Arch Linux

Scimmia

Fellow

Registered: 2012-09-01

Posts: 12,369

Re: filesystem Update Error /bin exists in filesystem

They will be symlinked, but if I understand correctly, future versions of pacman won't traverse the symlinks when installing, so the files need to be moved to /usr/bin in the package itself.

Allan

Pacman

From: Brisbane, AU

Registered: 2007-06-09

Posts: 11,503

Website

Re: filesystem Update Error /bin exists in filesystem

What would fix any package mean: 1) recompile by editing PKGBUILD or 2) manually move executables to /usr/bin? Of course recompiling is the best solution but I am asking in case I hit wall modifying PKGBUILD will it be okay to move files from /bin, /sbin, and /usr/sbin to /usr/bin by hand?

Recompiling is best, but you can move them if you update the filelist file in /var/lib/pacman/local/<pkgname>

Will /bin, /sbin, and /usr/sbin be deleted or symlinked to /usr/bin?

symlinks.

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Mr Green

Forum Fellow

From: U.K.

Registered: 2003-12-21

Posts: 5,920

Website

Re: filesystem Update Error /bin exists in filesystem

Just updated testing repo on a virtual machine

pacman -Syu --ignore filesystem
pacman -Su

without a problem, syslinux did not appear on reboot easy to fix, now working fine

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karol

Archivist

Registered: 2009-05-06

Posts: 25,440

Re: filesystem Update Error /bin exists in filesystem

Just updated testing repo on a virtual machine

pacman -Syu --ignore filesystem
pacman -Su

without a problem, syslinux did not appear on reboot easy to fix, now working fine

Why not

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

as the latest version of the instructions says?
https://mailman.archlinux.org/pipermail … 25043.html

Mr Green

Forum Fellow

From: U.K.

Registered: 2003-12-21

Posts: 5,920

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Re: filesystem Update Error /bin exists in filesystem

I never read instructions. Only this thread... I will reinstall and try again

:: Synchronizing package databases...
 testing is up to date
 core is up to date
 extra is up to date
 community-testing is up to date
 community is up to date
 archbang is up to date
:: Starting full system upgrade...
warning: bash: ignoring package upgrade (4.2.045-1 => 4.2.045-4)
warning: filesystem: ignoring package upgrade (2013.03-2 => 2013.05-2)
resolving dependencies...
warning: cannot resolve "libmbim", a dependency of "modemmanager"
warning: cannot resolve "libmbim", a dependency of "modemmanager"
:: The following package cannot be upgraded due to unresolvable dependencies:
      modemmanager

:: Do you want to skip the above package for this upgrade? [y/N] 

Last edited by Mr Green (2013-06-03 09:55:37)

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karol

Archivist

Registered: 2009-05-06

Posts: 25,440

Re: filesystem Update Error /bin exists in filesystem

If you're using [testing], you should be subscribed to arch-dev-public ML.

Mr Green

Forum Fellow

From: U.K.

Registered: 2003-12-21

Posts: 5,920

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Re: filesystem Update Error /bin exists in filesystem

Not sure I would be allowed...

warning: cannot resolve "libmbim", a dependency of "modemmanager"
:: The following package cannot be upgraded due to unresolvable dependencies:
      modemmanager

:: Do you want to skip the above package for this upgrade? [y/N] n
error: failed to prepare transaction (could not satisfy dependencies)
:: modemmanager: requires libmbim

Last edited by Mr Green (2013-06-03 09:57:17)

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HalosGhost

Forum Moderator

From: Twin Cities, MN

Registered: 2012-06-22

Posts: 2,097

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Re: filesystem Update Error /bin exists in filesystem

You should modify and rebuild the PKGBUILDs, and the extra bin directories will be symlinked to /usr/bin. The only files you should move by-hand are files existing in the to-be-symlinked directories which are unowned by any package (I.e., ones you manually put there).

All the best,

-HG

[Edit]: Wow, I totally failed to see the extra page of comments; sorry for the reply to a clearly already-answered question.

Last edited by HalosGhost (2013-06-03 10:54:28)

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karol

Archivist

Registered: 2009-05-06

Posts: 25,440

Re: filesystem Update Error /bin exists in filesystem

There is no way one can ban you from reading the ML, as the archives are public: https://mailman.archlinux.org/mailman/l … dev-public
Posting on that list is IIRC for devs and TUs only, so ... :-)

Edit: libmbim is in the repos: https://projects.archlinux.org/svntogit … es/libmbim
Maybe your package db is out of date?

Last edited by karol (2013-06-03 10:11:17)

Mr Green

Forum Fellow

From: U.K.

Registered: 2003-12-21

Posts: 5,920

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Re: filesystem Update Error /bin exists in filesystem

No new install fully up to date, symlink to bash does not look right

lrwxrwxrwx 1 root root 4 May 31 20:10 sh -> bash

(not that it helps much)

[live@archbang log]$ tail pacman.log 
[2013-06-03 10:52] [PACMAN] Running 'pacman -S bash'
[2013-06-03 10:52] [PACMAN] upgraded bash (4.2.045-1 -> 4.2.045-4)
[2013-06-03 10:52] [PACMAN] Running 'pacman -Su'
[2013-06-03 10:52] [PACMAN] starting full system upgrade

from logs

Last edited by Mr Green (2013-06-03 10:16:37)

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karol

Archivist

Registered: 2009-05-06

Posts: 25,440

Re: filesystem Update Error /bin exists in filesystem

Check your mirrorlist then.
What's the output of 'pacman -Syyu libmbim'?

Last edited by karol (2013-06-03 10:18:55)

Mr Green

Forum Fellow

From: U.K.

Registered: 2003-12-21

Posts: 5,920

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Re: filesystem Update Error /bin exists in filesystem

That might be the problem, however I cannot get back into build ;( might reinstall and refresh miirrorlist first

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Mr Green

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From: U.K.

Registered: 2003-12-21

Posts: 5,920

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Re: filesystem Update Error /bin exists in filesystem

[root@arch etc]# pacman -Ss mirrorlist
core/pacman-mirrorlist 20130601-1 [installed]
    Arch Linux mirror list for use by pacman

Ok updated syslinux and rebooted

[mrgreen@arch /]$ ls -la bin
lrwxrwxrwx 1 root root 7 May 31 19:40 bin -> usr/bin

Did use german mirrors instead....

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Mr Green I like Landuke!

Mr Green

Forum Fellow

From: U.K.

Registered: 2003-12-21

Posts: 5,920

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Re: filesystem Update Error /bin exists in filesystem

Just updated and rebooted my desktop, move went smoothly...

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t0m5k1

Member

From: overthere

Registered: 2012-02-10

Posts: 324

Re: filesystem Update Error /bin exists in filesystem

just wanted to know what repo names could be used in this:

Also check packages installed from non-official repos using:

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

I ask as I only use official repo's + aur, so I ran:

┌─(t0m5k1@b0x)-(1509/pts/0)-(03:29pm:03/06/13)-
└─>(%:~)
└─>> sudo paclist aur | awk ' { print $1 } ' | pacman -Ql - | grep ' /s\?bin/\| /usr/sbin/' | sprunge
error: repository "aur" was not found.

the list can be found here: http://sprunge.us/cgNF
but to me this looks like a list of pkg's from official repo's & not what I had installed via aur!!

I am sooooo confused lol

thnx for assistance

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Scimmia

Fellow

Registered: 2012-09-01

Posts: 12,369

Re: filesystem Update Error /bin exists in filesystem

The aur is not a pacman repo. That's what the first command about "non-official package" is for.

Last edited by Scimmia (2013-06-03 13:41:21)

karol

Archivist

Registered: 2009-05-06

Posts: 25,440

Re: filesystem Update Error /bin exists in filesystem

Also check packages installed from non-official repos

https://wiki.archlinux.org/index.php/Un … positories

How did you generate that list you pasted in sprunge?

Last edited by karol (2013-06-03 13:43:26)

t0m5k1

Member

From: overthere

Registered: 2012-02-10

Posts: 324

Re: filesystem Update Error /bin exists in filesystem

The aur is not a pacman repo. That's what the first command about "non-official package" is for.

I did think that but I am confused lol

Also check packages installed from non-official repos

https://wiki.archlinux.org/index.php/Un … positories

How did you generate that list you pasted in sprunge?

thnx for the url, that is a good reference

for sprunge I use a zsh function I got from GTMANFRED :

function sprunge() {
  if (($#)); then
if [[ -f $1 && -r $1 ]]; then
curl -F 'sprunge=<-' http://sprunge.us < "$1"
    else
printf 'file %s does not exist or is not readable\n' "$1" >&2
      return 1
    fi
else
curl -F 'sprunge=<-' http://sprunge.us
  fi
}

then you just use it as i did above (cmd pipe sprunge) :

┌─(t0m5k1@b0x)-(1509/pts/0)-(03:29pm:03/06/13)-
└─>(%:~)
└─>> sudo paclist aur | awk ' { print $1 } ' | pacman -Ql - | grep ' /s\?bin/\| /usr/sbin/' | sprunge

cheers again for the clarity

Last edited by t0m5k1 (2013-06-03 13:55:52)

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ROG Strix (GD30CI) - Intel Core i5-7400 CPU - 32Gb 2400Mhz - GTX1070 8GB - AwesomeWM (occasionally XFCE, i3)

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indianahorst

Member

Registered: 2008-08-23

Posts: 129

Re: filesystem Update Error /bin exists in filesystem

Please help....

First of all: I dont use testing or unofficial repos, just the official ones.

A few hours ago, I updated my system following the instructions on
https://www.archlinux.org/news/binaries … ervention/

Following Step 5, I did

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

When I came to # pacman -Su, I still got the "exists in filesystem" error. I hadn't the time to fix it at the moment, so I shutdown my system.

Now I startet it again and just get the error

Error: Root device mounted successfully, but /sbin/init does not exist.
Bailing out, you are on your own. Good Luck

[rootfs /]#

What can I do now to fix it?

HalosGhost

Forum Moderator

From: Twin Cities, MN

Registered: 2012-06-22

Posts: 2,097

Website

Re: filesystem Update Error /bin exists in filesystem

That was so much cleaner (for me) than the lib merges. Awesome work devs!

All the best,

-HG

---

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karol

Archivist

Registered: 2009-05-06

Posts: 25,440

Re: filesystem Update Error /bin exists in filesystem

When I came to # pacman -Su, I still got the "exists in filesystem" error. I hadn't the time to fix it at the moment, so I shutdown my system.

Why did you start updating at all then??

Use a liveCD / live USB, chroot, fix the 'exist in the filesystem' errors and open a separate thread if you need further help.

dwal42

Member

Registered: 2013-06-03

Posts: 2

Re: filesystem Update Error /bin exists in filesystem

UPDATE:
I personally fixed this by running '# rm -rf /bin; rm -rf /usr/sbin' then '# pacman -Su'. Seems to be working now but YMMV.
FYI this is also happening on NON-testing repos.

Packages (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 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: /usr/sbin exists in filesystem
Errors occurred, no packages were upgraded.

And my pacman.conf:

#
# /etc/pacman.conf
#
# See the pacman.conf(5) manpage for option and repository directives

#
# GENERAL OPTIONS
#
[options]
# The following paths are commented out with their default values listed.
# If you wish to use different paths, uncomment and update the paths.
#RootDir     = /
#DBPath      = /var/lib/pacman/
#CacheDir    = /var/cache/pacman/pkg/
#LogFile     = /var/log/pacman.log
#GPGDir      = /etc/pacman.d/gnupg/
HoldPkg     = pacman glibc
#XferCommand = /usr/bin/curl -C - -f %u > %o
#XferCommand = /usr/bin/wget --passive-ftp -c -O %o %u
#CleanMethod = KeepInstalled
#UseDelta    = 0.7
Architecture = auto

# Pacman won't upgrade packages listed in IgnorePkg and members of IgnoreGroup
#IgnorePkg   =
#IgnoreGroup =

#NoUpgrade   =
#NoExtract   =

# Misc options
#UseSyslog
#Color
#TotalDownload
CheckSpace
#VerbosePkgLists

# By default, pacman accepts packages signed by keys that its local keyring
# trusts (see pacman-key and its man page), as well as unsigned packages.
SigLevel    = Required DatabaseOptional
LocalFileSigLevel = Optional
#RemoteFileSigLevel = Required

# NOTE: You must run `pacman-key --init` before first using pacman; the local
# keyring can then be populated with the keys of all official Arch Linux
# packagers with `pacman-key --populate archlinux`.

#
# REPOSITORIES
#   - can be defined here or included from another file
#   - pacman will search repositories in the order defined here
#   - local/custom mirrors can be added here or in separate files
#   - repositories listed first will take precedence when packages
#     have identical names, regardless of version number
#   - URLs will have $repo replaced by the name of the current repo
#   - URLs will have $arch replaced by the name of the architecture
#
# Repository entries are of the format:
#       [repo-name]
#       Server = ServerName
#       Include = IncludePath
#
# The header [repo-name] is crucial - it must be present and
# uncommented to enable the repo.
#

# The testing repositories are disabled by default. To enable, uncomment the
# repo name header and Include lines. You can add preferred servers immediately
# after the header, and they will be used before the default mirrors.

#[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

# If you want to run 32 bit applications on your x86_64 system,
# enable the multilib repositories as required here.

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

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

[archlinuxfr]
SigLevel = Optional TrustAll
Server = http://repo.archlinux.fr/$arch

# An example of a custom package repository.  See the pacman manpage for
# tips on creating your own repositories.
#[custom]
#SigLevel = Optional TrustAll
#Server = file:///home/custompkgs

...and I just now realized that my system is hosed. The entire /bin directory has been wiped out.

Last edited by dwal42 (2013-06-03 14:42:48)

karol

Archivist

Registered: 2009-05-06

Posts: 25,440

Re: filesystem Update Error /bin exists in filesystem

FYI this is also happening on NON-testing repos.

Because it hit the non-testing repos now - see Arch home page.

Scimmia

Fellow

Registered: 2012-09-01

Posts: 12,369

Re: filesystem Update Error /bin exists in filesystem

dwal42, what's the output of pacman -Qo /usr/sbin

It should just be the filesystem package. If it's any other package, fix them.

Your system isn't "hosed", everything from /bin has just been moved to /usr/bin.

Last edited by Scimmia (2013-06-03 14:41:48)

dwal42

Member

Registered: 2013-06-03

Posts: 2

Re: filesystem Update Error /bin exists in filesystem

dwal42, what's the output of pacman -Qo /usr/sbin

It should just be the filesystem package. If it's any other package, fix them.

Your system isn't "hosed", everything from /bin has just been moved to /usr/bin.

I figured it out, thanks for the info!