filesystem Update Error /bin exists in filesystem

cfr · 2013-06-11 23:47:45

What command did you use to install libpng? If you used pacman -S libpng you should have been fine. So presumably you used something else. pacman -Sy libpng, maybe? What happened then? You can get relevant info from pacman.log.

WonderWoofy · 2013-06-12 00:42:09

@cfr, from reading trixrabbit's posts elsewhere, he has apparently been unknowingly partially upgrading. In essence, he must have been doing pacman -Sy, then installing packages without doing the -Su.

trixrabbit · 2013-06-12 02:55:03

WonderWoofy wrote:

@cfr, from reading trixrabbit's posts elsewhere, he has apparently been unknowingly partially upgrading. In essence, he must have been doing pacman -Sy, then installing packages without doing the -Su.

no no no, I always install packages pacman -S and update system with pacman -Syu, never used anything else. I don't know it's weird. I installed blender 3d, tried to run it, it didn't start because it said it was missing libpng...then I just did pacman -S libpng, tried again and blender started. Then I tried to open chromium, it wasn't working with my shortcut key, so tried in console, nothing. Tried with a bunch of other programs, same problem...so I rebooted my laptop (old windows habit) and after startx only a gray screen would appear and from my openbox menu nothing would start.

edit: I'll try to fix some stuff with the news i just read..I can't update system now because of the merging..
Well the step 1 shows a lot of packages, I don't know what to do with them..

Last edited by trixrabbit (2013-06-12 03:16:13)

WonderWoofy · 2013-06-12 03:01:05

@trixrabbit, the problem with that assumption is that if you always did pacman -S <package> and pacman -Syu only, then you would have not been able to install a newer version of blender that was incompatible with the old build of libpng. After libpng caused all kinds of compaibility problems, all affected packages were updated. So your sync database had to have been different from what the packages you had locally.

trixrabbit · 2013-06-12 03:22:49

@WonderWoofy, I'm not sure...but I never install with -Sy or -Su

Right now, pacman --root /mnt -Syu tries to update but I get the conflict error at the end, so I've been reading the news...Is there somewhere will clearer steps on what to do..
1) Fix any non-official packages with files in /bin, /sbin or /usr/sbin to put those files in /usr/bin. The list of packages that are not in a repo that need to be fixed can be generated using:

What do they mean by "fix"? Like so many packages appear with the command that it fills my screen.

WonderWoofy · 2013-06-12 04:10:46

trixrabbit wrote:

What do they mean by "fix"? Like so many packages appear with the command that it fills my screen.

Considering this has been answered over and over and over and over again in this thread, it would probably serve you well to go back and actualy read some of the thread you are now posting in.

If the list of packages are filling your screen, either you have a crazy number of unofficial/unsupported packages that are also unmaintained. Or you don't ever update those packages. Or more likely, you are probably entering the command wrong (which has also been covered over and over and over and over again in this thread).

darkreaper476 · 2013-06-12 04:39:33

cfr wrote:

@darkreaper476,
Please post the command you used to generate that list. If you followed the instructions in the news, those packages should not for the most part be identified as problematic.

grep '^s\?bin/\|usr/sbin' /var/lib/pacman/local/*/files | cut -d ":" -f 1 | uniq | cut -d "/" -f 6

Is one of them listed on the first page.
I made the list more forum friendly is all..

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

Found nothing.

I didn't even see the news. lol as many when people say the go to the front page I thought that meant page 1 of this thread...

Followed, fixed. lol thanks!

Scimmia · 2013-06-12 06:29:19

trixrabbit wrote:

WonderWoofy wrote:
@cfr, from reading trixrabbit's posts elsewhere, he has apparently been unknowingly partially upgrading. In essence, he must have been doing pacman -Sy, then installing packages without doing the -Su.
no no no, I always install packages pacman -S and update system with pacman -Syu, never used anything else

Did you ever cancel an update? That's the same as running pacman -Sy.

toni · 2013-06-12 15:04:39

Now I am trying to update arch by following what is said in arch home to update my system by following the steps, but I am a little newbie in this yet... So I highly appreciate if someone can guide me in the right direction. I have some doubts in the below steps:

1) Fix any non-official packages with files in /bin, /sbin or /usr/sbin to put those files in /usr/bin.
My list is the following:

$ pacman -Qqo /bin /sbin /usr/sbin | pacman -Qm -
grub 0.97-21
grub 0.97-21
tcp_wrappers 7.6-15
xrdp 0.6.0-3

so as I understand I have to move them into /usr/bin

Could someone say me how to move all the files listed above using only one terminal command?

2) Make sure any packages in IgnorePkg or IgnoreGroup do not have files in /bin, /sbin, or /usr/sbin. Fix them if necessary.

How to perform step 2? what I have to type in the terminal?

3) If you have files in /bin, /sbin or /usr/sbin that are unowned by any package, you need to move them. Find a list using:

$ LC_ALL=C find /bin /sbin /usr/sbin -exec pacman -Qo -- {} + >/dev/null
error: No package owns /sbin/suspend
error: No package owns /sbin/fsck.btrfs

In my case, from the output above, do I have to perform something?

4) Ensure all partitions are mounted if using autofs. They may not automount when needed later in this update.
How to check this?

Thanks!

Last edited by toni (2013-06-12 15:05:23)

HalosGhost · 2013-06-12 15:13:44

No, you don't want to just move the files into /usr/bin. "Fixing the packages" refers to having the PKGBUILDs themselves install the files into /usr/bin; however, none of those packages are officially supported anymore, so you should switch to something else (if you wish to keep grub 1.x for instance, use aur/grub-legacy).

For (2), if you aren't aware of how to check this, odds are you don't need to. But, for safety's sake, you should do it anyway. These settings are in your /etc/pacman.conf.

But do this one step at a time; deal with these two before moving onto the next steps.

All the best,

-HG

Last edited by HalosGhost (2013-06-12 15:19:26)

karol · 2013-06-12 15:15:39

@toni
https://bbs.archlinux.org/viewtopic.php … 6#p1283396

progandy · 2013-06-12 15:17:40

Could someone say me how to move all the files listed above using only one terminal command?

Replace grub with grub-legacy (AUR), update tcp_wrappers and xrdp.

How to perform step 2? what I have to type in the terminal?

If you don't have added packages to Ignore... in your pacman.conf, then don't do anything.

3) If you have files in /bin, /sbin or /usr/sbin that are unowned by any package, you need to move them. Find a list using:

I suggest you move suspend to /usr/local/bin. fsck.btrfs should be there too if possible (It maybe that some scripts needs it in /usr/bin though)

4) Ensure all partitions are mounted if using autofs. They may not automount when needed later in this update.
How to check this?

Access all mountpounts with cd, ls I guess.

toni · 2013-06-12 15:29:54

progandy wrote:

Could someone say me how to move all the files listed above using only one terminal command?
Replace grub with grub-legacy (AUR), update tcp_wrappers and xrdp.
How to perform step 2? what I have to type in the terminal?
If you don't have added packages to Ignore... in your pacman.conf, then don't do anything.
3) If you have files in /bin, /sbin or /usr/sbin that are unowned by any package, you need to move them. Find a list using:
I suggest you move suspend to /usr/local/bin. fsck.btrfs should be there too if possible (It maybe that some scripts needs it in /usr/bin though)
4) Ensure all partitions are mounted if using autofs. They may not automount when needed later in this update.
How to check this?
Access all mountpounts with cd, ls I guess.

Ok, all the steps solved except I have a doubt when you say:
I suggest you move suspend to /usr/local/bin. fsck.btrfs should be there too if possible (It maybe that some scripts needs it in /usr/bin though)

how to do this?

and last step, 5, is a little bit confusing, Do I hav to do only pacman -Syu or what is said:

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

Scimmia · 2013-06-12 15:30:40

is fsck.btrfs a symlink you made or something? There is no such program for btrfs, the closest thing is btrfsck, but it does different things and is not compatible with the fsck.x tools. I would suggest getting rid of it.

toni · 2013-06-12 15:36:28

Scimmia wrote:

is fsck.btrfs a symlink you made or something? There is no such program for btrfs, the closest thing is btrfsck, but it does different things and is not compatible with the fsck.x tools. I would suggest getting rid of it.

They are not symbolic links:

$ ls -l /sbin/suspend /sbin/fsck.btrfs 
-rwxr-xr-x 1 root root 27184 abr 26 03:29 /sbin/fsck.btrfs
-rwxr-xr-x 1 root root   252 oct 27  2011 /sbin/suspend

so Do I have to move them into /usr/bin by performing:

mv /sbin/fsck.btrfs /usr/bin
mv /sbin/suspend /usr/bin

Thanks.

Scimmia · 2013-06-12 15:42:47

So what is fsck.btrfs? There is no such thing. Try 'file /sbin/fsck.btrfs' If it's a script, 'cat /sbin/fsck.btrfs'

toni · 2013-06-12 15:48:17

Scimmia wrote:

So what is fsck.btrfs? There is no such thing. Try 'file /sbin/fsck.btrfs' If it's a script, 'cat /sbin/fsck.btrfs'

$ file /sbin/fsck.btrfs
/sbin/fsck.btrfs: ELF 64-bit LSB  executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.32, BuildID[sha1]=8be7f2dd7d4faafe47883fc26c0dd61d6f4ee0b1, stripped

and what to do with suspend?

$ cat /sbin/suspend
 #!/bin/sh

 ## Checking if you are a root or not
 if ! [ -w / ]; then
   echo >&2 "This script must be run as root"
   exit 1
 fi

 s2ram -f

 sleep 2

 /etc/rc.d/oss restart 2>/tmp/oss.txt ||
 echo "OSS restart failed, check /tmp/oss.txt for advice"

ewaller · 2013-06-12 15:48:52

Split other thread and merged part 2 with the stickied thread on the filesystem change after the other thread changed topic.

Last edited by ewaller (2013-06-12 15:50:59)

Scimmia · 2013-06-12 15:57:01

So you have a binary fsck.btrfs which belongs to no package. Since there is no such thing, I don't know what you should do with it. Since pacman didn't put it there, you must have done it, so you tell us what needs to happen with it.

On the suspend script, it's calling s2ram, which is not a file in the official repos. It's also calling rc.d, so the script is out of date at the very least. Do you use this script? If not, I would just delete it.

victorhooi · 2013-06-13 00:19:47

Hi,

Hmm, I tried following the steps here:

https://mailman.archlinux.org/pipermail … 25042.html

However, when I get to upgrading filesystem:

pacman -Su
<tries to install filesystem>
error: failed to commit transaction (conflicting files)
filesystem: /sbin exists in filesystem
filesystem: /usr/sbin exists in filesystem
Errors occured, no packages were upgraded

I then ran:

pacman -Qo /bin /sbin /usr/sbin
error: failed to read file '/bin': No such file or directory
/sbin is owned by sysvinit 2.88-9
/usr/sbin is owned by consolekit 0.4.6-4
/usr/sbin is owned by initscripts 2012.10.1-1

Any thoughts on what I could try next?

Cheers,
Victor

Trilby · 2013-06-13 00:23:56

You could try reading this tread. All three of those conflicting packages are covered ad naseum.

xref · 2013-06-13 06:14:04

Hello everyone.

I'm confused about what I have to do to fix the filesystem issue in the update. Im sorry if this has been covered before. I've seen a different post on it but I didnt get the solution.

Doing the update I folllowed the steps on the landing page for archlinux.org

Here is what I did:

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

Which returns:

error: No package owns /bin
error: No package owns /sbin
mdk3 v6-1

2. paclist <repo> | awk ' { print $1 } ' | pacman -Ql - | grep ' /s\?bin/\| /usr/sbin/'

(I tried this with multilib, community, core and extra)

Returns nothing.

3. find /bin /sbin /usr/sbin -exec pacman -Qo -- {} + >/dev/null

returns:

error: No package owns /bin
error: No package owns /sbin

4. pacman -Syu --ignore filesystem,bash

Returns:
:: Synchronizing package databases...
core is up to date
extra is up to date
community is up to date
multilib is up to date
atlassian is up to date
:: Starting full system upgrade...
warning: filesystem: ignoring package upgrade (2013.03-2 => 2013.05-2)
there is nothing to do

5. pacman -S bash -does a reinstall.

6. pacman -Su

:: Starting full system upgrade...
resolving dependencies...
looking for inter-conflicts...

Packages (1): filesystem-2013.05-2

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

:: Proceed with installation? [Y/n]
(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%
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.

Now my question is what to do here? Should I move all the files in /bin /sbin /usr/sbin somewhere? What am I missing?

I'm sorry for the lack of knowledge here but I'm begging someone to point me in the right direction, preferably with an explanation of what I'm doing wrong and how to fix it.

Thanks for reading my post.

Last edited by xref (2013-06-13 06:15:36)

Scimmia · 2013-06-13 06:20:49

It looks like the mdk3 package is causing your trouble. What is it? It's not in the official repos or in the AUR. It needs to be fixed to install it's files to /usr/bin. If it's not critical for your system, I would suggest uninstalling it, finishing the update, then fixing the package to reinstall it.

If /bin or /sbin are empty, you can delete them. If not, I'm guessing that whatever is in them belongs to that stray package?

jasonwryan · 2013-06-13 06:34:05

Merging with the sticky...

Lone_Wolf · 2013-06-13 12:12:33

@xref :

looking at

pacman -Syu --ignore filesystem,bash

Returns:
:: Synchronizing package databases...
core is up to date
extra is up to date
community is up to date
multilib is up to date
atlassian is up to date

you use 1 unofficial repo, atlassian .

do step 2 like this :

paclist atlassian | awk ' { print $1 } ' | pacman -Ql - | grep ' /s\?bin/\| /usr/sbin/'

Arch Linux

#501 2013-06-11 23:47:45

Re: filesystem Update Error /bin exists in filesystem

#502 2013-06-12 00:42:09

Re: filesystem Update Error /bin exists in filesystem

#503 2013-06-12 02:55:03

Re: filesystem Update Error /bin exists in filesystem

#504 2013-06-12 03:01:05

Re: filesystem Update Error /bin exists in filesystem

#505 2013-06-12 03:22:49

Re: filesystem Update Error /bin exists in filesystem

#506 2013-06-12 04:10:46

Re: filesystem Update Error /bin exists in filesystem

#507 2013-06-12 04:39:33

Re: filesystem Update Error /bin exists in filesystem

#508 2013-06-12 06:29:19

Re: filesystem Update Error /bin exists in filesystem

#509 2013-06-12 15:04:39

Re: filesystem Update Error /bin exists in filesystem

#510 2013-06-12 15:13:44

Re: filesystem Update Error /bin exists in filesystem

#511 2013-06-12 15:15:39

Re: filesystem Update Error /bin exists in filesystem

#512 2013-06-12 15:17:40

Re: filesystem Update Error /bin exists in filesystem

#513 2013-06-12 15:29:54

Re: filesystem Update Error /bin exists in filesystem

#514 2013-06-12 15:30:40

Re: filesystem Update Error /bin exists in filesystem

#515 2013-06-12 15:36:28

Re: filesystem Update Error /bin exists in filesystem

#516 2013-06-12 15:42:47

Re: filesystem Update Error /bin exists in filesystem

#517 2013-06-12 15:48:17

Re: filesystem Update Error /bin exists in filesystem

#518 2013-06-12 15:48:52

Re: filesystem Update Error /bin exists in filesystem

#519 2013-06-12 15:57:01

Re: filesystem Update Error /bin exists in filesystem

#520 2013-06-13 00:19:47

Re: filesystem Update Error /bin exists in filesystem

#521 2013-06-13 00:23:56

Re: filesystem Update Error /bin exists in filesystem

#522 2013-06-13 06:14:04

Re: filesystem Update Error /bin exists in filesystem

#523 2013-06-13 06:20:49

Re: filesystem Update Error /bin exists in filesystem

#524 2013-06-13 06:34:05

Re: filesystem Update Error /bin exists in filesystem

#525 2013-06-13 12:12:33

Re: filesystem Update Error /bin exists in filesystem

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