filesystem Update Error /bin exists in filesystem

[KNS]Kumo · 2013-06-22 18:17:08

Scimmia wrote:

FIX GUIDE: For those that screwed up the filesystem update and can't boot anymore because it can't find /sbin/init
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 following the above guide to fix my system, but I'm stuck.

1) No problem
2) I mount /dev/sda1 (root) in /mnt/root and /dev/sda2 (home) in /mnt/home. I have only these 2 partitons
3) When I execute pacman --root /mnt -Qo /mnt/bin /mnt/sbin /mnt/usr/sbin I get -> "error: failed to initialize alpm library (could not find or read directory)".

Pacman -Tv says:

Warning: Database file for core does not exists
" " " " extra " " "
" " " " community " " "
Root : /
Conf File : /etc/pacman.conf
DB Path : /var/lib/pacman/
Cache Dirs : /var/cache/pacman/pkg/
Lock file: /var/lib/pacman/db.lck
log file : /var/log/pacman.log
GPG Dir : /etc/pacman.d/gnupg
Targets : none

Am I doing something wrong? Guess something related to mounting the partitions?
Should I mount /mnt/root/var in /mnt/var and the same with /mnt/root/bin||/user||/sbin||/opt||/etc||...?

Ps: Sorry, but I've read some replies while I was looking for answers and when a so important update is not well documented in the front page and the thread is 28 pages long, full of problems some sort of replies like "this is not your linux" or "if you don't have spare time to fix it is not your distro" and others like those are simply absurd. One just can't not talk about doing stuff following a sort KISS philosophy and then say your $users has to be half-hackers to understand it/you.
I Like Arch. I don't understand some of the later updates, but I really like it. I've using for several years now and I think that kind of replies (and attitude) are useless and don't contribute to improve the distro or the user experiece. This update just didn't go well for a lot of people. We can learn something about this whole mess or repeat it in the next major upgrade until we run out of $users.

Last edited by [KNS]Kumo (2013-06-22 19:16:47)

60lpsdf250 · 2013-06-22 18:36:02

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.

Thank you Scimmia. This procedure got me unstuck without having to reinstall my system.

Scimmia · 2013-06-22 19:11:22

[KNS]Kumo wrote:

2) I mount /dev/sda1 (root) in /mnt/root and /dev/sda2 (home) in /mnt/home. I have only these 2 partitons
3) When I execute pacman --root /mnt -Qo /mnt/bin /mnt/sbin /mnt/usr/sbin I get -> "error: failed to initialize alpm library (could not find or read directory)".

The error you're seeing is because pacman can't find it's database. This is correct since you didn't mount your root partition to /mnt, which is what is specified in the --root option. If you want to mount the root partition to /mnt/root, you would need to mount home to /mnt/root/home and use --root /mnt/root in the pacman command.

cupcake1234 · 2013-06-22 20:09:03

In Allan's most recent post about migrating to /usr/bin

https://www.archlinux.org/news/binaries … ervention/

In the first step to updating, he says "Fix any non-official packages with files in ..." What exactly is meant by "fix"? I ran the line he gave to find packages that need to be fixed and got

grub 0.97-21
grub 0.97-21
sysvinit 2.88-9
consolekit 0.4.6-4
initscripts 2012.08.3-2

So, any help, maybe a link somewhere showing how to fix these packages would be appreciated. Thank you.

ewaller · 2013-06-22 20:12:36

Moving to Upgrade issues and merging with the Stickied thread.
Edit: Was meaning of "fix" in move to /usr/bin by cupcake1234

Last edited by ewaller (2013-06-22 20:14:58)

[KNS]Kumo · 2013-06-22 20:48:22

Scimmia wrote:

The error you're seeing is because pacman can't find it's database. This is correct since you didn't mount your root partition to /mnt, which is what is specified in the --root option. If you want to mount the root partition to /mnt/root, you would need to mount home to /mnt/root/home and use --root /mnt/root in the pacman command.

Thanks Scimmia. I've mounted root at /mnt as you said.

Now in step 3 I get:

/mnt/bin is owned by grub...
/mnt/sbin is owned by gent-init-cpio...
/mnt/sbin is owned by grub...
/mnt/usr/sbin is owned by consolekit...
/mnt/usr/sbin is owned by dcron...
/mnt/usr/sbin is owned by enemy-teritory...
/mnt/usr/sbin is owned by filesystem...
/mnt/usr/sbin is owned tcp-wrappers...

Now, If I've understood the guide, I should unistall or delete some packects. Beside Enemy territory, I don't know about the others. Can I simply do pacman --root /mnt -S <pkgname>? I mean, grub or others look important (althought the first is outdated I believe).

Edit: I've unistalled everything but filesystem and grub. I'm going to read some pages back about the last.

Last edited by [KNS]Kumo (2013-06-22 21:03:04)

Scimmia · 2013-06-22 21:04:08

Filesystem is correct, the others need some attention. All of them have been covered in this thread except enemy-territory. Looking at the AUR page for it, I think it's already been fixed there, so I would just uninstall it for now then rebuild and reinstall it once you get your system back up.

pacman -S won't do anything for them since none of those are in the repos.

[KNS]Kumo · 2013-06-22 21:42:50

Scimmia wrote:

Filesystem is correct, the others need some attention. All of them have been covered in this thread except enemy-territory. Looking at the AUR page for it, I think it's already been fixed there, so I would just uninstall it for now then rebuild and reinstall it once you get your system back up.
pacman -S won't do anything for them since none of those are in the repos.

Thanks Scimmia. I've edited the post as long as I was reading/progressing with the info of the thread. Now I only have doubts about grub. I don't want to break it more.

Last edited by [KNS]Kumo (2013-06-22 22:28:33)

Scimmia · 2013-06-22 21:49:35

Grub is your bootloader. You should update to a supported bootloader like syslinux or grub 2. If you really want to stay with grub 0.97, you should install grub-legacy from the AUR.

cfr · 2013-06-22 21:51:36

grub is no longer officially supported so you have to make a choice. Assuming that you are still using it as your boot loader, you could update to a different loader (grub2 or syslinux, for example), you could switch to legacy grub from AUR (which has been updated to cope with the filesystem changes), or you could use the trick for continuing with grub discussed in one of the forum threads on this. The last option was really invented because the AUR package had not been updated when the filesystem changes first occurred so I am not sure that it now has any advantages over just switching to the AUR package if you want to stay with legacy grub.

cupcake1234 · 2013-06-22 22:28:14

OK, I've installed syslinux, and it seems to work. Is there any way to see what the active boot loader is?

The other three that come up as in the old directories are

sysvinit 2.88-9
consolekit 0.4.6-4
initscripts 2012.08.3-2

Do I need them? What do I need to do to make them work in the new system?

[KNS]Kumo · 2013-06-22 22:30:28

Chrooted the system and instaled syslinux to remove grub (finger crossed).

Now in step 3 I get:
Error: No packages own /mnt/bin
Error: failed to read file '/mnt/sbin/': no such...
/mnt/usr/sbin is owned bu filesystem...

Worried about /mnt/bin still exists... step 4 shows find: missing argument to '-exec'

working on it.

@cupcake1234 If you moved to systemd you shouldn't need consolekit (old package) and initscripts.

Last edited by [KNS]Kumo (2013-06-22 22:32:05)

Scimmia · 2013-06-22 22:31:26

take a look at /mnt/bin. If there's nothing in it, delete it.

Lord Bo · 2013-06-22 22:56:58

Scimmia wrote:

take a look at /mnt/bin. If there's nothing in it, delete it.

...and otherwise do a "pacman --root 'whatever' -Qo" on the files inside it.

[KNS]Kumo · 2013-06-22 22:57:06

I just want to say that I'm writting right now from my main system, so it's fixed. And I want to express my thanks, a lot, to Scimmia for his help, explanations and patience.

MichaelRpdx · 2013-06-24 04:22:33

I'm here to get whacked with a clue stick. Here's what I've done:
download archlinux-2013.06.01-dual.iso and burned to CD
used the CD to do a fresh install using core-local
in package selection step add openssh, accept all other default settings
accept all defaults possible
Read the News About the /usr/bin migration (this is not the first install attempt ...)

For any non-official packages - nope, just the default core + openssh
Non-official repos - nope, just the standard from the install disk
Ignore{Pkg,Group} are both blank in /etc/pacman.conf
Do the check for unowned files in /bin /sbin /usr/sbin
hmmm, cannot determine ownership of /bin /sbin /usr/sbin
Nothing is using autofs

Update your system:
Having read the News I

pacman -Syu --ignore filesystem,bash

and eventually find that I'm in a catch 22 because many of the packages require glibc to be upgraded
but

:: glibc: requires filesystem>=2013.01

Is there a different install image I should be using?
What's the path to get glibc and filesystem upgraded?

WonderWoofy · 2013-06-24 04:25:48

core-local? That was something on the old installers with the Arch Installation Framework (AIF) which is no longer around. It has been replaced by some simple scripts called the arch-install-scripts. If you had done an install with a new install media like you mentioned above, you would have ended up with an up to date system because it always does a netinstall now. There are no packages on the new installer.

Scimmia · 2013-06-24 04:41:31

The error you're getting only happens if your system is at least 6 months out of date. What in the world are you installing with?

MichaelRpdx · 2013-06-24 04:59:51

I'm installing with archlinux-2013.06.01-dual.iso fetched from osuosl.org and a verification pulled from rit.edu.

Shouldn't that be up to date? <rhetorical_shrug/>

WonderWoofy · 2013-06-24 05:20:07

Okay... for a sanity check, can you do "pacman -Q filesystem" and post the result?

MichaelRpdx · 2013-06-24 05:37:13

And the sanity check says:

[root@barn ~]# pacman -Q filesystem
filesystem 2011.08-1

HalosGhost · 2013-06-24 05:43:48

MichaelRpdx wrote:

And the sanity check says:
[root@barn ~]# pacman -Q filesystem
filesystem 2011.08-1

And this is while booted with your livecd? Because, whatever environment you're in, it is ancient.

All the best,

-HG

WonderWoofy · 2013-06-24 06:24:06

Hence the dependency issues. So whatever you are installing from and booting from it is obviously not the June iso. As I said before, the new isos have no packages, so there is no possible way to get old packages with the new installation method. If this is a brand new installation, I would recommend going back and trying again. You didn't get worried when what you were doing didn't match the Installation Guide or the Beginners Guide?

MichaelRpdx · 2013-06-24 06:42:11

Well, I owe all of you a beer. I'd burned the wrong ISO to the CD.
meh

Now I have a new problem, at the end of the boot process dmesg (or dmesg like) logging fills the screen with

[  ##.#####] r8169 0000:04:00.0 emp4s0: rtl_phyar_cond == 0 (loop: 20, delay: 25)

soon as I get that to quit logging to console I'll be able to install.

apologies for the bone headedness

Updated: since r8169 googles out to a Realtec ethernet chipset I concluded disabling the embedded ethernet on the motherboard would solve that problem. And it did.

Now for a real install

Last edited by MichaelRpdx (2013-06-24 06:48:05)

WonderWoofy · 2013-06-24 06:50:08

This really goes beyond the scope of this thread. But I'll just throw this out there, and if it doens't work, start a new thread. I have a realtek card that would normally use the r8169 module, but it is a new revision of the card and have never quite worked right with that particular module. So I have to rely on the realtek provided r8168 module instead. It is in the official community repo. If this error just continues to clog the shit out of your screen, you are going to need to blacklist it from the kernel command line. Otherwise, you need to simply unload it. Then also have the r8168 package handy, since you cannot download it, and then use pacman to install it once you get booted. Beware though that the module is dependent on the kernel version being pretty specific, so you may have to go to the ARM (Arch Rollback Machine) to get an old package.

Edit: Oh I see you are just using wireless then.

Last edited by WonderWoofy (2013-06-24 06:50:54)

Arch Linux

#676 2013-06-22 18:17:08

Re: filesystem Update Error /bin exists in filesystem

#677 2013-06-22 18:36:02

Re: filesystem Update Error /bin exists in filesystem

#678 2013-06-22 19:11:22

Re: filesystem Update Error /bin exists in filesystem

#679 2013-06-22 20:09:03

Re: filesystem Update Error /bin exists in filesystem

#680 2013-06-22 20:12:36

Re: filesystem Update Error /bin exists in filesystem

#681 2013-06-22 20:48:22

Re: filesystem Update Error /bin exists in filesystem

#682 2013-06-22 21:04:08

Re: filesystem Update Error /bin exists in filesystem

#683 2013-06-22 21:42:50

Re: filesystem Update Error /bin exists in filesystem

#684 2013-06-22 21:49:35

Re: filesystem Update Error /bin exists in filesystem

#685 2013-06-22 21:51:36

Re: filesystem Update Error /bin exists in filesystem

#686 2013-06-22 22:28:14

Re: filesystem Update Error /bin exists in filesystem

#687 2013-06-22 22:30:28

Re: filesystem Update Error /bin exists in filesystem

#688 2013-06-22 22:31:26

Re: filesystem Update Error /bin exists in filesystem

#689 2013-06-22 22:56:58

Re: filesystem Update Error /bin exists in filesystem

#690 2013-06-22 22:57:06

Re: filesystem Update Error /bin exists in filesystem

#691 2013-06-24 04:22:33

Re: filesystem Update Error /bin exists in filesystem

#692 2013-06-24 04:25:48

Re: filesystem Update Error /bin exists in filesystem

#693 2013-06-24 04:41:31

Re: filesystem Update Error /bin exists in filesystem

#694 2013-06-24 04:59:51

Re: filesystem Update Error /bin exists in filesystem

#695 2013-06-24 05:20:07

Re: filesystem Update Error /bin exists in filesystem

#696 2013-06-24 05:37:13

Re: filesystem Update Error /bin exists in filesystem

#697 2013-06-24 05:43:48

Re: filesystem Update Error /bin exists in filesystem

#698 2013-06-24 06:24:06

Re: filesystem Update Error /bin exists in filesystem

#699 2013-06-24 06:42:11

Re: filesystem Update Error /bin exists in filesystem

#700 2013-06-24 06:50:08

Re: filesystem Update Error /bin exists in filesystem

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