filesystem Update Error /bin exists in filesystem

geo909 · 2013-07-11 15:25:48

Success!

jorge@flamingo:/$ sudo 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%
(1/1) checking available disk space                [#########################] 100%
(1/1) upgrading filesystem

So, I go on and reboot now, right?

EDIT: sounds like common sense but I'd rather be paranoid than sorry.

Last edited by geo909 (2013-07-11 15:32:07)

Scimmia · 2013-07-11 15:55:54

Yep, once filesystem upgrades successfully, you're OK to keep using the system like normal, including a reboot if you want.

geo909 · 2013-07-11 16:02:42

Scimmia wrote:

Yep, once filesystem upgrades successfully, you're OK to keep using the system like normal, including a reboot if you want.

Indeed, I rebooted and everything seems to be fine. Thanks a lot for your advice!!

anthillsocial · 2013-07-17 10:24:56

Hi,

I Just ran:

$ sudo pacman -Su

And got this error:

(512/512) 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.

As per these instructions:
https://www.archlinux.org/news/binaries … ervention/

I ran:

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

Which output:

grub-common 2.00-1
hfsprogs 332.25-6
samsung-unified-driver 4.00.39-3

Now i'm a little confused by what I need to do next as I don't quite understand the instruction (from link above ) to:

1) Fix any non-official packages with files in /bin, /sbin or /usr/sbin to put those files in /usr/bin

Does this mean move all the files in /bin to /usr/bin ?
(Which doesn't feel quite right)

Or does it mean move files related to; grub-common 2.00-1, hfsprogs 332.25-6 and samsung-unified-driver 4.00.39-3 to /usr/bin?
In which case I'm not sure which those are?

As always any help gratefully received.
Tom

Last edited by anthillsocial (2013-07-17 11:53:11)

IsSuE · 2013-07-17 10:31:15

Update those packages, grub from offical repos and the other two from AUR, this should fix your problems.

anthillsocial · 2013-07-17 11:52:31

Excellent - worked perfectly - thank you.

davidm · 2013-07-21 18:32:41

ilesystem: /bin exists in filesystem
filesystem: /sbin exists in filesystem
filesystem: /usr/sbin exists in filesystem
Errors occurred, no packages were upgraded.

[root@archreborn ~]# pacman -Qqo /bin /sbin /usr/sbin | pacman -Qm -
grub-common 2.00-1
zfs-fuse 0.7.0-5

(zfs-fuse doesn't seem to be updated in AUR and it is not critical so I planned to sort it out later and simply removed it)

[root@archreborn ~]# pacman -R zfs-fuse
checking dependencies...

Packages (1): zfs-fuse-0.7.0-5

Total Removed Size:   4.30 MiB

:: Do you want to remove these packages? [Y/n] 
(1/1) removing zfs-fuse                                                                                 [#############################################################] 100%
warning: /etc/conf.d/zfs-fuse saved as /etc/conf.d/zfs-fuse.pacsave

resolving dependencies...
looking for inter-conflicts...
:: grub and grub-common are in conflict. Remove grub-common? [y/N] y
:: grub and grub-bios are in conflict. Remove grub-bios? [y/N] y

Packages (3): grub-bios-2.00-1 [removal]  grub-common-2.00-1 [removal]  grub-2.00.5043-2

Total Installed Size:   17.86 MiB
Net Upgrade Size:       2.29 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%
(3/3) checking available disk space                                                                     [#############################################################] 100%
(1/2) removing grub-common                                                                              [#############################################################] 100%
warning: /boot/grub/grub.cfg saved as /boot/grub/grub.cfg.pacsave
(2/2) removing grub-bios                                                                                [#############################################################] 100%
(1/1) installing grub                                                                                   [#############################################################] 100%
Copying /boot/grub/grub.cfg.pacsave to /boot/grub/grub.cfg
Generating grub.cfg.example config file...
This may fail on some machines running a custom kernel.
done.
Optional dependencies for grub
    freetype2: For grub-mkfont usage [installed]
    fuse: For grub-mount usage [installed]
    dosfstools: For grub-mkrescue FAT FS and EFI support
    efibootmgr: For grub-install EFI support
    libisoburn: Provides xorriso for generating grub rescue iso using grub-mkrescue
    os-prober: To detect other OSes when generating grub.cfg in BIOS systems
    mtools: For grub-mkrescue FAT FS support

[root@archreborn ~]# pacman -Qqo /bin /sbin /usr/sbin | pacman -Qm -
[root@archreborn ~]# pacman -Syu
:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
:: Starting full system upgrade...
:: Replace pyqt-common with extra/pyqt4-common? [Y/n] 
:: Replace python2-pyqt with extra/python2-pyqt4? [Y/n] 
resolving dependencies...
warning: dependency cycle detected:
warning: torsocks will be installed before its tor dependency
looking for inter-conflicts...

Total Installed Size:   2508.42 MiB
Net Upgrade Size:       -74.17 MiB

:: Proceed with installation? [Y/n] 
(525/525) checking keys in keyring                                                                      [#############################################################] 100%
(525/525) checking package integrity                                                                    [#############################################################] 100%
(525/525) loading package files                                                                         [#############################################################] 100%
(525/525) 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.

[root@archreborn ~]# pacman -Qqo /bin /sbin /usr/sbin | pacman -Qm -
[root@archreborn ~]#

No special other repos are enabled.

#[testing]
#Include = /etc/pacman.d/mirrorlist

[core]
Include = /etc/pacman.d/mirrorlist

[extra]
Include = /etc/pacman.d/mirrorlist

#[community-testing]
#Include = /etc/pacman.d/mirrorlist

[community]
Include = /etc/pacman.d/mirrorlist

[root@archreborn ~]# find /bin /sbin /usr/sbin -exec pacman -Qo -- {} + >/dev/null
[root@archreborn ~]#

I have a few things compiled from tarballs but they use /usr/local/

Any hints?

Trilby · 2013-07-21 18:36:40

Read step 5 again - you need to execute the three commands there in proper sequence. `pacman -Syu` is expected to fail, which is why this was a news-worthy item.

davidm · 2013-07-21 18:57:58

Trilby wrote:

Read step 5 again - you need to execute the three commands there in proper sequence. `pacman -Syu` is expected to fail, which is why this was a news-worthy item.

D'oh! Sorry.

Anyway I manually upgraded a bunch of packages which were using the old structure and am in the middle of a 'pacman -Syu' now which appears to be working thus far (141/476 in on upgrading packages). So we'll see how that goes. I have a couple terminals open just in case.

edit:

......and I rebooted. Success! Thanks again.

Last edited by davidm (2013-07-21 19:34:09)

ariel · 2013-07-21 19:30:26

Hi all,

I post this reply with hope it may help others with similar situation.

I also had this issue with filesystem. I solved it with

 $ yaourt -Syu --ignore filesystem

which worked well, but I shouldn't use yaourt for this task because

1. I couldn't install filesystem via yaourt

 $ yaourt -Su
bash: /usr/bin/yaourt: /bin/bash: bad interpreter: No such file or directory

2. I couldn't use su

$ su
su: failed to execute /bin/bash: No such file or directory

both because bash is now in /usr/bin, and I needed root access to change it...

my solution:

$ cp /usr/bin/yaourt ~/yaourt/xyz 
$ chown $myusername$ ~/yaourt/xyz
(here I changed the first line in xyz to #!/usr/bin/bash)
$ /home/$myusername$/yaourt/xyz -Su

==> Software upgrade (new version) :
core/filesystem 2013.03-2 -> 2013.05-2

==> Continue upgrade ? [Y/n]
==> [V]iew package detail   [M]anually select packages
==> --------------------------------------------------

...

(1/1) upgrading filesystem                         [###########] 100%

Done!

cfr · 2013-07-21 20:44:49

Ingenious but wouldn't it have been easier to just use pacman?

Trilby · 2013-07-21 21:03:04

Or you could have ignored filesystem and bash, like the original instructions said to.

As you didn't, you may have created many currently unseen problems due to failed post-install scripts in any package that was upgraded.

b0f00narch · 2013-07-30 16:26:48

After update, I have only grub. How do you boot in system from grub ?
How do I load kernel ?

I did
setup (hd0)
kernel (hd0,0)/boot/vmlinuz26
boot

kernel panic: unable to mount root fs on unknown block(0,0)

Last edited by b0f00narch (2013-07-30 16:47:54)

LinuxFTW · 2013-07-30 21:29:06

sudo pacman -Qqo /bin /sbin /usr/sbin | pacman -Qm -
gconf-thread 3.2.5-3
initscripts 2012.10.1-1
lightdm-bzr 1632-1
lightdm-gtk3-greeter-bzr 92-1

I'm extremely lost. How do I "fix" these packages? I know I need to move them to /usr/bin but when I can't find them in those directories (unless the file name is diff?). Can someone please explain this to me.

jasonwryan · 2013-07-30 21:31:49

You uninstall/replace/rebuild them. AUR packages are your responsibility to manage, not pacman's.

WorMzy · 2013-07-30 21:58:39

b0f00narch wrote:

After update, I have only grub. How do you boot in system from grub ?
How do I load kernel ?
I did
setup (hd0)
kernel (hd0,0)/boot/vmlinuz26
boot
kernel panic: unable to mount root fs on unknown block(0,0)

I suggest you boot a LiveCD and fix grub from there. Unless you're incredibly out of date, you won't have a "vmlinuz26", Arch has had a "standard" 3.x kernel since mid-2011, and a "lts" 3.x kernel since early 2012.

cfr · 2013-07-31 00:31:55

@LinuxFTW,
Have you updated your system to use systemd? I notice you still have initscripts installed.

If not, update your system to use systemd (following the instructions in the wiki) before starting the latest update as it will be a lot easier to do one thing at a time.

If you are already using systemd, install systemd-sysvcompat (and let pacman remove initscripts). Then (optionally) remove the init=/usr/lib/systemd/systemd option from your kernel command line. That will simplify things somewhat and will at least deal with one of the obstructing packages.

Last edited by cfr (2013-07-31 00:33:31)

LinuxFTW · 2013-07-31 02:29:50

Yes, I am using systemd.

WonderWoofy · 2013-07-31 02:46:22

Okay, that is good LinuxFTW. So update the lightdm stuff through the AUR. Then install gconf from the repos. Then remove initscripts (which wil occur automatically if you install systemd-sysvcompat). Then you should be good to go.

LinuxFTW · 2013-07-31 03:08:05

I got it to update the packages. Now to see if it survives restart.

pielgrzym · 2013-08-02 08:42:21

Any way to make it quickly work? I just need to set up nfs share and move stuff out of hd (leaving Arch - just need some basic reliability when it comes to updating the system, don't have patience to fix such failiures anymore, just need a slim distro that works. Crunchbang perhaps?).

Tried running it with kernel opt 'init=/usr/bin/init' but unfortunately partition is encrypted and boot stalls on some system-mapper errors

Last edited by pielgrzym (2013-08-02 08:47:24)

Trilby · 2013-08-02 11:37:15

??? Pielgrzym, first, you haven't posted on any problem, so how can we know what you need to do to get "it" to work?

If you haven't screwed up this update by not following the instructions, there is a *very* quick way to get it to work: follow the instructions. They might take as little as a minute, or should be no more than 10 minutes if you have many outdated/aur packages.

But, if you are leaving arch, why do you need to update it in the first place? This has nothing to do with having access to the files on the disk. Any other distro or OS should be able to access disks just fine even if this upgrade was completely botched. (edit: I just saw you have encrypted partitions - I guess that *might* be different, I'm not sure. But I'm pretty sure other distros can use encrypted filesystems just as well as arch to just access data).

Last edited by Trilby (2013-08-02 11:38:22)

pielgrzym · 2013-08-06 12:14:51

Trilby, sorry - I had a problem with binaries missing due to improper filesystem update. Wanted to make it work to copy the files asap. Didn't come up with any reasonable solution so just fell back to baking an usb stick with live installation and decrypting the partitions manually.

Bye.

yiuin · 2013-08-07 19:50:50

ariel wrote:

Hi all,
I post this reply with hope it may help others with similar situation.
I also had this issue with filesystem. I solved it with
 $ yaourt -Syu --ignore filesystem 
which worked well, but I shouldn't use yaourt for this task because
1. I couldn't install filesystem via yaourt
 $ yaourt -Su
bash: /usr/bin/yaourt: /bin/bash: bad interpreter: No such file or directory 
2. I couldn't use su
$ su
su: failed to execute /bin/bash: No such file or directory
both because bash is now in /usr/bin, and I needed root access to change it...
my solution:
$ cp /usr/bin/yaourt ~/yaourt/xyz 
$ chown $myusername$ ~/yaourt/xyz
(here I changed the first line in xyz to #!/usr/bin/bash)
$ /home/$myusername$/yaourt/xyz -Su

==> Software upgrade (new version) :
core/filesystem 2013.03-2 -> 2013.05-2

==> Continue upgrade ? [Y/n]
==> [V]iew package detail   [M]anually select packages
==> --------------------------------------------------

...

(1/1) upgrading filesystem                         [###########] 100%
Done!

Much easier to just use

su -s /usr/bin/bash

Trilby · 2013-08-07 20:21:56

Much much easier to use pacman - and to follow the instructions in the news item. Lets not give the impression that very odd workarounds that worked for one user should be recommended. That is *not* a good solution.

Arch Linux

#801 2013-07-11 15:25:48

Re: filesystem Update Error /bin exists in filesystem

#802 2013-07-11 15:55:54

Re: filesystem Update Error /bin exists in filesystem

#803 2013-07-11 16:02:42

Re: filesystem Update Error /bin exists in filesystem

#804 2013-07-17 10:24:56

Re: filesystem Update Error /bin exists in filesystem

#805 2013-07-17 10:31:15

Re: filesystem Update Error /bin exists in filesystem

#806 2013-07-17 11:52:31

Re: filesystem Update Error /bin exists in filesystem

#807 2013-07-21 18:32:41

Re: filesystem Update Error /bin exists in filesystem

#808 2013-07-21 18:36:40

Re: filesystem Update Error /bin exists in filesystem

#809 2013-07-21 18:57:58

Re: filesystem Update Error /bin exists in filesystem

#810 2013-07-21 19:30:26

Re: filesystem Update Error /bin exists in filesystem

#811 2013-07-21 20:44:49

Re: filesystem Update Error /bin exists in filesystem

#812 2013-07-21 21:03:04

Re: filesystem Update Error /bin exists in filesystem

#813 2013-07-30 16:26:48

Re: filesystem Update Error /bin exists in filesystem

#814 2013-07-30 21:29:06

Re: filesystem Update Error /bin exists in filesystem

#815 2013-07-30 21:31:49

Re: filesystem Update Error /bin exists in filesystem

#816 2013-07-30 21:58:39

Re: filesystem Update Error /bin exists in filesystem

#817 2013-07-31 00:31:55

Re: filesystem Update Error /bin exists in filesystem

#818 2013-07-31 02:29:50

Re: filesystem Update Error /bin exists in filesystem

#819 2013-07-31 02:46:22

Re: filesystem Update Error /bin exists in filesystem

#820 2013-07-31 03:08:05

Re: filesystem Update Error /bin exists in filesystem

#821 2013-08-02 08:42:21

Re: filesystem Update Error /bin exists in filesystem

#822 2013-08-02 11:37:15

Re: filesystem Update Error /bin exists in filesystem

#823 2013-08-06 12:14:51

Re: filesystem Update Error /bin exists in filesystem

#824 2013-08-07 19:50:50

Re: filesystem Update Error /bin exists in filesystem

#825 2013-08-07 20:21:56

Re: filesystem Update Error /bin exists in filesystem

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