filesystem Update Error /bin exists in filesystem

young lust · 2013-06-09 09:50:08

hello, dudes.

what i do wrong?

according to the front page i do following steps:

pacman -Qqo /bin /sbin /usr/sbin | pacman -Qm -
nothing gave...

find /bin /sbin /usr/sbin -exec pacman -Qo -- {} + >/dev/null
nothing gave too...

and what i should use instead of <repo> in
paclist <repo> | awk ' { print $1 } ' | pacman -Ql - | grep ' /s\?bin/\| /usr/sbin/'

msthev · 2013-06-09 09:59:32

If you don't use any unofficial repositories, you can skip this step. Check your pacman.conf to see if you use any.

theking2 · 2013-06-09 11:52:41

msthev wrote:

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).

I honestly don't know why I didn't read the instructions on the front page, msthev.

I could get rid of gen-init-cpio, tcp_wrappers and tgt. with

pacman -Rc ...

However, the update in filesystem required me to update grub-legacy to grub. which isn't possible on my system as http://wiki.gentoo.org/wiki/GRUB2#No_post-MBR_gap. A simple filesystem update causes quite some more trouble than is covered in the frontpage instructions. As this is only partial related to filesystem update (requiring a grub2 upgrade) I will post this in another thread.

Last edited by theking2 (2013-06-09 12:58:59)

msthev · 2013-06-09 11:56:26

Remove this outdated grub and install grub-legacy from AUR: https://aur.archlinux.org/packages/grub-legacy/
Then it should be straightforward to do the /usr/bin update.

karol · 2013-06-09 11:56:38

theking2, if you updated grub-legacy (which is unsupported) to grub2 or syslinux earlier, it would have been a smoother ride.
Please don't blame your lack of maintenance on e.g. Arch devs.

krork · 2013-06-09 12:40:57

Trilby wrote:

I don't know if this would be the best idea, krork, but it wouldn't be quite the worst: use sed to fix all the file lists.
sed -i 's|^bin/|usr/bin/' /var/lib/pacman/local/*/files
sed -i 's|^sbin/|usr/bin/|' /var/lib/pacman/local/*/files
sed -i 's|^usr/sbin/|usr/bin/|' /var/lib/pacman/local/*/files
EDIT: there are no leading slashes in the files files, I've modified the command appropriately.

Thank you Trilby, when I ran the first command I got this error:

sed: -e expression #1, char 16: unterminated `s' command

.

Thanks, because that finally made me read up on how to use sed, which is awesome.

For anyone interested: The correct code would be:

sed -i 's|^bin/|usr/bin/|' /var/lib/pacman/local/*/files

, i.e. the third "|" delimiter was typo-ed into non-existence.
If anybody, like me, has let their own mistakes with the update lure them into further learning about the gnu/linux world, I'm currently reading this tutorial on http://www.grymoire.com/Unix/Sed.html#uh-0 which I can highly recommend. Sed is really awesome.

I have not yet gone further with the update, since I'm nervous about ruining my system. All I've done so far is stupidly copy all bins from /bin /sbin /usr/sbin to /usr/bin and done some magical sed damage repair with the help of Trilby. I need to upload some finished work tonight, so I will wait a day or two, read up and then continue the update..
..with

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

?
Would that be the next step? I'm unsure, still rather new to Arch.

Thank you all so far, and good luck to all the other strugglers reading this thread.

karol · 2013-06-09 12:46:23

Next step is going on with your life.
After the update you should have a working system and you can do whatever you want.

Trilby · 2013-06-09 12:52:21

Sorry about the typo. I usually use / as a sed delimiter, but I figured escaping the / with \/ int all the paths would be confusing to others. I ended up confusing myself instead - I'll edit the previous post.

theking2 · 2013-06-09 13:00:23

karol wrote:

theking2, if you updated grub-legacy (which is unsupported) to grub2 or syslinux earlier, it would have been a smoother ride.
Please don't blame your lack of maintenance on e.g. Arch devs.

update to grub2 was not possible with my system. please see my (edited) reply. And I didn't blame anyone, did I?

Last edited by theking2 (2013-06-09 13:23:41)

yungtrizzle · 2013-06-09 15:17:40

ewaller wrote:

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 %

Results :

[root@none] ls -l /sbin
[root@none] ls : cannot access /sbin : no such file or directory
[root@none] ls /usr/bin/init
/usr/bin/init
[root@none] ls -l /usr/bin/init
/usr/bin/init -> ../lib/systemd/systemd

Last edited by yungtrizzle (2013-06-09 15:22:12)

Scimmia · 2013-06-09 15:37:25

Wait a minute, earlier you said you confirmed that /sbin was a symlink to usr/bin. If it's not, reinstall the filesystem package.

yungtrizzle · 2013-06-09 16:50:52

liveCD chroot said /sbin was symlinked apparently it really wasn't. I reinstalled filesystem and fsck'ed a couple a times before rebuilding grug.cfg

esuhl · 2013-06-09 18:44:50

As a result of all binaries being moved to /usr/bin recently, I followed the instructions to update my desktop PC and (having uninstalled tcp_wrappers, gen-init-cpio and consolekit), everything updated smoothly.

I did the same on my Asus EEE 901 netbook and, on running pacman -Syu --ignore filesystem,bash, a handful of packages showed an error message relating to one of the binary directories not being found.

When the update finished, I was no longer able to connect to either wired or wireless networks. I also lost the ability to mount USB drives (because 'vfat' was not recognised as a valid filesystem).

After a lot of troubleshooting, I (stupidly) rebooted, but I get the following 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 /]#

I'm completely out of my league! Can anyone help me understand what I need to do to get the system up and running again?

Scimmia · 2013-06-09 18:48:29

Try this: https://bbs.archlinux.org/viewtopic.php … 3#p1283343

karol · 2013-06-09 18:48:32

Please search the forum, the wiki ...

Chroot using a liveCD/liveUSB and install systemd-sysvcompat.

jasonwryan · 2013-06-09 18:57:13

Merging with the mega-sticky...

Trilby · 2013-06-09 19:25:44

jasonwryan wrote:

Merging with the mega-sticky...

Sounds like the subtitle to a really bad SciFi B movie.

Edit: Now playing at a theater near you: "The Stink Monsters From Uranus II: Merging with the mega-sticky"

Edit: they had to make a sequel, it just wouldn't be right without a good number 2.

Last edited by Trilby (2013-06-09 20:35:11)

WorMzy · 2013-06-09 20:33:31

Stink monsters for Uranus was a classic, they should stop trying to milk the series.

esuhl: If you get that error, you either:

1) were using initscripts (unsupported for half a year now) and uninstalled them to get the update to go through but didn't install systemd-sysvcompat or update your bootloader with init=/usr/lib/systemd/systemd
or
2) didn't complete the update before you restarted, and your filesystem package is out-of-date.

Your post isn't clear as to which situation you're in; no doubt you can find a solution by reading through the topic though.

Let us know which of these better represents the situation you're in, if you can't find a solution, and we can better advise you.

tiaschaer · 2013-06-09 20:59:09

Hi guys,

unfortunately, after about 3 years that I am using Archlinux (and about 10 that I am using Linux), I am forced to write for the first time into a forum to get help.
I looked long time for a solution in the forums but this time I had no luck...

I basically followed the instructions for the upgrade, but I did some very stupid things (just because I was in a hurry).
Command

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

listed 3 things: 2 of them were "grub*" while the 3. one I do not remember. First stupid thing: I ignored them. I then went on till the end of the procedure but the last command

pacman -Su

gave some error which I also do not remember. But for sure the update has not been installed. Second stupid thing: I turned off my PC (thinking to finish the update in a second moment...)

The result at the next boot was
Normal boot
What I already find strange is that it is looking for "initrd" while I am using "systemd"since long time.
As a next trial I modified the booting line involving the kernel by adding "init=/usr/lib/systemd/systemd"
Boot option
And the result is that the system can not boot (because of mounting issues? I.e. related to the filesystem?)
Boot with option

At this point I really do not know what I should do... But I am sure that you guys can help me!

Thanks for the help,
Mattia

DaTa · 2013-06-09 21:12:58

I want to mention that the last step in the recipe in the news fails when pacman is configured with XferCommand.

For some reason it tries to update filesystem, deletes /bin, and then executes wget with "/bin/sh -c 'wget ...".

Recreating the directories /bin /sbin /usr/sbin, disabling the XferCommand and running the command again solved that.

WonderWoofy · 2013-06-09 21:16:12

Yes, it creates a shell for itself to run the command in. This has been covered several times through this mega-thread. I'm glad you figured this out for yourself here, but it is not news.

jasonwryan · 2013-06-09 21:18:06

Merging with the sticky...

Scimmia · 2013-06-09 21:21:40

tiaschaer wrote:

I basically followed the instructions for the upgrade, but I did some very stupid things (just because I was in a hurry).
Command
$ pacman -Qqo /bin /sbin /usr/sbin | pacman -Qm -
listed 3 things: 2 of them were "grub*" while the 3. one I do not remember. First stupid thing: I ignored them. I then went on till the end of the procedure but the last command
pacman -Su
gave some error which I also do not remember. But for sure the update has not been installed. Second stupid thing: I turned off my PC (thinking to finish the update in a second moment...)

https://bbs.archlinux.org/viewtopic.php … 3#p1283343

Foxboron · 2013-06-09 23:58:57

Helluw.
So i borked my install by fucking over everything, i cant even remember what i did, but /bin /sbin and /usr/sbin was gone. I couldn't boot and just symlinked /usr/bin too /bin, /sbin and /usr/sbin. Now, i am trying to fix it, but if i remove any symlinks, i get:

 Error: `git` command not found

the line from the fix outputs:

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

error: No package owns /bin
error: No package owns /sbin
error: No package owns /usr/sbin
adobe-air 2.1-1
adobe-air-sdk 2.6-5
android-udev 39.ff4469c-1
asoundconf 1:1.0.1-3
asus-kbd-backlight 1.1-1
asus-screen-brightness 1.0-1
awoken-icons 2.5.1-1
bbswitch-dkms 0.7-1
chromium-pepper-flash-stable 11.7.700.203-1
delorean-dark-theme-3.6 2.56-3
destroytwitter 2.1.5-1
downgrade 3.3-1
dropbox 2.0.22-1
dropbox-cli 1-14
dropbox-daemon 0.8-8
empathy-theme-ubuntu-adium-bzr 12-1
gdm3setup 20130207-1
gdm3setup-utils 20130207-1
gnome-defaults-list 3.6.2-7
gnome-shell-theme-elegance 20130105-1
go-mtpfs-git 20130404-1
google-talkplugin 3.19.1.0-2
ldm 0.4.1-1
lib32-libxslt 1.1.28-1
libsmi 0.4.8-2
libxml-perl 0.08-4
libxnvctrl 319.23-1
lighttable 0.4.9-1
mpd-git 20130404-1
nautilus-dropbox 1.6.0-1
netcfg 3.1-3
otf-source-code-pro-powerline-git 20130309-2
package-query 1.2-2
perl-data-random 0.08-2
perl-goo-canvas 0.06-2
perl-gtk2-imageview 0.05-2
perl-gtk2-unique 0.05-2
perl-mouse 1.06-1
perl-net-dropbox-api 1.9-2
perl-net-oauth 0.28-2
perl-net-pcap 0.17-2
perl-proc-processtable 0.47-1
perl-proc-simple 1.30-1
perl-yaml-tiny 1.51-2
psgrep 1.0.6-1
python-powerline-git 20130412-1
rssh 2.3.4-1
rxvt-unicode-patched 9.18-2
shutter 0.90-2
sl 5.0-2
slimlock-git 20130505-1
smlnj 110.75-1
speedtest-cli 20130218-3
sublime-text 2.0.1-2
sublime-text-nightly 3.3035-1
tmux-solarized-git 20130603-1
toluapp 1.0.93-6
urlview 0.9-7
xbindkeys_config 0.1.3-2
xcalib 0.8-4
xfce-theme-blackbird 0.4-1
yaourt 1.3-1
zramswap 1.1-1

I am not really sure what i should to fix this, any guidance?

Last edited by Foxboron (2013-06-10 00:03:06)

cfr · 2013-06-10 00:35:16

You are getting those results with /bin, /sbin and /usr/sbin as symbolic links? That is not going to tell you what you need to know. That command was designed to identify problematic packages if run *before* commencing the upgrade.

Did you move things manually from those directories to /usr/bin? If so, you need to identify the problematic packages in some other way.

grep "\(^usr\/sbin\)\|\(^sbin\)\|\(^bin\)" /var/lib/pacman/local/*/files

should tell you which packages pacman thinks own files in those directories. Many of these will be in the official repos. You are looking for those which also appear in the list you posted above. So start off by figuring out which those are.

Then you will need to remove or update those packages. Some are obsolete e.g. netcfg should be replaced. Others should not appear in the new list e.g. psgrep. Others may need to be updated or replaced.

When you've done that, you can proceed with the rest of the upgrade. However, you will probably need to boot the install media to update filesystem since you are going to have to remove the symbolic links you've created manually in order to do that.

Arch Linux

#426 2013-06-09 09:50:08

Re: filesystem Update Error /bin exists in filesystem

#427 2013-06-09 09:59:32

Re: filesystem Update Error /bin exists in filesystem

#428 2013-06-09 11:52:41

Re: filesystem Update Error /bin exists in filesystem

#429 2013-06-09 11:56:26

Re: filesystem Update Error /bin exists in filesystem

#430 2013-06-09 11:56:38

Re: filesystem Update Error /bin exists in filesystem

#431 2013-06-09 12:40:57

Re: filesystem Update Error /bin exists in filesystem

#432 2013-06-09 12:46:23

Re: filesystem Update Error /bin exists in filesystem

#433 2013-06-09 12:52:21

Re: filesystem Update Error /bin exists in filesystem

#434 2013-06-09 13:00:23

Re: filesystem Update Error /bin exists in filesystem

#435 2013-06-09 15:17:40

Re: filesystem Update Error /bin exists in filesystem

#436 2013-06-09 15:37:25

Re: filesystem Update Error /bin exists in filesystem

#437 2013-06-09 16:50:52

Re: filesystem Update Error /bin exists in filesystem

#438 2013-06-09 18:44:50

Re: filesystem Update Error /bin exists in filesystem

#439 2013-06-09 18:48:29

Re: filesystem Update Error /bin exists in filesystem

#440 2013-06-09 18:48:32

Re: filesystem Update Error /bin exists in filesystem

#441 2013-06-09 18:57:13

Re: filesystem Update Error /bin exists in filesystem

#442 2013-06-09 19:25:44

Re: filesystem Update Error /bin exists in filesystem

#443 2013-06-09 20:33:31

Re: filesystem Update Error /bin exists in filesystem

#444 2013-06-09 20:59:09

Re: filesystem Update Error /bin exists in filesystem

#445 2013-06-09 21:12:58

Re: filesystem Update Error /bin exists in filesystem

#446 2013-06-09 21:16:12

Re: filesystem Update Error /bin exists in filesystem

#447 2013-06-09 21:18:06

Re: filesystem Update Error /bin exists in filesystem

#448 2013-06-09 21:21:40

Re: filesystem Update Error /bin exists in filesystem

#449 2013-06-09 23:58:57

Re: filesystem Update Error /bin exists in filesystem

#450 2013-06-10 00:35:16

Re: filesystem Update Error /bin exists in filesystem

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