch boot disk so you can use pacman with the -r option to reinstall things. Start with systemd-sysvcompat and bash then see if you can arch-chroot.

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#84 2013-06-03 15:28:12

karol
Archivist
Registered: 2009-05-06
Posts: 25,440

Re: filesystem Update Error /bin exists in filesystem

indianahors wrote:

The /bin, /sbin, and /usr/sbin dirs exist, but they are just symlinks to /usr/bin/.

Good.

indianahors wrote:

It wasn't clear to me, that after the execution of

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

would be in an unbootable stage! There is nowhere a hint in this direction!

The news item and the update instructions said you need to

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

Why did you assume that some parts are optional or can be performed later?

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#85 2013-06-03 15:46:14

ewaller
Administrator
From: Pasadena, CA
Registered: 2009-07-13
Posts: 16,443

Re: filesystem Update Error /bin exists in filesystem

This has gone mainstream.  Moving from testing to Pacman & Package Upgrade Issues.

Note to other moderators:  As this is someone exceptional, I left a forwarding link for this in 'Testing' on purpose.

Last edited by ewaller (2013-06-03 15:48:52)


Nothing is too wonderful to be true, if it be consistent with the laws of nature -- Michael Faraday
Sometimes it is the people no one can imagine anything of who do the things no one can imagine. -- Alan Turing
---
How to Ask Questions the Smart Way

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#86 2013-06-03 15:53:47

Scimmia
Bug Wrangler
Registered: 2012-09-01
Posts: 7,198

Re: filesystem Update Error /bin exists in filesystem

Oh, and once you get in, just run "pacman -Syu" and see if everything's fine afterwards. If not, try "pacman -Q | pacman -Qk | grep warning" to see what packages need reinstalled.

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#87 2013-06-03 18:10:07

Visp
Member
From: Valencia (Spain)
Registered: 2013-03-02
Posts: 11

Re: filesystem Update Error /bin exists in filesystem

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

[rootfs /]#

Same problem here...

But i can't execute "pacman -S bash"... pacman not exists...

Last edited by Visp (2013-06-03 18:14:45)

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#88 2013-06-03 18:11:19

jasonwryan
Anarchist
From: .nz
Registered: 2009-05-09
Posts: 26,978
Website

Re: filesystem Update Error /bin exists in filesystem

Merging with the stickied thread...


Arch + dwm   •   Mercurial repos  •   Github

Registered Linux User #482438

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#89 2013-06-03 18:18:29

meijin
Member
From: Israel
Registered: 2009-03-05
Posts: 92

Re: filesystem Update Error /bin exists in filesystem

Visp wrote:
Error: Root device mounted successfully, but /sbin/init does not exist.
Bailing out, you are on your own. Good Luck

[rootfs /]#

Same problem here...

But i can't execute "pacman -S bash"... pacman not exists...

mount "new_root" to /mnt
then pacman -Ur /mnt/var/cache/pkg/bash....
same for filesystem...

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#90 2013-06-03 18:43:58

Visp
Member
From: Valencia (Spain)
Registered: 2013-03-02
Posts: 11

Re: filesystem Update Error /bin exists in filesystem

meijin wrote:

mount "new_root" to /mnt
then pacman -Ur /mnt/var/cache/pkg/bash....
same for filesystem...

Thanks for your answer.

But i have this error when "pacman -Su bash"

error: could not open file: /etc/mtab: No such file or directory
error: could not determine filesystem mount points
error: failed to commit transaction (unexpected error)
Errors ocurred, no packages were upgraded.

Last edited by Visp (2013-06-03 19:04:46)

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#91 2013-06-03 18:51:54

ergoschnuffel
Member
Registered: 2013-06-03
Posts: 12

Re: filesystem Update Error /bin exists in filesystem

Hello,

well i kinda tried to upgrade ...

First i got stuck with that nice move /bin.. pacma's msg, so i quckly checked and just moved all in /usr/bin -> reboot and nothing. Then i booted from another hdd (got replaced by ssd a while back, rsynced) and mounted the ssd and was be able to install the filesystem update with.

pacman --root /mnt -S filesystem

Rebooted and still the same: cant find sbin/init.

So i checked and iam stuck here now.

sbin is "now" only owned by filesystem:

pacman --root /mnt -Qo /mnt/usr/sbin
/mnt/usr/sbin is owned by filesystem 2013.05-2

Any tips how to get ti up and running?


Some Intel CPU + HD6970 repos: [all testing] + [mesa-git]

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#92 2013-06-03 18:53:53

Scimmia
Bug Wrangler
Registered: 2012-09-01
Posts: 7,198

Re: filesystem Update Error /bin exists in filesystem

What exactly did you do when you say "just moved all in /usr/bin"?

Do /bin and /sbin exist? They should be symlinks to usr/bin.

Last edited by Scimmia (2013-06-03 18:54:13)

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#93 2013-06-03 18:56:28

jqvillanova
Member
From: Madrid, Spain
Registered: 2013-04-25
Posts: 17

Re: filesystem Update Error /bin exists in filesystem

Read the news before upgrading or subscribe to arch-announcement mailing list, your issue is well covered. I updated with no issues.

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#94 2013-06-03 19:00:37

jasonwryan
Anarchist
From: .nz
Registered: 2009-05-09
Posts: 26,978
Website

Re: filesystem Update Error /bin exists in filesystem

Merging with the stickied thread...


Arch + dwm   •   Mercurial repos  •   Github

Registered Linux User #482438

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#95 2013-06-03 19:03:35

ergoschnuffel
Member
Registered: 2013-06-03
Posts: 12

Re: filesystem Update Error /bin exists in filesystem

I moved all real files and links on no "bin" files in /usr/bin from [/bin, /sbin, /usr/bin].

#ls -l /mnt/

 
bin -> usr/bin
...
sbin -> usr/bin
...

#ls -l /mnt/usr/

...
sbin -> bin
...

Some Intel CPU + HD6970 repos: [all testing] + [mesa-git]

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#96 2013-06-03 19:07:35

Scimmia
Bug Wrangler
Registered: 2012-09-01
Posts: 7,198

Re: filesystem Update Error /bin exists in filesystem

ergoschnuffel, just how much did you move?!? You should have only moved files like that that you put there, anything put there by pacman should be moved by pacman. Try "pacman -Syu --root /mnt", see if you get errors.

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#97 2013-06-03 19:28:13

ergoschnuffel
Member
Registered: 2013-06-03
Posts: 12

Re: filesystem Update Error /bin exists in filesystem

I moved all, tho did a remount and update via host pacman (pacman -Syu --root /mnt). Rebooted on ssd and its working ... kinda robust thingy.
Well thanks Scimmia.


Some Intel CPU + HD6970 repos: [all testing] + [mesa-git]

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#98 2013-06-03 20:17:00

electric_indigo
Member
Registered: 2011-05-12
Posts: 89

Re: filesystem Update Error /bin exists in filesystem

For those who ended up in an unbootable state. I assume you have previous versions of all recently updated packages in pacman's cache.
1. Boot into a LiveCD.
2. Open terminal, log in as root.
3.

# cd /
# mkdir BrokenArch
# mount /dev/[Arch's partition here] BrokenArch
# cd BrokenArch
# ln -s usr/bin bin
# ln -s usr/sbin sbin
# mount --bind /dev dev
# mount --bind /proc proc
# mount --bind /run run
# mount --bind /sys sys
# chroot .

4. Open /BrokenArch/var/log/pacman.log and find the recently updated packages.
5.

# cd /var/cache/pacman/pkg
# pacman -U [list all the previous versions of recently updated packages here, use full filenames with *.pkg.tar.xz estensions. probably just few of the packages caused the problem, but I reinstalled them all]

5. Before confirming downgrade in pacman, open another terminal and log in as root.
6. In the new terminal

# rm /BrokenArch/bin
# rm /BrokenArch/sbin

7. Now you can confirm the downgrade in the first terminal.
8. When the downgrade is complete, perform it once more to correctly execute all post-install scripts.
EDIT: 8.5.

# exit

9. (edited)

# cd /
# umount /BrokenArch

10. reboot

Last edited by electric_indigo (2013-06-03 20:38:13)

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#99 2013-06-03 21:13:33

czubek
Member
From: Alliance College
Registered: 2012-03-08
Posts: 137

Re: filesystem Update Error /bin exists in filesystem

Upgrades of this type typically result in me performing a complete re-installation of Arch Linux. Much to my surprise there were no problems. My thanks to the AUR maintainers. None of the 9 AUR packages I have installed required re-packaging.

Edit: I have read nearly all the posts under this topic and I am amazed that I survived this upgrade. Granted, I was fortunate to have no AUR packages requiring re-building, but is it possible I'm actually learning something, even if it is only to read the current news.

Last edited by czubek (2013-06-13 19:28:09)


Arch Linux is suited to the competent user.
Which ranks me right up there at highly incompetent.

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#100 2013-06-03 21:31:27

Torxed
Member
Registered: 2013-01-10
Posts: 157

Re: filesystem Update Error /bin exists in filesystem

Trying to do the regular sudo pacman -Syu and get:

Total Installed Size:   587.90 MiB
Net Upgrade Size:       -19.05 MiB

:: Proceed with installation? [Y/n] y
(93/93) checking keys in keyring                   [######################] 100%
(93/93) checking package integrity                 [######################] 100%
(93/93) loading package files                      [######################] 100%
(93/93) checking for file conflicts                [######################] 100%
error: failed to commit transaction (conflicting files)
filesystem: /bin exists in filesystem
filesystem: /sbin exists in filesystem
filesystem: /usr/sbin exists in filesystem
systemd-sysvcompat: /usr/bin/poweroff exists in filesystem
Errors occurred, no packages were upgraded.

I have no clue why it's complaining about /bin, /sbin, /usr/sbin and my poweroff script that i've linked in containing:

shutdown -h now

I'm almost afraid of rebooting the machine now because i'm not sure of the severity of /bin being in my "filesystem" (which it should, it just frightens me that it complains about such a thing).

Any ideas to why or how to begin debugging this?

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