filesystem Update Error /bin exists in filesystem

maggie · 2013-06-04 19:31:02

I read the instructions but still ended up with this error.

Step 1 worked with no output:

sh-4.2# pacman -Qqo /bin /sbin /usr/sbin | pacman -Qm -
sh-4.2# paclist repo-ck  | awk ' { print $1 } ' | pacman -Ql - | grep ' /s\?bin/\| /usr/sbin/'

Step 2 was easy because I dont use my ignorepkg or group.

Step 3 worked:

sh-4.2# find /bin /sbin /usr/sbin -exec pacman -Qo -- {} + >/dev/null

Step 4 was easy because I dont use autofs.

Step 5a worked:

sh-4.2# pacman -Syu --ignore filesystem,bash
:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 repo-ck is up to date
:: Starting full system upgrade...
warning: bash: ignoring package upgrade (4.2.045-1 => 4.2.045-4)
warning: filesystem: ignoring package upgrade (2013.03-2 => 2013.05-2)
warning: syslinux: local (5.01-2) is newer than core (4.06-2)
resolving dependencies...

warning: dependency cycle detected:
warning: torsocks will be installed before its tor dependency
looking for inter-conflicts...

...

Step 5b worked:

sh-4.2# pacman -S bash
resolving dependencies...
looking for inter-conflicts...

Packages (1): bash-4.2.045-4

Total Download Size:    0.77 MiB
Total Installed Size:   3.51 MiB
Net Upgrade Size:       -0.10 MiB

:: Proceed with installation? [Y/n]
:: Retrieving packages ...
pa bash-4.2.045-4-x86_64                              538.4 KiB   704K/s 00:00 [#############################---------------]  6cm bash-4.2.045-4-x86_64                              792.2 KiB  1075K/s 00:01 [############################################] 100%
(1/1) checking keys in keyring                                               [############################################] 100%
(1/1) checking package integrity                                             [############################################] 100%
(1/1) loading package files                                                  [############################################] 100%
(1/1) checking for file conflicts                                            [############################################] 100%
an(1/1) upgrading bash                                                         [--------------------------------------------]    (1/1) upgrading bash                                                         [############################################] 100%

But step 5c does not work.

sh-4.2# pacman -Su
:: Synchronizing package databases...
:: Starting full system upgrade...
warning: syslinux: local (5.01-2) is newer than core (4.06-2)
resolving dependencies...
looking for inter-conflicts...

Packages (1): filesystem-2013.05-2

Total Download Size:    0.01 MiB
Total Installed Size:   0.01 MiB
Net Upgrade Size:       -0.30 MiB

:: Proceed with installation? [Y/n]
:: Retrieving packages ...
 filesystem-2013.05-2-x86_64                          8.4 KiB   195K/s 00:00 [############################################] 100%
(1/1) checking keys in keyring                                               [############################################] 100%
(1/1) checking package integrity                                             [############################################] 100%
(1/1) loading package files                                                  [############################################] 100%
bb/1) checking for file conflicts                                            [--------------------------------------------]   0%
exit(1/1) checking for file conflicts                                            [############################################] 100%
error: failed to commit transaction (conflicting files)
filesystem: /usr/sbin exists in filesystem
Errors occurred, no packages were upgraded.

I do not want to break my laptop so I will just wait with an open xterm until a professional can help me

Scimmia · 2013-06-04 19:35:23

warning: syslinux: local (5.01-2) is newer than core (4.06-2)

This line is your problem, you need to upgrade to 5.01-4. Cherry picking things from testing isn't a good idea.

jasonwryan · 2013-06-04 19:36:07

Merging with the stickied thread...

karol · 2013-06-04 19:40:25

Scimmia wrote:

warning: syslinux: local (5.01-2) is newer than core (4.06-2)
This line is your problem, you need to upgrade to 5.01-4. Cherry picking things from testing isn't a good idea.

I found no signs of 4.06-2 even being in [core]. syslinux 5 was introduced in December so ...?

What's the output of

ls -l /usr/sbin

Scimmia · 2013-06-04 19:41:17

karol wrote:

Scimmia wrote:
warning: syslinux: local (5.01-2) is newer than core (4.06-2)
This line is your problem, you need to upgrade to 5.01-4. Cherry picking things from testing isn't a good idea.
I found no signs of 4.06-2 even being in [core]. syslinux 5 was introduced in December so ...?
What's the output of
ls -l /usr/sbin

No, 4.06-2 is current in core, version 5 is only in testing

https://www.archlinux.org/packages/?q=syslinux

maggie · 2013-06-04 19:42:20

Thank you for the suggestion. I dont know how I got this version of syslinux but I updated it from testing repo and everything works now. I will just keep this version since it boots without problems.

akanski · 2013-06-04 19:45:56

krash wrote:

But it seems to me that I will need to use LiveUSB (or something similar) because even if I use init=/usr/lib/systemd/systemd - systemd doesn't see /bin/mount...
but we need to know how far you got in the update
Too far ). Filesystem was the only thing that wasn't updated before reboot ).

Hi @krash,

If you are using GRUB, try this,

1. Type `e` to edit booting options.
2. In 'linux' section, change ro to rw and type init=/usr/bin/bash, or edit it.
3. CTRL + X to boot.
4. Use `ls -l` command, if there is no directory for /bin and /sbin, then make these two symlinks:

ln -s usr/bin /bin
ln -s usr/bin /sbin

5. If there is some directory (/bin, /sbin), then back it up and act accordingly (making symlinks, finding out whether you have some critical binaries in that previous backup before copying them to '/usr/bin' at your own risk, and so on).
6. Wait a little more 30 seconds (1, 2, 3) and press CTRL + ALT + DEL (or much better, and without further ado, use Magic SysRq).
7. When everything is running well, then install this troublesome package:

pacman -Sy filesystem

8. If there is some error or warning, act accordingly. For example, removing the previous symlinks (or forcing installation whether you are sure of what to do).
___

P.S.

(1) Anyone can try this stuff. However, it's much better and cleaner to fix this issue using chroot unless no pen drive or LiveCD is at hand.

(2) After making symlinks for /bin and /sbin, whoever chooses to copy backed-up binaries to /usr/bin should not have trouble with that unless those symlinks are removed in the future. Nevertheless, it's advisable to upgrade non-official packages with files in /bin, /sbin or /usr/sbin as soon as possible.

Last edited by akanski (2013-06-30 22:15:01)

karol · 2013-06-04 19:54:22

Scimmia wrote:

karol wrote:
Scimmia wrote:
This line is your problem, you need to upgrade to 5.01-4. Cherry picking things from testing isn't a good idea.
I found no signs of 4.06-2 even being in [core]. syslinux 5 was introduced in December so ...?
What's the output of
ls -l /usr/sbin
No, 4.06-2 is current in core, version 5 is only in testing
https://www.archlinux.org/packages/?q=syslinux

You're right. I checked two other places that have no mention of syslinux 4.06-2, one of them being https://projects.archlinux.org/svntogit … s/syslinux ...

This looked pretty weird, but fortunately it was just an error on my part :-)

Edit: Maybe 4.06-2 missing from svntogit is the result of https://bugs.archlinux.org/task/30734

Last edited by karol (2013-06-04 20:04:58)

brokengestalt · 2013-06-04 20:17:22

I want to be really sure on this:

pacman -Qqo /bin /sbin /usr/sbin | pacman -Qm -

is the correct command, and not

pacman -Qqo /bin /sbin /usr/sbin | pacman -Qm

, so that last hyphen is intended/important?

I ask this because I also tried the second command, and got a list of all packages from the AUR that I have installed, which seems like the sorta things this command is intended to list.

Please verify/advise.

karol · 2013-06-04 20:20:16

Yes, it's the first command, hyphen is important.

man pacman wrote:

Additionally, if stdin is not from a terminal and a single dash (-) is passed as an argument, targets will be read from stdin.

Last edited by karol (2013-06-04 20:24:50)

doblerone · 2013-06-04 21:02:51

diterius wrote:

Today faced with this situation:
ERROR: Root device mounted successfully, but /sbin/init does not exist.
Bailing out, you are on your own.
sh: can't access tty; job control turned off
[rootfs/]#
but successfully solved it with live usb
I did everything what electric_indigo adviced to point 4
electric_indigo wrote:
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
then
#chroot . /usr/bin/bash
#pacman -S filesystem
/bin exists...etc
ok...rename /bin to /bin_old, /usr/sbin/ to /usr/sbin_old, remove /sbin link at all
then again
#pacman -S filesystem
it installs without any errors
At last reboot and remove live usbflash

Which one is Arch's partition???

christian1337 · 2013-06-04 21:16:07

hi,

today I "pacman -Syu"-ed my system but then I first had to do this (https://www.archlinux.org/news/binaries … ervention/). So far so good. I think something went wrong there, but all, besides "filesystem" updated correctly, so I thought it would be ok and I just wait for the next update.. After the next reboot I realised that this was totally wrong...

After this I get the following error at boot:

ERROR: Root device mounted successfully, but /sbin/init does not exist.
Bailing out.... 

sh: can't access tty: job control turned off

rootfs /#

then I booted my fallback debian to look for the init in sbin but there wasn't any.. I created just a empy file called init.. but yeah, I "know" this was totally wrong. Also I updated my grub config with grub-mkconfig... After that, also my Debian failed to start... Perfect :-/
Now I'm on my "fallback" Win7 and totally f****ed and have no clue what I'm doing now..

the following errors are coming now when I boot:
arch:

debian:

grub entries:
arch:

debian:

I also had the idea that I somehow crashed the filesystem, but I can access both filesystems(at the moment with a filesystem"reader" for win7)...

Can anyone help me please?

If its totally broken something, is there a possibility to rescue at least my arch system? In case, what files need to be backup-ed? Then I just install a "fresh" arch linux and copy the files over? The problem is that I have many configuration and stuff which would take long time to reconfigure and also I have installed a lot I really need, how do I get all my packages back?

Thank you soooo much in advance.

-- mod edit: read the Forum Etiquette and only post thumbnails http://wiki.archlinux.org/index.php/For … s_and_Code [jwr] --

Scimmia · 2013-06-04 21:18:59

Why do so many people seem to think the filesystem package is optional?

You need to boot from an install disk, mount your partitions to /mnt, then update filesystem with pacman --root /mnt -Su. If it gets errors, you need to fix them.

jakobcreutzfeldt · 2013-06-04 21:22:34

Do as Scimmia says.

Also, you'll have to change your Arch init line to be init=/usr/lib/systemd/systemd, unless you have systemd-sysvcompat, in which case you can just go without an init line.

christian1337 · 2013-06-04 21:24:00

mh, when so many people think that, why don't advice them that it IS mandatory?
but anyway, really thank you for your answer.
So I need to boot from, e.g. a boot stick like knoppix? Then mount ok. But how do I update my arch linux with pacman when I can't login to my arch?

€: @jakobcreutzfeldt: also thank you. I will do that when I'm getting to that, hopefully

Last edited by christian1337 (2013-06-04 21:25:37)

Scimmia · 2013-06-04 21:28:31

The instructions I gave you don't require you to log in, but they only work from an Arch install disk. If you're using Knoppix, you'll have to chroot in the old way: https://wiki.archlinux.org/index.php/Chroot

Know that you'll be in a pretty crippled system until you get the filesystem package installed.

christian1337 · 2013-06-04 21:33:49

ah right with chroot. Yeah ok, then I better try it with a arch usb install. You mean a arch "live" usb stick right?
But how does the shell I'm running then in "live mode" know that I want to update/install the actual broken arch system filesystem package and not the one from the currently running usb arch system? I'm sorry for maybe dumb questions, but it's late, I'm confused and normally totally busy with study stuff at the moment

Scimmia · 2013-06-04 21:35:44

that's what "--root /mnt" is for

Janusz11 · 2013-06-04 21:36:50

electric_indigo wrote:

For those who ended up in an unbootable state. [snip!]

Dude, you're my hero!

Thanks a bunch!

christian1337 · 2013-06-04 21:39:36

awesome, I wondered for what that is, thank you very much <3

jasonwryan · 2013-06-04 22:25:52

Merging with the stickied thread...

christian1337 · 2013-06-05 00:45:51

ok now I've done it. Big thanks, even though it was more a dumb thing because of not thinking update, to all how helped me. It worked

edit: for those who are unsure if you can delete /sbin and /usr/sbin or something to update filesystem package. do it! (just fyi)

Last edited by christian1337 (2013-06-05 00:47:16)

ill · 2013-06-05 01:09:54

I consulted the news article about it but still get the error. My term output:

[~] pacman -Qqo /bin /sbin /usr/sbin | pacman -Qm -
[~] paclist archlinuxfr | awk ' { print $1 } ' | pacman -Ql - | grep ' /s\?bin/\| /usr/sbin/'
[~] find /bin /sbin /usr/sbin -exec pacman -Qo -- {} + >/dev/null
[~] sudo pacman -Syu
[sudo] password for nikon: 
:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
 archlinuxfr is up to date
:: Starting full system upgrade...
resolving dependencies...
warning: dependency cycle detected:
warning: lib32-gcc-libs will be installed before its gcc-libs-multilib dependency
looking for inter-conflicts...

Packages (53): bash-4.2.045-4  bitcoin-qt-0.8.2-1  bluez-4.101-2  cdrkit-1.1.11-3
               chromium-27.0.1453.110-1  coreutils-8.21-2  cryptsetup-1.6.1-2  device-mapper-2.02.98-4
               dhcpcd-5.6.8-3  e2fsprogs-1.42.7-2  filesystem-2013.05-2  fuse-2.9.2-3  gcc-4.8.1-1
               gcc-libs-multilib-4.8.1-1  gconf-3.2.6-2  giflib-4.2.1-2  glibc-2.17-6  gnutls-3.2.1-1
               inetutils-1.9.1-6  iproute2-3.9.0-2  iptables-1.4.19.1-1  kmod-13-2
               lib32-gcc-libs-4.8.1-1  libatasmart-0.19-2  libbonobo-2.32.1-4  libltdl-2.4.2-9
               libogg-1.3.1-1  libsasl-2.1.26-4  libtool-2.4.2-9  libx11-1.6.0-1  libxml2-2.9.1-2
               lsof-4.87-2  lvm2-2.02.98-4  nilfs-utils-2.1.5-2  opencl-headers-2:1.1.20110526-1
               pm-utils-1.4.1-6  ppp-2.4.5-6  python2-mako-0.8.1-1  rtmpdump-20121203-2
               ruby-2.0.0_p195-1  sed-4.2.2-3  shadow-4.1.5.1-6  strigi-0.7.8-3  systemd-204-3
               systemd-sysvcompat-204-3  sysvinit-tools-2.88-11  tar-1.26-4  udisks2-2.1.0-3
               usbmuxd-1.0.8-2  util-linux-2.23.1-2  v4l-utils-0.9.5-2  zsh-5.0.2-2  zvbi-0.2.33-6

Total Installed Size:   395.07 MiB
Net Upgrade Size:       -11.85 MiB

:: Proceed with installation? [Y/n] 
(53/53) checking keys in keyring                               [##################################] 100%
(53/53) checking package integrity                             [##################################] 100%
(53/53) loading package files                                  [##################################] 100%
(53/53) 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
Errors occurred, no packages were upgraded.

What did I do wrong?

Scimmia · 2013-06-05 01:13:31

Re-read step 5. Read the whole thing, not just the first sentence.

jasonwryan · 2013-06-05 01:19:53

Merging with the stickied thread..

Arch Linux

#176 2013-06-04 19:31:02

Re: filesystem Update Error /bin exists in filesystem

#177 2013-06-04 19:35:23

Re: filesystem Update Error /bin exists in filesystem

#178 2013-06-04 19:36:07

Re: filesystem Update Error /bin exists in filesystem

#179 2013-06-04 19:40:25

Re: filesystem Update Error /bin exists in filesystem

#180 2013-06-04 19:41:17

Re: filesystem Update Error /bin exists in filesystem

#181 2013-06-04 19:42:20

Re: filesystem Update Error /bin exists in filesystem

#182 2013-06-04 19:45:56

Re: filesystem Update Error /bin exists in filesystem

#183 2013-06-04 19:54:22

Re: filesystem Update Error /bin exists in filesystem

#184 2013-06-04 20:17:22

Re: filesystem Update Error /bin exists in filesystem

#185 2013-06-04 20:20:16

Re: filesystem Update Error /bin exists in filesystem

#186 2013-06-04 21:02:51

Re: filesystem Update Error /bin exists in filesystem

#187 2013-06-04 21:16:07

Re: filesystem Update Error /bin exists in filesystem

#188 2013-06-04 21:18:59

Re: filesystem Update Error /bin exists in filesystem

#189 2013-06-04 21:22:34

Re: filesystem Update Error /bin exists in filesystem

#190 2013-06-04 21:24:00

Re: filesystem Update Error /bin exists in filesystem

#191 2013-06-04 21:28:31

Re: filesystem Update Error /bin exists in filesystem

#192 2013-06-04 21:33:49

Re: filesystem Update Error /bin exists in filesystem

#193 2013-06-04 21:35:44

Re: filesystem Update Error /bin exists in filesystem

#194 2013-06-04 21:36:50

Re: filesystem Update Error /bin exists in filesystem

#195 2013-06-04 21:39:36

Re: filesystem Update Error /bin exists in filesystem

#196 2013-06-04 22:25:52

Re: filesystem Update Error /bin exists in filesystem

#197 2013-06-05 00:45:51

Re: filesystem Update Error /bin exists in filesystem

#198 2013-06-05 01:09:54

Re: filesystem Update Error /bin exists in filesystem

#199 2013-06-05 01:13:31

Re: filesystem Update Error /bin exists in filesystem

#200 2013-06-05 01:19:53

Re: filesystem Update Error /bin exists in filesystem

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