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#1 2013-05-31 15:48:22

Alcasa
Member
Registered: 2013-05-18
Posts: 33

filesystem Update Error /bin exists in filesystem

Hello,

everytime I try to update filesystem to 2013.05, I get this error. Does anyone know a solution to this. I would guess that it could be related to file corruption in pacman, as my system is otherwise working just fine.

Here is the response I get, when I try to reinstall filesystem:

arch # pacman -S filesystem
resolving dependencies...
looking for inter-conflicts...

Packages (1): filesystem-2013.05-1

Total Installed Size:   0,01 MiB
Net Upgrade Size:       -0,30 MiB

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

Last edited by Alcasa (2013-05-31 15:49:07)

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#2 2013-05-31 15:50:47

teateawhy
Member
From: GER
Registered: 2012-03-05
Posts: 1,001
Website

Re: filesystem Update Error /bin exists in filesystem

Are you using [testing] ?

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#3 2013-05-31 15:52:59

Scimmia
Bug Wrangler
Registered: 2012-09-01
Posts: 4,695

Re: filesystem Update Error /bin exists in filesystem

Always subscribe to arch-dev-public when running testing.

https://mailman.archlinux.org/pipermail … 25003.html

Very late edit: Do not follow these instructions. They were a draft from when this update was in testing. Always follow the instructions on the front page.

Last edited by Scimmia (2013-06-06 17:34:24)

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#4 2013-05-31 15:55:11

WorMzy
Forum Moderator
From: England
Registered: 2010-06-16
Posts: 4,862

Re: filesystem Update Error /bin exists in filesystem

If you're going to use testing, you should really keep up to date with the mailing lists.


...in fact, you should really keep up to date with the mailing lists anyway, but it's especially important for [testing] users.

Relevant thread: https://mailman.archlinux.org/pipermail … 24908.html


Sakura:-
Mobo: ASUS P8Z77-V PRO // Processor: Intel Core i7-3770K 3.4GHz // GFX: nVidia GeForce GTX 970 Ti // RAM: 32GB (4x 8GB) Corsair DDR3 (@ 2133MHz) // Storage: 1x 3TB Seagate SATAII 5x 1TB Samsung SATAII, 2x 120GB Corsair SSD

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#5 2013-05-31 16:16:28

Gusar
Member
Registered: 2009-08-25
Posts: 3,398

Re: filesystem Update Error /bin exists in filesystem

I was waiting for a thread like this to appear smile

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#6 2013-05-31 16:50:50

WonderWoofy
Member
From: Los Gatos, CA
Registered: 2012-05-19
Posts: 8,412

Re: filesystem Update Error /bin exists in filesystem

Gusar wrote:

I was waiting for a thread like this to appear smile

It was surely inevitable.  I was very shcoed to see how fast this move was actually done after Allan announced he was bored and wanted to get moving on it.  I went through the update this morning and it went smooth as butter.  But I first found all the AUR packages that I had that were still utilizing /usr/sbin, /bin, and /sbin and took care of those first.  I was surprised to find I only had four that were potential conflicts (f2fs-tools-git, connman-git, hfsprogs, and hostsblock).

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#7 2013-05-31 16:52:19

WorMzy
Forum Moderator
From: England
Registered: 2010-06-16
Posts: 4,862

Re: filesystem Update Error /bin exists in filesystem

Gusar wrote:

I was waiting for a thread like this to appear smile

Same. There's going to be a lot in the coming weeks.

For anyone who's encountered this problem, do not use pacman's --force flag to install the filesystem update.

Check your AUR packages for updates, and update them. Remove or rebuild (after modifying the PKGBUILD) any unsupported packages that still place binaries in /bin, /sbin or /usr/sbin. If you have untracked files in those directories, remove them, or move them to /usr/local/bin.

Get a list of packages that owns files in /bin, /sbin, and /usr/sbin (tested in bash and zsh):

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

Find unpackaged files in /bin, /sbin, and /usr/sbin:

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

Again, do NOT use pacman's --force flag to install the filesystem update.


Sakura:-
Mobo: ASUS P8Z77-V PRO // Processor: Intel Core i7-3770K 3.4GHz // GFX: nVidia GeForce GTX 970 Ti // RAM: 32GB (4x 8GB) Corsair DDR3 (@ 2133MHz) // Storage: 1x 3TB Seagate SATAII 5x 1TB Samsung SATAII, 2x 120GB Corsair SSD

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#8 2013-05-31 16:52:30

ewaller
Administrator
From: Pasadena, CA
Registered: 2009-07-13
Posts: 12,253

Re: filesystem Update Error /bin exists in filesystem

Moving to testing


Nothing is too wonderful to be true, if it be consistent with the laws of nature -- Michael Faraday
Like you, I have no idea what you are doing, but I am pretty sure it is wrong...Jasonwryan
----
How to Ask Questions the Smart Way

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#9 2013-05-31 16:54:21

WonderWoofy
Member
From: Los Gatos, CA
Registered: 2012-05-19
Posts: 8,412

Re: filesystem Update Error /bin exists in filesystem

WorMzy wrote:

For anyone who's encountered this problem, do not use pacman's --force flag to install the filesystem update.
...
Again, do NOT use pacman's --force flag to install the filesystem update.

Though this is good advice, I would like to point out that pacman in its current form will not actually let you replace a directory with a file.  The symlink coulnts as a file, so the force won't happen anyway.  Of course this assumes that pacman itself is up to date.

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#10 2013-05-31 16:57:15

WorMzy
Forum Moderator
From: England
Registered: 2010-06-16
Posts: 4,862

Re: filesystem Update Error /bin exists in filesystem

I hadn't checked, though I did see Allan saying something like that. It never hurts to remind people not to force things though.


Sakura:-
Mobo: ASUS P8Z77-V PRO // Processor: Intel Core i7-3770K 3.4GHz // GFX: nVidia GeForce GTX 970 Ti // RAM: 32GB (4x 8GB) Corsair DDR3 (@ 2133MHz) // Storage: 1x 3TB Seagate SATAII 5x 1TB Samsung SATAII, 2x 120GB Corsair SSD

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#11 2013-05-31 17:15:37

Gusar
Member
Registered: 2009-08-25
Posts: 3,398

Re: filesystem Update Error /bin exists in filesystem

WonderWoofy wrote:

I was very shcoed to see how fast this move was actually done after Allan announced he was bored and wanted to get moving on it.

Yeah, I too was surprised to see it already.

WonderWoofy wrote:

I went through the update this morning and it went smooth as butter.

I was actually sad at how uneventful it was smile. I expected my systems to explode. But nothing. Then I thought "ok, maybe they work now, but on a reboot things will surely go to hell". Nope, after the reboot the system came up as always. Boring smile

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#12 2013-05-31 20:34:50

jasonwryan
Forum & Wiki Admin
From: .nz
Registered: 2009-05-09
Posts: 18,086
Website

Re: filesystem Update Error /bin exists in filesystem

Gusar wrote:

I was waiting for a thread like this to appear smile

Stickying until it passes through...


Arch + dwm   •   Mercurial repos  •   Github

Registered Linux User #482438

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#13 2013-05-31 21:22:51

combuster
Member
From: Serbia
Registered: 2008-09-30
Posts: 711
Website

Re: filesystem Update Error /bin exists in filesystem

Do NOT, I repeat DO NOT exit the terminal with root priviliges untill you do a

pacman -Su

after

pacman -Syu --ignore filesystem

I had to chroot from flash and pacstrap the filesystem package from testing to boot at all. Even in the  same session I couldn't get a terminal with root privileges. My mistake... smile

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#14 2013-05-31 22:10:57

Jristz
Member
From: America/Santiago
Registered: 2011-06-11
Posts: 903

Re: filesystem Update Error /bin exists in filesystem

I recommend using su and update all trow pacman after return to normal user on terminal
only for safenessness

Allan announced he was bored

me too, I moved to testing temporally for the fact of /usr/bin-iness
Now I only noticed any change only a sistem Megas more light... I was deceptionated, now make the same for usr/local/sbin (any can say that I give a +1 to that?)


Well, I suppose that this is somekind of signature, no?

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#15 2013-06-01 02:25:44

Jodell
Member
Registered: 2009-10-09
Posts: 285

Re: filesystem Update Error /bin exists in filesystem

combuster wrote:

Do NOT, I repeat DO NOT exit the terminal with root priviliges untill you do a

pacman -Su

after

pacman -Syu --ignore filesystem

I had to chroot from flash and pacstrap the filesystem package from testing to boot at all. Even in the  same session I couldn't get a terminal with root privileges. My mistake... smile

Are you sure? I used sudo to do the upgrade and I was fine.

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#16 2013-06-01 02:31:28

WonderWoofy
Member
From: Los Gatos, CA
Registered: 2012-05-19
Posts: 8,412

Re: filesystem Update Error /bin exists in filesystem

What he means is that you need to update filesystem before you reboot.  By moving everything into /usr/bin, and then not putting in place the symlinks necessary to resolve paths like /sbin, /bin, and /usr/bin you will render your system unbootable because it will not be able to find many of the necessary binaries to get your system going.

Whether you used sudo or su doesn't really matter as long as you do both steps.

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#17 2013-06-01 02:39:03

Trilby
Forum Moderator
From: Massachusetts, USA
Registered: 2011-11-29
Posts: 13,373
Website

Re: filesystem Update Error /bin exists in filesystem

WonderWoofy wrote:

I was very shcoed to see how fast this move was actually done after Allan announced he was bored.

If Allan gets bored, stuff gets broken.


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#18 2013-06-01 02:56:19

WonderWoofy
Member
From: Los Gatos, CA
Registered: 2012-05-19
Posts: 8,412

Re: filesystem Update Error /bin exists in filesystem

That is why it was so shocking to see things get done so damn smoothly.  In this case, it would seem that Allan broke his ways of breaking shit.

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#19 2013-06-01 03:27:54

progandy
Member
Registered: 2012-05-17
Posts: 2,143

Re: filesystem Update Error /bin exists in filesystem

What happens with post-install scripts if binaries cannot be found? There are absolute references to /usr/sbin, /sbin, /bin in some scripts I think.
This was my updatepath:
- sync databases
- get list of pacakges with files in /bin, /sbin, /usr/sbin.
- update packages from this list
- make sure /bin, /sbin, /usr/sbin are clean.
- update filesystem
- reinstall packages from said list (make sure install scripts are executed properly)
- update everything

Another idea:
- move everything to /usr/bin
- symlink /bin, /sbin, /usr/sbin.
- update everything, ignore filesystem
- remove symlinks
- update filesystem
(- update everything)

Btw: As soon as I get a conflict during a normal update, I open a root busybox shell. This means I have a backup shell to fix a borked system without reboots and bootcds (worst case: use pacman cache and extract some old packages manually and delete broken upgrades)

Last edited by progandy (2013-06-01 03:40:53)

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#20 2013-06-01 03:55:58

donniezazen
Member
From: Salt Lake City
Registered: 2011-06-24
Posts: 671
Website

Re: filesystem Update Error /bin exists in filesystem

WorMzy wrote:

For anyone who's encountered this problem, do not use pacman's --force flag to install the filesystem update.

And that should be enough...   With pacman-4.1 (and the patched 4.0.x
versions in our repos since the /lib move), anybody just doing a "pacman
-Syu" will get a conflict.  Using --force in pamcan-4.1 will not break
things (I think...) as --force does not allow overwriting a directory
with a file.
   People using pacman-4.0.x and --force could still break
their system.

Allan

For sake of curiosity, are we talking about different things here?

Last edited by donniezazen (2013-06-01 03:56:46)

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#21 2013-06-01 05:39:28

Allan
Developer
From: Brisbane, AU
Registered: 2007-06-09
Posts: 10,327
Website

Re: filesystem Update Error /bin exists in filesystem

progandy wrote:

What happens with post-install scripts if binaries cannot be found? There are absolute references to /usr/sbin, /sbin, /bin in some scripts I think.

There should not be...  post_install scripts should not use the full path.

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#22 2013-06-01 05:58:22

Allan
Developer
From: Brisbane, AU
Registered: 2007-06-09
Posts: 10,327
Website

Re: filesystem Update Error /bin exists in filesystem

WorMzy wrote:

Get a list of packages that owns files in /bin, /sbin, and /usr/sbin (tested in bash and zsh):

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

Impressive....

pacman -Qo /bin /sbin /usr/sbin

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#23 2013-06-01 06:38:51

WorMzy
Forum Moderator
From: England
Registered: 2010-06-16
Posts: 4,862

Re: filesystem Update Error /bin exists in filesystem

Allan wrote:
WorMzy wrote:

Get a list of packages that owns files in /bin, /sbin, and /usr/sbin (tested in bash and zsh):

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

Impressive....

pacman -Qo /bin /sbin /usr/sbin

Oh yeah.. x_x

donniezazen wrote:

For sake of curiosity, are we talking about different things here?

No, I think pamcan is a typo. Also see post #9 and #10.


Sakura:-
Mobo: ASUS P8Z77-V PRO // Processor: Intel Core i7-3770K 3.4GHz // GFX: nVidia GeForce GTX 970 Ti // RAM: 32GB (4x 8GB) Corsair DDR3 (@ 2133MHz) // Storage: 1x 3TB Seagate SATAII 5x 1TB Samsung SATAII, 2x 120GB Corsair SSD

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#24 2013-06-01 07:03:41

Alambre
Member
Registered: 2011-11-30
Posts: 11

Re: filesystem Update Error /bin exists in filesystem

in my case, just move the folders, and delete it (when it empty), I did not know the final result

[root@bootstrap:/home/alambre] # ls /usr/sbin /sbin /bin -la                                                       
lrwxrwxrwx 1 root root 7 may 31 15:40 /bin -> usr/bin
lrwxrwxrwx 1 root root 7 may 31 15:40 /sbin -> usr/bin
lrwxrwxrwx 1 root root 3 may 31 15:40 /usr/sbin -> bin

cp /my/usr/sbin/* /bin
cp /my/bin/* /bin

Last edited by Alambre (2013-06-01 07:18:49)

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#25 2013-06-01 07:08:22

HalosGhost
Member
From: Twin Cities, MN
Registered: 2012-06-22
Posts: 1,485
Website

Re: filesystem Update Error /bin exists in filesystem

Alambre wrote:

in my case, just move the folders, and delete it (when it empty), I did not know the final result
[root@bootstrap:/home/alambre] # ls /usr/sbin /sbin /bin -la                                                       
lrwxrwxrwx 1 root root 7 may 31 15:40 /bin -> usr/bin
lrwxrwxrwx 1 root root 7 may 31 15:40 /sbin -> usr/bin
lrwxrwxrwx 1 root root 3 may 31 15:40 /usr/sbin -> bin

cp /my/usr/sbin/* /bin
cp /my/bin/* /bin

Two things.

1. code tags are your friends

2. For the love of god, don't use that ugly workaround.

All the best,

-HG


"All errors are ᴘᴇʙᴋᴀᴄ errors—It's just a matter of narrowing down which keyboard and chair." -Trilby
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