filesystem Update Error /bin exists in filesystem

archoriano · 2013-09-07 18:07:59

Hey guys, i need help, i f*ckd up.

I didnt update my system for like 7 months, for college assignments sake, and now i was having a hard time updating but i did it. Unfortunally i cant boot now and im going to emergency shell.

What i did was update everything exept filesystem, then removing tlp because it had somthing in sbin, then update the filesystem. I forgot to ignore bash, so i only had 1 shell but after filesystem update shell was working again, so i tought i could reboot but as it turns out i cant

I know i shouldnt let arch get 7 months outdated but i dont really want to make a fresh install.

Please Help

WorMzy · 2013-09-07 18:17:16

You can't boot now because your initial ramdisk (initrd) doesn't have the modules for your current kernel. This is because, by not holding back the bash package during the main part of the update, various packages were unable to execute their .install scripts -- one of these was the linux package which uses this script to generate a new initrd.

The solution, which is documented multiple times in this thread, is to boot a liveCD, chroot into your installation, and manually run the mkinitcpio script. Alternatively chroot in and reinstall the linux package, which will trigger a re-run of the install script.

gizzard · 2013-09-15 16:33:38

Scimmia wrote:

FIX GUIDE: For those that screwed up the filesystem update and can't boot anymore because it can't find /sbin/init
(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.

I'm really sorry to post here for help, but I have run into the "can't find /sbin/init, bailing out error" after trying to follow the home page instructions. I had to first replace grub-common with grub (2.00-1) before upgrading the remaining packages (ignoring filesystem and bash). In looking at pacman.log, I only received these warnings during the the kernel build:

WARNING: Possibly missing firmware for module: aic94xx
WARNING: Possibly missing firmware for module: bfa
WARNING: Possibly missing firmware for module: smsmdtv

I didn't think these modules needed to be dealt with at this point. I also got a message about SNA being used in the xf86-input-evdev package.

I then upgraded bash without any problems (at least according to pacman.log) and the next entry is "Running 'pacman -Su' but there are no additional errors or messages. At this point I think I tried to restart the system and I am not sure if filesystem was fully upgraded properly or not.

Now, on boot I get:

*** Warning ***
* The root device is not configured to be mounted *
* read-write@ It may be fsck'd again later. *
***
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 /]#

In following Scimmia's instructions above, I booted using an archiso USB (with filesystem 2012.10-1) and mounted the root and var partitions to /mnt and /mnt/var, respectively, and at step 3 I get:

root@archiso /mnt # pacman --root /mnt -Qo /mnt/bin /mnt/sbin /mnt/usr/sbin
error: failed to read file '/mnt/bin': No such file or directory
error: cannot determine ownership of directory '/mnt/sbin'
error: cannot determine ownership of directory '/mnt/usr/sbin'

In the /mnt directory, the /mnt/bin folder does not exist, and /mnt/sbin and /mnt/usr/sbin both exist as directories (ie not symlinks) and are empty.

I thought perhaps the linux package was not installed properly at the beginning, so I tried this to reinstall it:

root@archiso / # pacman --root /mnt -S linux
warning: linux-3.10.10-1 is up to date -- reinstalling
<snip>
(1/1) upgrading linux [###] 100%
call to execv failed (No such file or directory)
error: command failed to execute correctly
pacman --root /mnt -S linux  6.48s user 0.68s system 5% cpu 2:05.60 total

Any help would be appreciated. Again, sorry to be yet another user with difficulties.

WorMzy · 2013-09-15 16:48:03

By the looks of things, your problem is two-fold: 1) you haven't upgraded the filesystem package, and 2) the existing filesystem package installed on your system is in an inconsistent state.

I expect that 2) is the reason for 1), as when you try to install the update, you will recieve "exists in filesystem" errors for any number of directories. Try running the final step of the upgrade again from the liveCD:

pacman -r /mnt -Syu

Make a note of which files are conflicting, and report back (full output in [ code ] tags is preferable, you can use sprunge or similar utility to upload output from a tty).

You can ignore the firmware errors mkinitcpio spits out, chances are you don't need them.

Scimmia · 2013-09-15 16:52:30

If /bin doesn't exist and /sbin does as a dir, there's no way the filesystem package updated correctly. Since it's empty, go ahead and delete /sbin and try reinstalling the filesystem package.

gizzard · 2013-09-15 17:41:03

Thanks for both of your replies. Here's the entire output from WorMzy's command:

root@archiso /mnt # pacman -r /mnt -Syu
:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
:: Starting full system upgrade...
resolving dependencies...
looking for inter-conflicts...

Targets (1): filesystem-2013.05-2

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

Proceed with installation? [Y/n] Y
(1/1) Checking package integrity [###] 100%
(1/1) loading package files [###} 100%
(1/1) checking for file conflicts [###] 100%
error: failed to commit transaction (conflicting files)
filesystem: /mnt/sbin exists in the filesystem
Errors occurred, no packages were upgraded.

I removed the /sbin directory and tried the above command again, and this time filesystem updated without any errors and the system booted appropriately. Thanks again to both of you.

WorMzy · 2013-09-15 17:51:12

Ah, it is just the one directory. Go ahead with Scimmia's suggestion, that should fix it.

EDIT: Missed the bottom of your post. Glad you got it sorted.

Last edited by WorMzy (2013-09-15 17:52:01)

mjohnson · 2013-10-14 23:49:15

My Arch system has been mostly dormant for the last 9-12 months, but I fired it up again and wanted to get things up to date. I've read the instructions, but I don't understand several of the steps.

Namely, after I run the command `pacman -Qqo /bin /sbin /usr/sbin | pacman -Qm -` I get a humongous list:

error: cannot determine ownership of directory '/bin'
error: cannot determine ownership of directory '/sbin'
error: cannot determine ownership of directory '/usr/sbin'
acpitool 0.5.1-6
apiextractor 0.10.10-1
archlinux-themes-kde 1.5-2
bin32-4l 1.0r6-5
bin32-lightscribe 1.18.24.1-1
consolekit 0.4.5-2
d1x-rebirth 0.57.3-1
d2x-rebirth 0.57.3-1
db4.5 4.5.20-5
dbus-core 1.4.16-1
dbus-python 0.84.0-1
dcron 4.5-2
django 1.3.1-2
django-piston 0.2.2-3
downgrader 1.2.0-1
eclipse-emf 2.7.1-1
eclipse-gef 3.7.2-1
eclipse-pydev 2.4.0-1
eclipse-wtp-wst 3.3.1-8
eject 2.1.5-7
farsight2 0.0.31-1
freenx 0.7.3-10
gen-init-cpio 2.6.36-1
generatorrunner 0.6.16-1
ggz-client-libs 0.0.14.1-3
gnupg2 2.0.18-1
google-appengine 1.4.0-1
google-talkplugin 2.6.1.0-2
gscan2pdf 1.0.0-2
hal-info 0.20091130-1
heirloom-mailx 12.5-3
icedtea-web 1.1.4-2
initscripts 2012.02.1-1
ipython2-docs 0.12-2
javacc 5.0-2
kdeadmin-system-config-printer-kde 4.8.0-1
kdebase-kappfinder 4.4.5-1
kdegames-kbattleship 4.8.0-1
kdegames-ktron 4.8.0-1
kdegames-libkdegames 4.8.0-1
kdegames-libkmahjongg 4.8.0-1
kdemultimedia-kioslave 4.8.0-1
kdepim-wizards 4.7.4-1
kdeplasma-addons-applets-kdeobservatory 4.8.0-1
kdesdk-kbugbuster 4.5.4-1
kdesdk-kdeaccounts-plugin 4.8.0-1
kdesdk-kdepalettes 4.8.0-1
kdesdk-kioslave 4.8.0-1
kdesdk-kmtrace 4.8.0-1
kdesdk-kpartloader 4.8.0-1
kdesdk-kprofilemethod 4.8.0-1
kdesdk-kstartperf 4.8.0-1
kdesdk-kuiviewer 4.8.0-1
kdesdk-scripts 4.8.0-1
kdesdk-strigi-analyzer 4.8.0-1
kdetoys-kweather 4.4.5-1
kdeutils-printer-applet 4.8.0-1
khrplatform-devel 7.11.2-1
lessc-git 20120315-1
lib32-dbus-core 1.4.16-1
lib32-libgl 7.11.2-3
lib32-libglapi 7.11.2-3
lib32-openssl-compatibility 0.9.8-4
lib32-qt 4.8.0-2
lib32-sqlite3 3.7.10-1
libegl 7.11.2-1
libfetch 2.33-3
libggz 0.0.14.1-3
libgl 7.11.2-1
libglapi 7.11.2-1
libgles 7.11.2-1
libmysqlclient 5.5.20-1
libreoffice-extension-ct2n 3.4.5-2
libreoffice-extension-diagram 3.4.5-2
libreoffice-extension-hunart 3.4.5-2
libreoffice-extension-numbertext 3.4.5-2
libreoffice-extension-oooblogger 3.4.5-2
libreoffice-extension-pdfimport 3.4.5-2
libreoffice-extension-presenter-screen 3.4.5-2
libreoffice-extension-report-builder 3.4.5-2
libreoffice-extension-typo 3.4.5-2
libreoffice-extension-watch-window 3.4.5-2
libshiboken 1.1.0-1
libsoup-gnome 2.36.1-1
libusb 1.0.8-2
libwebkit 1.6.3-1
libwebkit3 1.6.3-1
lucene 2.9.4-1
mx 1.4.1-1
mysql 5.5.20-1
mysql-clients 5.5.20-1
mysql-workbench 1:5.2.35-1
netcfg 2.8.3-1
ntfsprogs 2012.1.15-1
ntrack 1:16-1
nx-common 3.5.0-3
nxclient 3.5.0.7-1
nxserver 3.5.0-5
openjdk6 6.b24_1.11.1-1
openssl-compatibility 0.9.8-3
perl-b-keywords 1.11-1
perl-config-general 2.50-1
perl-critic 1.116-1
perl-devel-stacktrace 1.26-1
perl-exception-class 1.32-1
perl-font-ttf 0.45-2
perl-goo-canvas 0.06-2
perl-gtk2-ex-simple-list 0.50-2
perl-gtk2-imageview 0.05-2
perl-lib-base 2.15-1
perl-pdf-api2 2.019-1
perl-pod-spell 1.01-1
perl-ppi 1.215-1
perl-ppix-regexp 0.025-1
perl-ppix-utilities 1.001000-3
perl-proc-processtable 0.45-2
perl-readonly 1.03-2
perl-readonly-xs 1.05-1
perl-sane 0.03-2
perl-set-intspan 1.13-1
perl-string-format 1.16-1
perl-task-weaken 1.04-1
perl-test-critic 1.02-1
picasa 3.0_5744.02-6
pngcrush 1.7.24-1
poppler-qt 0.18.3-2
procps 3.2.8-4
pycrypto 2.3-1
pyqt 4.9.1-1
pyside 1.1.0-1
pyside-tools 0.2.13-5
python-beautifulsoup 3.2.0-2
python-distribute 0.6.24-1
python-fuse 0.2.1-3
python-imaging 1.1.7-4
python-paramiko 1.7.7.1-1
python-pexpect 2.3-5
python-pysqlite 2.6.3-1
python-utidylib 0.2-4
python2-distribute 0.6.24-1
python2-pyqt 4.9.1-1
python2-suds 0.4-3
python25 2.5.6-2
python25-pil 1.1.7-2
python25-ssl 1.15-1
python26 2.6.7-1
qt 4.8.0-4
qt-doc 4.8.0-1
shibokengenerator 1.1.0-1
spe 0.8.4.h-1
sqlite3 3.7.10-1
system-config-printer-common 1.3.7-1
sysvinit 2.88-3
tcp_wrappers 7.6-15
telepathy-farsight 0.0.19-1
telepathy-qt4 0.8.0-1
ttf-ms-fonts 2.0-3
tunepimp 0.5.3-9
udev 181-2
virtualbox-additions 4.1.8-1
virtualbox-modules 4.1.8-3
xf86-video-radeonhd 1.3.0-3
xorg-res-utils 1.0.3-3
yuicompressor 2.4.7-1

The instructions say to "fix" them. What exactly does this entail? I'm reading about people manually copying/moving files, but I have more than three or four files here... And do the errors at the top of that list mean anything important?

Second, I tried the command to check files from non-official repos (I have some stuff installed from archlinuxfr), but `paclist` just tells me "command not found." What do I need to do to get paclist installed?

It also wants me to update pacman, but of course I can't because the new version depends on things that won't update due to the above issues...

I've been trying to get this working for a while now, and I'm wondering if nuking and starting over might be the best option! But then I'd lose all of the time I spent getting things set up just how I like them...

karol · 2013-10-15 00:01:42

mjohnson, I think that reinstalling and keeping your Arch up to date from now on will be faster and easier.

mjohnson wrote:

'd lose all of the time I spent getting things set up just how I like them...

If you like it so much, why haven't you kept it updated? :-)

mjohnson · 2013-10-15 00:21:16

karol wrote:

mjohnson, I think that reinstalling and keeping your Arch up to date from now on will be faster and easier.

[sigh] I thought that might be the case.

karol wrote:

mjohnson wrote:
I'd lose all of the time I spent getting things set up just how I like them...
If you like it so much, why haven't you kept it updated? :-)

I have Arch on a desktop which used to be my primary machine, but about a year go I got a new, fast laptop that became my primary machine. But even though I don't use my desktop much these days, I still like it to be customized just the way I have it for when I do use it. I started using Arch about four years ago and really like its customizability and bleeding-edge updates.

Is Arch not meant to be usable/recoverable if you don't update it every couple of months? (I'm just surprised that by letting it sit for a little while there's no good way to get back up to speed.) If that's the case, maybe it's just not the right fit for a lesser-used, secondary/backup machine...as much as I hate the idea of switching to something else!

karol · 2013-10-15 00:26:46

I think updating it e.g. weekly is preferable. After half a year many changes pile up and this can make updating a real PITA.

mjohnson wrote:

maybe it's just not the right fit for a lesser-used, secondary/backup machine

I'm afraid it's not.

Pse · 2013-10-15 03:55:47

mjohnson wrote:

I have Arch on a desktop which used to be my primary machine, but about a year go I got a new, fast laptop that became my primary machine.

The same thing happened to me. I switched my desktop (which is used less) to Fedora, and I've been quite pleased. Fairly easy to maintain, recent packages, delta-RPMs (fast update downloads), similar configs to Arch (systemd). I keep Arch on my laptop, which is used day to day.

mjohnson · 2013-10-15 06:05:03

Pse wrote:

mjohnson wrote:
I have Arch on a desktop which used to be my primary machine, but about a year go I got a new, fast laptop that became my primary machine.
The same thing happened to me. I switched my desktop (which is used less) to Fedora, and I've been quite pleased. Fairly easy to maintain, recent packages, delta-RPMs (fast update downloads), similar configs to Arch (systemd). I keep Arch on my laptop, which is used day to day.

Thanks for the suggestion! I haven't tried Fedora out yet, but that's something to keep in mind. (I've done more with Debian and Ubuntu, personally.) I ended up reinstalling Arch; I have dmcrypt + LVM set up, and I wasn't sure how easy it would be to configure the same setup in another distro. Even in Arch it took me a while to remember how I had it set up, but after that point reinstalling Arch wasn't bad, and I'm back up and running!

cfr · 2013-10-15 22:53:09

I've configured lvm-on-luks on a machine running Fedora, as well as on my Arch laptop. (Again, not needing to keep up with updates was the key reason to go Fedora - though selinux was also a consideration for that machine.) The biggest hassle is fighting the installer but it may be easier if you don't go with the KDE spin but the standard one - I'm not sure.

jasonwryan · 2013-10-15 23:12:24

This thread was about the /usr/bin move: clearly it has served it's purpose.

Please be aware that not every thread needs to devolve into a discussion on the required frequency of updating Arch (Allan's Law)...

Closing.

Arch Linux

#826 2013-09-07 18:07:59

Re: filesystem Update Error /bin exists in filesystem

#827 2013-09-07 18:17:16

Re: filesystem Update Error /bin exists in filesystem

#828 2013-09-15 16:33:38

Re: filesystem Update Error /bin exists in filesystem

#829 2013-09-15 16:48:03

Re: filesystem Update Error /bin exists in filesystem

#830 2013-09-15 16:52:30

Re: filesystem Update Error /bin exists in filesystem

#831 2013-09-15 17:41:03

Re: filesystem Update Error /bin exists in filesystem

#832 2013-09-15 17:51:12

Re: filesystem Update Error /bin exists in filesystem

#833 2013-10-14 23:49:15

Re: filesystem Update Error /bin exists in filesystem

#834 2013-10-15 00:01:42

Re: filesystem Update Error /bin exists in filesystem

#835 2013-10-15 00:21:16

Re: filesystem Update Error /bin exists in filesystem

#836 2013-10-15 00:26:46

Re: filesystem Update Error /bin exists in filesystem

#837 2013-10-15 03:55:47

Re: filesystem Update Error /bin exists in filesystem

#838 2013-10-15 06:05:03

Re: filesystem Update Error /bin exists in filesystem

#839 2013-10-15 22:53:09

Re: filesystem Update Error /bin exists in filesystem

#840 2013-10-15 23:12:24

Re: filesystem Update Error /bin exists in filesystem

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